treatments-xml/data/03/D2/A0/03D2A0512862FFC83C7CDEA40E4BF69F.xml

<document ID-DOI="http://doi.org/10.5281/zenodo.5616102" ID-GBIF-Dataset="f6d4770f-2380-4376-a80d-92745d739c09" ID-GBIF-Taxon="127696782" ID-Zenodo-Dep="5616102" checkinTime="1487928914059" checkinUser="plazi" docAuthor="Dieter Slos, Walter Sudhaus, Lewis Stevens, Wim Bert &amp; Mark Blaxter" docDate="2017" docId="03D2A0512862FFC83C7CDEA40E4BF69F" docLanguage="en" docName="10.1186s40850-017-0013-2_OCR.pdf" docOrigin="BMC Zoology 2 (4)" docStyle="DocumentStyle{}" docTitle="Caenorhabditis monodelphis Slos &amp; Sudhaus 2017" docType="treatment" docVersion="10" lastPageId="11" lastPageNumber="12" masterDocId="FFEBD8292860FFC33967D8220606FFF9" masterDocTitle="Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis" masterLastPageNumber="15" masterPageNumber="1" pageId="2" pageNumber="3" updateTime="1635507854601" updateUser="ExternalLinkService">
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<mods:title>Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis</mods:title>
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<mods:namePart>Dieter Slos</mods:namePart>
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<mods:namePart>Walter Sudhaus</mods:namePart>
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<mods:namePart>Lewis Stevens</mods:namePart>
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<mods:namePart>Wim Bert</mods:namePart>
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<mods:namePart>Mark Blaxter</mods:namePart>
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<taxonomicName authority="Slos &amp; Sudhaus, 2017" authorityName="Slos &amp; Sudhaus" authorityYear="2017" box="[1307,1793,1670,1706]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="species" species="monodelphis">
<emphasis box="[1307,1793,1670,1706]" italics="true" pageId="2" pageNumber="3">Caenorhabditis monodelphis</emphasis>
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1 sp. n. Slos &amp; Sudhaus
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= 
<taxonomicName box="[1343,1594,1770,1806]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="genus">
<emphasis box="[1343,1594,1770,1806]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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sp. SB341 [
<bibRefCitation author="Kiontke K &amp; Gavin NP &amp; Raynes Y &amp; Roehrig C &amp; Piano F &amp; Fitch DHA." box="[1796,1816,1770,1806]" journalOrPublisher="Proc Natl Acad Sei U S A" pageId="2" pageNumber="3" pagination="9003 - 8" part="101" refString="7. Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DHA. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sei U S A. 2004; 101: 9003 - 8." title="Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss" type="journal article" year="2004">7</bibRefCitation>
]
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</paragraph>
<paragraph blockId="2.[1306,2209,1767,2106]" pageId="2" pageNumber="3">
= 
<taxonomicName box="[1343,1594,1820,1856]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="genus">
<emphasis box="[1343,1594,1820,1856]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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sp. SB341 and 
<taxonomicName box="[1858,2110,1820,1856]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="genus" status="sp. n.">
<emphasis box="[1858,2110,1820,1856]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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SB341 [
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]
</paragraph>
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= 
<taxonomicName box="[1343,1594,1920,1956]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="genus" status="sp. n.">
<emphasis box="[1343,1594,1920,1956]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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<taxonomicNameLabel box="[1609,1696,1920,1956]" pageId="2" pageNumber="3" rank="species">sp. n.</taxonomicNameLabel>
1 (SB341) and (lapse)
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<taxonomicName box="[1307,1558,1970,2006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="2" pageNumber="3" phylum="Nematoda" rank="genus" status="sp. n.">
<emphasis box="[1307,1558,1970,2006]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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<taxonomicNameLabel box="[1573,1660,1970,2006]" pageId="2" pageNumber="3" rank="species">sp. n.</taxonomicNameLabel>
4 (SB341) [
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]
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= 
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<emphasis box="[1343,1594,2020,2056]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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sp. 1 SB341 [
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, 
<bibRefCitation author="Nuez I &amp; Felix M-A." box="[1871,1890,2020,2056]" journalOrPublisher="PLoS ONE" pageId="2" pageNumber="3" pagination="29811" part="7" refString="8. Nuez I, Felix M-A. Evolution of susceptibility to ingested double-stranded RNAs in Caenorhabditis nematodes. PLoS ONE. 2012; 7: e 29811." title="Evolution of susceptibility to ingested double-stranded RNAs in Caenorhabditis nematodes" type="journal article" year="2012">8</bibRefCitation>
, 
<bibRefCitation author="Felix M-A." box="[1911,1950,2020,2056]" journalOrPublisher="Curr Biol" pageId="2" pageNumber="3" pagination="103 - 14" part="17" refString="37. Felix M-A. Cryptic quantitative evolution of the vulva intercellular signaling network in Caenorhabditis. Curr Biol. 2007; 17: 103 - 14." title="Cryptic quantitative evolution of the vulva intercellular signaling network in Caenorhabditis" type="journal article" year="2007">37</bibRefCitation>
]
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= 
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<emphasis box="[1343,1594,2070,2106]" italics="true" pageId="2" pageNumber="3">Caenorhabditis</emphasis>
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sp. 4 SB341 [
<bibRefCitation author="Akimkina T &amp; Yook K &amp; Curnock S &amp; Hodgkin J." box="[1828,1868,2070,2106]" journalOrPublisher="FEMS Microbiol Lett" pageId="2" pageNumber="3" pagination="145 - 51" part="264" refString="38. Akimkina T, Yook K, Curnock S, Hodgkin J. Genome characterization, analysis of virulence and transformation of Microbacterium nematophilum, a coryneform pathogen of the nematode Caenorhabditis elegans. FEMS Microbiol Lett. 2006; 264: 145 - 51." title="Genome characterization, analysis of virulence and transformation of Microbacterium nematophilum, a coryneform pathogen of the nematode Caenorhabditis elegans" type="journal article" year="2006">38</bibRefCitation>
]
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<heading box="[1307,1776,2170,2206]" fontSize="11" level="4" pageId="2" pageNumber="3" reason="1">
(
<figureCitation box="[1318,1426,2170,2206]" captionStart="Fig. 1" captionStartId="3.[264,311,2428,2455]" captionTargetBox="[237,2247,365,2408]" captionText="Fig. 1 Line draw ings o f Caenorhabditis monodelphis sp. n. a Fem ale, schem atic overview, b-i Male, b: Male, lateral; c Anterior end in ventral view; d Tail in lateral view; e Tail in ventral view; f Pharyngeal region; g Gubernaculum in ventral view; h Gubernaculum in lateral view; i Spiculum in ateral view" httpUri="https://zenodo.org/record/322317/files/figure.png" pageId="2" pageNumber="3">Figs. 1</figureCitation>
, 
<figureCitation box="[1448,1469,2170,2206]" captionStart="Fig. 2" captionStartId="4.[265,310,878,908]" captionTargetBox="[279,1175,399,850]" captionText="Fig. 2 Cae o abolts mo ode ph s sp. n., matu e spe matozoa fema e post- ıte e sac, TEM A ovvs = spe m ce s" httpUri="https://zenodo.org/record/322318/files/figure.png" pageId="2" pageNumber="3">2</figureCitation>
, 
<figureCitation box="[1491,1509,2170,2206]" captionStart="Fig. 3" captionStartId="5.[263,310,2635,2662]" captionTargetBox="[236,2245,369,2617]" captionTargetPageId="5" captionText="Fig. 3 Light m icroscopic im ages o f Caenorhabditis monodelphis sp. n. a G en eralo verview of a dauer larva; b: Ventral view of fem ale reproductive system; c Detailed ventralview of vulva; d Anterior region of male; e Male tailin ventral view, showing seven ventral (v 1 - 7) and tw o dorsal (ad, pd) genital papi llae. The phasmids are not visibl e in this pl ane; f Male tai lin latera l view; g Detai l o f the spicu le; h Detail o f the gubernacu lum s ____________________________________________________________________________________________________________________________________________________________________________________________________________________" httpUri="https://zenodo.org/record/322319/files/figure.png" pageId="2" pageNumber="3">3</figureCitation>
and 
<figureCitation box="[1597,1618,2170,2206]" captionStart="Fig. 4" captionStartId="6.[264,311,2504,2531]" captionTargetBox="[268,2215,393,2476]" captionTargetPageId="6" captionText="Fig. 4 Scanning electron m icrographs o f Caenorhabditis monodelphis sp. n. a, d Anterior end of fem ale; b, c Anterior end o f male; e Fem ale vulva; f. g Lateral field o f fem ale and male, respectively; h Fem ale anus and tail; ij Male bursa with genital papillae indicated; k Detail of cloaca region with postcloacal sensillae; I Detail o f male spiculum" httpUri="https://zenodo.org/record/322320/files/figure.png" pageId="2" pageNumber="3">4</figureCitation>
; 
<tableCitation box="[1640,1761,2170,2206]" captionStart="Table 1" captionStartId="7.[238,329,368,401]" captionTargetBox="[237,1212,477,2661]" captionTargetPageId="7" captionText="Table 1 Measurements (in | jm) of heat relaxed specimens of Caenorhabditis monodelphis sp. n." httpUri="http://table.plazi.org/id/DF0441CF2867FFC43989D95204E2FE46" pageId="2" pageNumber="3" tableUuid="DF0441CF2867FFC43989D95204E2FE46">Table 1</tableCitation>
)
</heading>
</paragraph>
<paragraph blockId="2.[1272,2245,2270,3057]" box="[1272,1361,2270,2305]" pageId="2" pageNumber="3">
<heading bold="true" box="[1272,1361,2270,2305]" fontSize="12" level="2" pageId="2" pageNumber="3" reason="0">
<emphasis bold="true" box="[1272,1361,2270,2305]" pageId="2" pageNumber="3">Adult</emphasis>
</heading>
</paragraph>
<paragraph blockId="2.[1272,2245,2270,3057]" lastBlockId="4.[239,1216,1021,1210]" lastPageId="4" lastPageNumber="5" pageId="2" pageNumber="3">
Small species (female 0.72 - 1.04 mm, male 0.65 - 0.77 mm); cuticle thin, ca. 1 pm wide and finely annulated, 0.8 pm wide at midbody. Lateral field inconspicuous, about 9% of body width, consisting one ridge that can be 
<emphasis bold="true" box="[1272,1374,2520,2556]" pageId="2" pageNumber="3">traced</emphasis>
anteriorly to the level of the median bulb and posteriorly at level of rectum in females and about 1% spicules length anterior of the cloacal aperture in males. Six lips slightly protruding, each with one apical papilliform labial sensillum and a second circle of four sublateral cephalic sensilla in both 
<emphasis bold="true" box="[1537,1625,2770,2806]" pageId="2" pageNumber="3">sexes</emphasis>
; amphids opening on the lateral lips, hardly discernible. Buccal tube long and slender, more than twice the width in lip region, pharyngeal sleeve envelopes nearly half of the stoma, the anterior as well as the posterior end of the tube appear slightly thickened, 
<emphasis bold="true" box="[1273,1462,3020,3056]" pageId="2" pageNumber="3">cheilostom</emphasis>
inconspicuous, arcade cells forming the gymnostom sometimes visible; glottoid apparatus completely absent. Pharynx with a prominent median bulb, diameter more than 90% of diameter of terminal bulb; terminal bulb pyriform, with double chambered haustrulum, the anterior chamber smallish; cardia conspicuous, opens funnel-like in intestine. Nerve ring encircles isthmus in its anterior part in living specimens, m ore to the middle of the isthmus in heat relaxed or preserved specimens; deirids usually conspicuous in the lateral field at level of beginning of terminal bulb, sometimes not visible in heat relaxed animals; pore of excretory-secretory system hard to discern posterior of deirid level. Two gland cells ventral and slightly posterior of term inal bulb conspicuous in live specimens. Lateral canals visible in live specimens extending anteriorly to two stoma length from the anterior end and ending at rectum level in the female. Postdeirids usually very conspicuous dorsally of the lateral field at about 75% of body length in both 
<emphasis bold="true" box="[239,328,1025,1061]" pageId="4" pageNumber="5">sexes</emphasis>
and about half the length between vulva and beginning of rectum (or at level of posterior end of uterus remnant) in females, sometimes not visible in heat relaxed specimens.
</paragraph>
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<paragraph pageId="3" pageNumber="4">
Fig. 1 Line drawings of 
<taxonomicName box="[589,781,2428,2455]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="3" pageNumber="4" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
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<taxonomicNameLabel box="[966,1034,2431,2454]" pageId="3" pageNumber="4" rank="species">sp. n.</taxonomicNameLabel>
a Female, schematic overview, b-i Male, b: Male, lateral; c Anterior end in ventral view; d Tail in lateral view; e Tail in ventral view; f Pharyngeal region; g Gubernaculum in ventral view; h Gubernaculum in lateral view; i Spiculum in ateral view
</paragraph>
</caption>
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<paragraph blockId="4.[264,1111,877,950]" pageId="4" pageNumber="5">Fig. 2 Cae o abolts mo ode ph s sp. n., matu e spe matozoa fema e post- ıte e sac, TEM A ovvs=spe m ce s</paragraph>
</caption>
<paragraph blockId="4.[238,1219,1275,2664]" box="[241,359,1275,1310]" pageId="4" pageNumber="5">
<heading bold="true" box="[241,359,1275,1310]" fontSize="12" level="2" pageId="4" pageNumber="5" reason="0">
<emphasis bold="true" box="[241,359,1275,1310]" pageId="4" pageNumber="5">Female</emphasis>
</heading>
</paragraph>
<paragraph blockId="4.[238,1219,1275,2664]" pageId="4" pageNumber="5">
Maximum body diameter clearly anterior of the vulva, vulva position 65% body length, a transverse slit, bordered in both ends by cuticular longitudinal flaps, vulva lips moderately protruding, four diagonal vulval muscles conspicuous; one pseudocoelomocyte exists anterior of gonad flexure ventrally. Genital tracts asymmetrical; posterior branch rudimentary, sac like, on the left hand side of intestine, without flexure, almost as long as body diameter at the level of the vulva, containing spermatozoa (
<figureCitation box="[328,428,1776,1812]" captionStart="Fig. 2" captionStartId="4.[265,310,878,908]" captionTargetBox="[279,1175,399,850]" captionText="Fig. 2 Cae o abolts mo ode ph s sp. n., matu e spe matozoa fema e post- ıte e sac, TEM A ovvs = spe m ce s" httpUri="https://zenodo.org/record/322318/files/figure.png" pageId="4" pageNumber="5">Fig. 2</figureCitation>
); anterior branch right of intestine, reflexed dorsally close to the pharynx, flexure more than half the length of the gonad (measured from vulva to flexure); at the flexure oocytes in several rows, downstream in one row, oocytes predominantly growing in the last position, where granules are stored inside; sphincter between oviduct and uterus, only a few sperm cells in oviduct, most of them in uterus and blind sac; oviparous, one egg at a time in uterus (rarely two), segmentation starts in the uterus. Rectum a little S-shaped, rectal gland cells very small, posterior anal lip slightly protuberant. Tail short, panagrolaimid, dorsally convex, with offset tip tapering, smooth to somewhat telescope-like by cuticle forming a sleeve-like structure; tail tip with tiny hooks, mostly one dorsal, but also subventral (compare with 
<emphasis box="[962,1215,2478,2514]" italics="true" pageId="4" pageNumber="5">
<taxonomicName box="[962,1193,2478,2514]" class="Secernentea" family="Rhabditidae" genus="Poikilolaimus" kingdom="Animalia" order="Rhabditida" pageId="4" pageNumber="5" phylum="Nematoda" rank="genus">Poikilolaimus</taxonomicName>
);
</emphasis>
opening of phasmids located at 60-65% of tail length, shortly anterior of tip, phasmid glands not reaching anus level.
</paragraph>
<paragraph blockId="4.[238,1217,2728,3067]" box="[240,320,2729,2764]" pageId="4" pageNumber="5">
<heading box="[240,320,2729,2764]" fontSize="12" level="3" pageId="4" pageNumber="5" reason="1">Male</heading>
</paragraph>
<paragraph blockId="4.[238,1217,2728,3067]" pageId="4" pageNumber="5">Testis right of intestine, ventrally reflexed in a certain distance posterior of pharynx; flexure relatively short. One pseudocoelomocyte between pharynx and flexure ventrally. Bursa well developed, peloderan, anteriorly open, with smooth margin and sometimes terminally indented, posterior part of velum transversely striated.</paragraph>
<paragraph blockId="4.[1276,2255,368,1210]" pageId="4" pageNumber="5">
Nine pairs of genital papillae (GP) present, two of them anterior of the cloaca, genital papilla 1 (GP1) and GP2 spaced, GP3 to GP6 and GP7 to GP9 clustered, GP5 and GP7 point to the dorsal side of the velum, GP6 slightly bottle shaped, GP8 and GP9 fused at base, GP2 and GP8 not reaching the margin of velum. Phasmids forming small tubercles to the ventral side posterior of the last GP; formula of GPs: vl,v2/(v3,v4,ad,v5) (pd,v6,v7)ph. Precloacal sensillum small, precloacal lip simple (according to type A of W Sudhaus and K Kiontke [
<bibRefCitation author="Sudhaus W &amp; Kiontke K." box="[2076,2120,823,859]" journalOrPublisher="J Zool Syst Evol Res" pageId="4" pageNumber="5" pagination="217 - 33" part="34" refString="39. Sudhaus W, Kiontke K. Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda). J Zool Syst Evol Res. 1996: 34: 217 - 33." title="Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda)" type="journal article" year="1996">39</bibRefCitation>
]), postcloacal sensilla long filamentous. Spicules short and stout, tawny, separate, slightly curved, with prominent head; shaft with a transverse seam, with a prominent longitudinal ridge, a dorsal lamella, and an oval “window”, the tip notched. Gubernaculum dorsally projecting, flexible, in the distal part following the contour of the spicules, spoon shaped in ventral view.
</paragraph>
<paragraph blockId="4.[1276,2253,1278,1716]" box="[1278,1468,1279,1314]" pageId="4" pageNumber="5">
<heading bold="true" box="[1278,1468,1279,1314]" fontSize="12" level="2" pageId="4" pageNumber="5" reason="0">
<emphasis bold="true" box="[1278,1468,1279,1314]" pageId="4" pageNumber="5">Dauer larva</emphasis>
</heading>
</paragraph>
<paragraph blockId="4.[1276,2253,1278,1716]" pageId="4" pageNumber="5">Unsheathed, mouth closed; stoma long, slender. Pharyngeal sleeve covering about half of the stoma; pharynx with welldeveloped median and terminal bulbs; corpus length ca. 52% of pharynx length. Nerve ring somewhat in the middle between the middle and terminal bulb. Genital primordium at about 60% of body length, elongated oval in shape. Tail conical. Amphids, lateral lines, position excretory pore, deirids and phasmids not observed.</paragraph>
<paragraph blockId="4.[1274,2253,1826,2013]" box="[1274,1446,1829,1860]" pageId="4" pageNumber="5">
<emphasis box="[1274,1446,1829,1860]" italics="true" pageId="4" pageNumber="5">Aberration</emphasis>
</paragraph>
<paragraph blockId="4.[1274,2253,1826,2013]" pageId="4" pageNumber="5">In one female a second set of “sensilla” were observed a short distance posterior to postdeirids, possibly a duplication of the postdeirids.</paragraph>
</subSubSection>
<subSubSection lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5" type="materials_examined">
<paragraph blockId="4.[1276,2255,2123,2612]" box="[1278,1669,2126,2157]" pageId="4" pageNumber="5">
<emphasis bold="true" box="[1278,1353,2126,2157]" pageId="4" pageNumber="5">Type</emphasis>
<emphasis box="[1364,1669,2126,2157]" italics="true" pageId="4" pageNumber="5">
carrier and 
<emphasis bold="true" box="[1553,1669,2126,2157]" italics="true" pageId="4" pageNumber="5">locality</emphasis>
</emphasis>
</paragraph>
<paragraph blockId="4.[1276,2255,2123,2612]" pageId="4" pageNumber="5">
Holotype and paratypes of 
<taxonomicName box="[1763,2252,2173,2209]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="4" pageNumber="5" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1763,2252,2173,2209]" italics="true" pageId="4" pageNumber="5">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1276,1372,2224,2260]" pageId="4" pageNumber="5" rank="species">sp. n.</taxonomicNameLabel>
were isolated from the tunnels of 
<taxonomicName authority="Herbst, 1793" authorityName="Herbst" authorityYear="1793" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="4" pageNumber="5" phylum="Arthropoda" rank="species" species="castaneus">
<emphasis box="[2017,2252,2224,2260]" italics="true" pageId="4" pageNumber="5">Cis castaneus</emphasis>
(Herbst, 1793)
</taxonomicName>
(
<taxonomicName box="[1548,1654,2274,2310]" class="Insecta" family="Ciidae" kingdom="Animalia" order="Coleoptera" pageId="4" pageNumber="5" phylum="Arthropoda" rank="family">Ciidae</taxonomicName>
, 
<taxonomicName box="[1678,1857,2274,2310]" class="Insecta" kingdom="Animalia" order="Coleoptera" pageId="4" pageNumber="5" phylum="Arthropoda" rank="order">Coleoptera</taxonomicName>
) in the bracket fungus 
<taxonomicName box="[1278,1692,2324,2360]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="4" pageNumber="5" phylum="Basidiomycota" rank="species" species="applanatum">
<emphasis box="[1278,1692,2324,2360]" italics="true" pageId="4" pageNumber="5">Ganoderma applanatum</emphasis>
</taxonomicName>
(
<taxonomicName box="[1723,1912,2324,2360]" class="Agaricomycetes" kingdom="Fungi" order="Polyporales" pageId="4" pageNumber="5" phylum="Basidiomycota" rank="order">Polyporales</taxonomicName>
) on a stump of the common beech (
<emphasis box="[1595,1883,2374,2410]" italics="true" pageId="4" pageNumber="5">
<taxonomicName box="[1595,1871,2374,2410]" class="Magnoliopsida" family="Fagaceae" genus="Fagus" kingdom="Plantae" order="Fagales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="sylvatica">Fagus sylvatica</taxonomicName>
)
</emphasis>
a few centimetres above the ground in Berlin-Grunewald in April 2001. The same sample included individuals of 
<taxonomicName box="[2035,2253,2474,2510]" class="Secernentea" family="Rhabditidae" genus="Diploscapter" kingdom="Animalia" order="Rhabditida" pageId="4" pageNumber="5" phylum="Nematoda" rank="genus">
<emphasis box="[2035,2253,2474,2510]" italics="true" pageId="4" pageNumber="5">Diploscapter</emphasis>
</taxonomicName>
sp., 
<taxonomicName box="[1350,1471,2525,2561]" class="Adenophorea" family="Plectidae" genus="Plectus" kingdom="Animalia" order="Araeolaimida" pageId="4" pageNumber="5" phylum="Nematoda" rank="genus">
<emphasis box="[1350,1471,2525,2561]" italics="true" pageId="4" pageNumber="5">Plectus</emphasis>
</taxonomicName>
sp., 
<taxonomicName box="[1567,1899,2525,2561]" class="Secernentea" family="Rhabditidae" genus="Oscheius" higherTaxonomySource="GBIF" kingdom="Animalia" order="Rhabditida" pageId="4" pageNumber="5" phylum="Nematoda" rank="species" species="dolichura">
<emphasis box="[1567,1899,2525,2561]" italics="true" pageId="4" pageNumber="5">Oscheius dolichura</emphasis>
</taxonomicName>
and one individual dorylaimid and mononchid.
</paragraph>
<paragraph blockId="4.[1275,2256,2679,3067]" box="[1278,1498,2682,2713]" pageId="4" pageNumber="5">
<emphasis bold="true" box="[1278,1353,2682,2713]" pageId="4" pageNumber="5">Type</emphasis>
<emphasis box="[1364,1498,2682,2713]" italics="true" pageId="4" pageNumber="5">material</emphasis>
</paragraph>
<paragraph blockId="4.[1275,2256,2679,3067]" lastBlockId="5.[237,1214,2818,3057]" lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5">
Holotype male (collection num ber 
<emphasis box="[1906,1943,2728,2764]" italics="true" pageId="4" pageNumber="5">W</emphasis>
T 3684) and five female and four male paratypes (WT 3685, W T 3686) are deposited in the National Plant Protection Organization Wageningen, The Netherlands. In addition, four female and four male paratypes, are deposited in the collection of Museum Voor Dierkunde at Ghent University, Ghent, Belgium, five female and three male paratypes in Museum für Naturkunde an der Humboldt-Universität zu Berlin, Berlin, Germany. Additional paratypes are available in the UGent Nematode Collection (slides UGnem158, 159 &amp; 160) of the Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.
</paragraph>
</subSubSection>
<caption httpUri="https://zenodo.org/record/322319/files/figure.png" pageId="5" pageNumber="6" targetBox="[236,2245,369,2617]" targetPageId="5">
<paragraph pageId="5" pageNumber="6">
Fig. 3 Light microscopic images of 
<taxonomicName box="[744,934,2635,2662]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
<taxonomicName box="[945,1110,2635,2662]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[1120,1188,2638,2661]" pageId="5" pageNumber="6" rank="species">sp. n.</taxonomicNameLabel>
a General o verview of a dauer larva; b: Ventral view of fem ale reproductive system; c Detailed ventral view of vulva; d Anterior region of male; e Male tailin ventral view, showing seven ventral (v1-7) and tw o dorsal(ad, pd) genital papillae. The phasmids are not visible in this pl ane; f Male tai lin lateral view; g Detai l o f the spicu le; h Detail of the gubernacu lum
</paragraph>
<paragraph box="[240,2234,2753,2770]" pageId="5" pageNumber="6">s____________________________________________________________________________________________________________________________________________________________________________________________________________________</paragraph>
</caption>
<subSubSection lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6" type="diagnosis">
<paragraph blockId="5.[1271,2243,2820,3057]" box="[1271,1700,2823,2854]" pageId="5" pageNumber="6">
<heading bold="true" box="[1271,1700,2823,2854]" fontSize="9" level="5" pageId="5" pageNumber="6" reason="6">
<emphasis bold="true" box="[1271,1700,2823,2854]" italics="true" pageId="5" pageNumber="6">Diagnosis and relationship</emphasis>
</heading>
</paragraph>
<paragraph blockId="5.[1271,2243,2820,3057]" lastBlockId="6.[238,1213,2766,3056]" lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6">
<taxonomicName box="[1273,1758,2870,2906]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1273,1758,2870,2906]" italics="true" pageId="5" pageNumber="6">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1775,1867,2870,2906]" pageId="5" pageNumber="6" rank="species">sp. n.</taxonomicNameLabel>
can be recognised as a 
<taxonomicName box="[1309,1566,2920,2956]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="genus">
<emphasis box="[1309,1566,2920,2956]" italics="true" pageId="5" pageNumber="6">Caenorhabditis</emphasis>
</taxonomicName>
based on the thickened GP6 and the clearly visible postdeirids. 
<taxonomicName box="[1712,2186,2970,3006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1712,2186,2970,3006]" italics="true" pageId="5" pageNumber="6">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel pageId="5" pageNumber="6" rank="species">sp. n.</taxonomicNameLabel>
is distinguished from all other described 
<taxonomicName box="[1992,2242,3020,3056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="5" pageNumber="6" phylum="Nematoda" rank="genus">
<emphasis box="[1992,2242,3020,3056]" italics="true" pageId="5" pageNumber="6">Caenorhabditis</emphasis>
</taxonomicName>
species by the presence of a monodelphic genital tract in the female with a blind sac posterior the vulva, a panagrolaimid female tail shape, adults with only one ridge on the lateral field, a very long and slender stoma without visible glottoid apparatus and male with short, stout spicule with bifurcate tip.
</paragraph>
</subSubSection>
<caption httpUri="https://zenodo.org/record/322320/files/figure.png" pageId="6" pageNumber="7" targetBox="[268,2215,393,2476]" targetPageId="6">
<paragraph pageId="6" pageNumber="7">
Fig. 4 Scanning electron micrographs of 
<taxonomicName box="[820,1186,2504,2531]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="6" pageNumber="7" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">Caenorhabditis monodelphis</taxonomicName>
<taxonomicNameLabel box="[1196,1264,2507,2530]" pageId="6" pageNumber="7" rank="species">sp. n.</taxonomicNameLabel>
a,d Anterior end of fem ale; b,c Anterior end of male; e Female vulva; f.g Lateral field of female and male, respectively; h Female anus and tail; ij Male bursa with genital papillae indicated; k Detail of cloaca region with postcloacal sensillae; I Detail of male spiculum
</paragraph>
</caption>
<subSubSection lastPageId="7" lastPageNumber="8" pageId="6" pageNumber="7" type="biology_ecology">
<paragraph blockId="6.[1272,2246,2769,3056]" box="[1272,1602,2772,2803]" pageId="6" pageNumber="7">
<emphasis box="[1272,1472,2772,2803]" italics="true" pageId="6" pageNumber="7">
<emphasis bold="true" box="[1272,1398,2772,2803]" italics="true" pageId="6" pageNumber="7">Ecology</emphasis>
and
</emphasis>
biology
</paragraph>
<paragraph blockId="6.[1272,2246,2769,3056]" lastBlockId="7.[1270,2246,365,1306]" lastPageId="7" lastPageNumber="8" pageId="6" pageNumber="7">
<taxonomicName box="[1274,1769,2820,2856]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="6" pageNumber="7" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1274,1769,2820,2856]" italics="true" pageId="6" pageNumber="7">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1795,1896,2820,2856]" pageId="6" pageNumber="7" rank="species">sp. n.</taxonomicNameLabel>
is a gonochoristic species with both males and females. Females are oviparous and carry only one egg (rarely two eggs). Development from egg to adult took about 5-6 days in juice prepared from brown algae at room temperature. Development from dauer larva to adults was completed in less than 3 days at 20 °C on NA seeded with OP50. The lifespan of adults is at m inim um 14 days for males and 17 days for females. One pair of adults produced 167 offspring in 8 days and the daily production of fertile eggs was 6-31 (mean 18; 
<emphasis box="[1455,1514,368,404]" italics="true" pageId="7" pageNumber="8">n =</emphasis>
14). After the reproductive phase, females lived 9-1 4 days 
<emphasis box="[1555,1626,418,454]" italics="true" pageId="7" pageNumber="8">(n =</emphasis>
3) with males present.
</paragraph>
<caption ID-Table-UUID="DF0441CF2867FFC43989D95204E2FE46" httpUri="http://table.plazi.org/id/DF0441CF2867FFC43989D95204E2FE46" pageId="7" pageNumber="8" targetBox="[237,1212,477,2661]" targetIsTable="true" targetPageId="7">
<paragraph blockId="7.[238,1161,368,447]" pageId="7" pageNumber="8">
<emphasis bold="true" box="[238,355,368,401]" pageId="7" pageNumber="8">Table 1</emphasis>
Measurements (in |jm) of heat relaxed specimens of 
<taxonomicName box="[239,651,416,447]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[239,651,416,447]" italics="true" pageId="7" pageNumber="8">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[664,740,416,447]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
</paragraph>
</caption>
<paragraph lastBlockId="7.[237,1101,2164,2749]" pageId="7" pageNumber="8">
<table box="[237,1212,477,2661]" gridcols="4" gridrows="38" pageId="7" pageNumber="8">
<tr box="[237,1212,477,501]" gridrow="0" pageId="7" pageNumber="8">
<th box="[237,601,477,501]" gridcol="0" gridrow="0" pageId="7" pageNumber="8">Character</th>
<th box="[677,816,477,501]" gridcol="1" gridrow="0" pageId="7" pageNumber="8">Female</th>
<th box="[890,1006,477,501]" gridcol="2" gridrow="0" pageId="7" pageNumber="8">Male</th>
<th box="[1087,1212,477,501]" gridcol="3" gridrow="0" pageId="7" pageNumber="8">Dauer</th>
</tr>
<tr box="[237,1212,532,556]" gridrow="1" pageId="7" pageNumber="8">
<th box="[237,601,532,556]" gridcol="0" gridrow="1" pageId="7" pageNumber="8">N</th>
<td box="[677,816,532,556]" gridcol="1" gridrow="1" pageId="7" pageNumber="8">11</td>
<td box="[890,1006,532,556]" gridcol="2" gridrow="1" pageId="7" pageNumber="8">10</td>
<td box="[1087,1212,532,556]" gridcol="3" gridrow="1" pageId="7" pageNumber="8">10</td>
</tr>
<tr box="[237,1212,590,614]" gridrow="2" pageId="7" pageNumber="8" rowspan-0="1">
<td box="[677,816,590,614]" gridcol="1" gridrow="2" pageId="7" pageNumber="8">870 ± 105</td>
<td box="[890,1006,590,614]" gridcol="2" gridrow="2" pageId="7" pageNumber="8">694 ± 36</td>
<td box="[1087,1212,590,614]" gridcol="3" gridrow="2" pageId="7" pageNumber="8">
456 
<emphasis box="[1143,1160,591,614]" italics="true" pageId="7" pageNumber="8">±</emphasis>
2 4
</td>
</tr>
<tr box="[237,1212,648,672]" gridrow="3" pageId="7" pageNumber="8">
<th box="[237,601,648,672]" gridcol="0" gridrow="3" pageId="7" pageNumber="8">
<emphasis box="[238,254,648,671]" italics="true" pageId="7" pageNumber="8">A</emphasis>
</th>
<td box="[677,816,648,672]" gridcol="1" gridrow="3" pageId="7" pageNumber="8">
17.1 ± 
<emphasis bold="true" box="[760,797,648,671]" pageId="7" pageNumber="8">0.8</emphasis>
</td>
<td box="[890,1006,648,672]" gridcol="2" gridrow="3" pageId="7" pageNumber="8">22 ± 1.6</td>
<td box="[1087,1212,648,672]" gridcol="3" gridrow="3" pageId="7" pageNumber="8">23 ± 1.2</td>
</tr>
<tr box="[237,1212,707,731]" gridrow="4" pageId="7" pageNumber="8">
<th box="[237,601,707,731]" gridcol="0" gridrow="4" pageId="7" pageNumber="8">B</th>
<td box="[677,816,707,731]" gridcol="1" gridrow="4" pageId="7" pageNumber="8">4.9 ± 0.5</td>
<td box="[890,1006,707,731]" gridcol="2" gridrow="4" pageId="7" pageNumber="8">4.1 ±0.3</td>
<td box="[1087,1212,707,731]" gridcol="3" gridrow="4" pageId="7" pageNumber="8">
3.6 ± 
<emphasis bold="true" box="[1150,1187,708,731]" pageId="7" pageNumber="8">0.1</emphasis>
</td>
</tr>
<tr box="[237,1212,765,789]" gridrow="5" pageId="7" pageNumber="8">
<th box="[237,601,765,789]" gridcol="0" gridrow="5" pageId="7" pageNumber="8">C</th>
<td box="[677,816,765,789]" gridcol="1" gridrow="5" pageId="7" pageNumber="8">20.5 ± 2.6</td>
<td box="[890,1006,765,789]" gridcol="2" gridrow="5" pageId="7" pageNumber="8">22 ± 2.3</td>
<td box="[1087,1212,765,789]" gridcol="3" gridrow="5" pageId="7" pageNumber="8">
9.8 ± 
<emphasis bold="true" box="[1154,1191,766,789]" pageId="7" pageNumber="8">0.7</emphasis>
</td>
</tr>
<tr box="[237,1212,823,847]" gridrow="6" pageId="7" pageNumber="8">
<th box="[237,601,823,847]" gridcol="0" gridrow="6" pageId="7" pageNumber="8">c'</th>
<td box="[677,816,823,847]" gridcol="1" gridrow="6" pageId="7" pageNumber="8">
1.99 ± 
<emphasis bold="true" box="[760,813,823,846]" pageId="7" pageNumber="8">0.17</emphasis>
</td>
<td box="[890,1006,823,847]" gridcol="2" gridrow="6" pageId="7" pageNumber="8">
<emphasis bold="true" box="[895,928,823,846]" pageId="7" pageNumber="8">1.8</emphasis>
± 0.2
</td>
<td box="[1087,1212,823,847]" gridcol="3" gridrow="6" pageId="7" pageNumber="8">3.9 ± 0.30</td>
</tr>
<tr box="[237,1212,881,908]" gridrow="7" pageId="7" pageNumber="8">
<th box="[237,601,881,908]" gridcol="0" gridrow="7" pageId="7" pageNumber="8">
<emphasis box="[237,253,882,905]" italics="true" pageId="7" pageNumber="8">V</emphasis>
</th>
<td box="[677,816,881,908]" gridcol="1" gridrow="7" pageId="7" pageNumber="8">
65 ± 
<emphasis bold="true" box="[746,778,882,905]" pageId="7" pageNumber="8">1.8</emphasis>
</td>
<td box="[890,1006,881,908]" gridcol="2" gridrow="7" pageId="7" pageNumber="8">
<emphasis bold="true" box="[892,904,881,908]" pageId="7" pageNumber="8">-</emphasis>
</td>
<td box="[1087,1212,881,908]" gridcol="3" gridrow="7" pageId="7" pageNumber="8">
<emphasis bold="true" box="[1089,1099,884,907]" pageId="7" pageNumber="8">-</emphasis>
</td>
</tr>
<tr box="[237,1212,940,964]" gridrow="8" pageId="7" pageNumber="8">
<th box="[237,601,940,964]" gridcol="0" gridrow="8" pageId="7" pageNumber="8">
<emphasis bold="true" box="[240,305,940,963]" pageId="7" pageNumber="8">Body</emphasis>
width
</th>
<td box="[677,816,940,964]" gridcol="1" gridrow="8" pageId="7" pageNumber="8">
51 ± 
<emphasis bold="true" box="[738,775,941,964]" pageId="7" pageNumber="8">6.9</emphasis>
</td>
<td box="[890,1006,940,964]" gridcol="2" gridrow="8" pageId="7" pageNumber="8">32 ± 3</td>
<td box="[1087,1212,940,964]" gridcol="3" gridrow="8" pageId="7" pageNumber="8">20 ± 0.6</td>
</tr>
<tr box="[237,1212,998,1022]" gridrow="9" pageId="7" pageNumber="8">
<th box="[237,601,998,1022]" gridcol="0" gridrow="9" pageId="7" pageNumber="8">Stoma length</th>
<td box="[677,816,998,1022]" gridcol="1" gridrow="9" pageId="7" pageNumber="8">27 ± 2.3</td>
<td box="[890,1006,998,1022]" gridcol="2" gridrow="9" pageId="7" pageNumber="8">
<emphasis bold="true" box="[893,923,998,1021]" pageId="7" pageNumber="8">27</emphasis>
± 2
</td>
<td box="[1087,1212,998,1022]" gridcol="3" gridrow="9" pageId="7" pageNumber="8">21 ±1.1</td>
</tr>
<tr box="[237,1212,1057,1081]" gridrow="10" pageId="7" pageNumber="8">
<th box="[237,601,1057,1081]" gridcol="0" gridrow="10" pageId="7" pageNumber="8">
Stoma diam 
<emphasis box="[398,448,1057,1080]" italics="true" pageId="7" pageNumber="8">eter</emphasis>
</th>
<td box="[677,816,1057,1081]" gridcol="1" gridrow="10" pageId="7" pageNumber="8">1.9 ± 0.6</td>
<td box="[890,1006,1057,1081]" gridcol="2" gridrow="10" pageId="7" pageNumber="8">1.2 ± 0.2</td>
<td box="[1087,1212,1057,1081]" gridcol="3" gridrow="10" pageId="7" pageNumber="8">0.6 ±0.1</td>
</tr>
<tr box="[237,1212,1115,1141]" gridrow="11" pageId="7" pageNumber="8">
<th box="[237,601,1115,1141]" gridcol="0" gridrow="11" pageId="7" pageNumber="8">Cheilostom</th>
<td box="[677,816,1115,1141]" gridcol="1" gridrow="11" pageId="7" pageNumber="8">2.5 ±0.2</td>
<td box="[890,1006,1115,1141]" gridcol="2" gridrow="11" pageId="7" pageNumber="8">2.4 ± 0,2</td>
<td box="[1087,1212,1115,1141]" gridcol="3" gridrow="11" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1173,1199]" gridrow="12" pageId="7" pageNumber="8">
<th box="[237,601,1173,1199]" gridcol="0" gridrow="12" pageId="7" pageNumber="8">Gym nostom</th>
<td box="[677,816,1173,1199]" gridcol="1" gridrow="12" pageId="7" pageNumber="8">10 ± 0.7</td>
<td box="[890,1006,1173,1199]" gridcol="2" gridrow="12" pageId="7" pageNumber="8">
9.7 
<emphasis box="[936,955,1174,1197]" italics="true" pageId="7" pageNumber="8">±</emphasis>
0.9
</td>
<td box="[1087,1212,1173,1199]" gridcol="3" gridrow="12" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1232,1257]" gridrow="13" pageId="7" pageNumber="8">
<th box="[237,601,1232,1257]" gridcol="0" gridrow="13" pageId="7" pageNumber="8">Stegostom</th>
<td box="[677,816,1232,1257]" gridcol="1" gridrow="13" pageId="7" pageNumber="8">15 ± 1.5</td>
<td box="[890,1006,1232,1257]" gridcol="2" gridrow="13" pageId="7" pageNumber="8">
15 
<emphasis box="[926,945,1232,1255]" italics="true" pageId="7" pageNumber="8">±</emphasis>
1.5
</td>
<td box="[1087,1212,1232,1257]" gridcol="3" gridrow="13" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1290,1314]" gridrow="14" pageId="7" pageNumber="8" rowspan-3="1">
<th box="[237,601,1290,1314]" gridcol="0" gridrow="14" pageId="7" pageNumber="8">Pharyngeal sleeve</th>
<td box="[677,816,1290,1314]" gridcol="1" gridrow="14" pageId="7" pageNumber="8">12.42 ± 1.6</td>
<td box="[890,1006,1290,1314]" gridcol="2" gridrow="14" pageId="7" pageNumber="8">13 ± 1.2</td>
</tr>
<tr box="[237,1212,1349,1372]" gridrow="15" pageId="7" pageNumber="8">
<th box="[237,601,1349,1372]" gridcol="0" gridrow="15" pageId="7" pageNumber="8">Pharynx length</th>
<td box="[677,816,1349,1372]" gridcol="1" gridrow="15" pageId="7" pageNumber="8">150 ± 6.7</td>
<td box="[890,1006,1349,1372]" gridcol="2" gridrow="15" pageId="7" pageNumber="8">141 ± 9.2</td>
<td box="[1087,1212,1349,1372]" gridcol="3" gridrow="15" pageId="7" pageNumber="8">107 ± 3.3</td>
</tr>
<tr box="[237,1212,1408,1434]" gridrow="16" pageId="7" pageNumber="8">
<th box="[237,601,1408,1434]" gridcol="0" gridrow="16" pageId="7" pageNumber="8">Procorpus length</th>
<td box="[677,816,1408,1434]" gridcol="1" gridrow="16" pageId="7" pageNumber="8">55 ±3.1</td>
<td box="[890,1006,1408,1434]" gridcol="2" gridrow="16" pageId="7" pageNumber="8">52 ± 3.6</td>
<td box="[1087,1212,1408,1434]" gridcol="3" gridrow="16" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1466,1492]" gridrow="17" pageId="7" pageNumber="8">
<th box="[237,601,1466,1492]" gridcol="0" gridrow="17" pageId="7" pageNumber="8">M etacorpus length</th>
<td box="[677,816,1466,1492]" gridcol="1" gridrow="17" pageId="7" pageNumber="8">26 ±2.1</td>
<td box="[890,1006,1466,1492]" gridcol="2" gridrow="17" pageId="7" pageNumber="8">22.8 ±1.1</td>
<td box="[1087,1212,1466,1492]" gridcol="3" gridrow="17" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1524,1550]" gridrow="18" pageId="7" pageNumber="8">
<th box="[237,601,1524,1550]" gridcol="0" gridrow="18" pageId="7" pageNumber="8">Isthmus length</th>
<td box="[677,816,1524,1550]" gridcol="1" gridrow="18" pageId="7" pageNumber="8">39 ± 3.2</td>
<td box="[890,1006,1524,1550]" gridcol="2" gridrow="18" pageId="7" pageNumber="8">40 ± 4.9</td>
<td box="[1087,1212,1524,1550]" gridcol="3" gridrow="18" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1583,1609]" gridrow="19" pageId="7" pageNumber="8">
<th box="[237,601,1583,1609]" gridcol="0" gridrow="19" pageId="7" pageNumber="8">
Nerve ring 
<emphasis box="[388,414,1583,1606]" italics="true" pageId="7" pageNumber="8">to</emphasis>
terminal bulb
</th>
<td box="[677,816,1583,1609]" gridcol="1" gridrow="19" pageId="7" pageNumber="8">11 ± 4.9</td>
<td box="[890,1006,1583,1609]" gridcol="2" gridrow="19" pageId="7" pageNumber="8">19 ± 3.3</td>
<td box="[1087,1212,1583,1609]" gridcol="3" gridrow="19" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1641,1668]" gridrow="20" pageId="7" pageNumber="8">
<th box="[237,601,1641,1668]" gridcol="0" gridrow="20" pageId="7" pageNumber="8">
<emphasis box="[237,300,1641,1664]" italics="true" pageId="7" pageNumber="8">Term</emphasis>
inal bulb length
</th>
<td box="[677,816,1641,1668]" gridcol="1" gridrow="20" pageId="7" pageNumber="8">30 ± 1.8</td>
<td box="[890,1006,1641,1668]" gridcol="2" gridrow="20" pageId="7" pageNumber="8">27 ± 1.7</td>
<td box="[1087,1212,1641,1668]" gridcol="3" gridrow="20" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1699,1723]" gridrow="21" pageId="7" pageNumber="8">
<th box="[237,601,1699,1723]" gridcol="0" gridrow="21" pageId="7" pageNumber="8">Diam eter o f median bulb</th>
<td box="[677,816,1699,1723]" gridcol="1" gridrow="21" pageId="7" pageNumber="8">22 ± 2.5</td>
<td box="[890,1006,1699,1723]" gridcol="2" gridrow="21" pageId="7" pageNumber="8">
17 
<emphasis box="[930,948,1699,1722]" italics="true" pageId="7" pageNumber="8">±</emphasis>
1.3
</td>
<td box="[1087,1212,1699,1723]" gridcol="3" gridrow="21" pageId="7" pageNumber="8">9 ± 0 5</td>
</tr>
<tr box="[237,1212,1757,1783]" gridrow="22" pageId="7" pageNumber="8">
<th box="[237,601,1757,1783]" gridcol="0" gridrow="22" pageId="7" pageNumber="8">Diam eter o f terminal bulb</th>
<td box="[677,816,1757,1783]" gridcol="1" gridrow="22" pageId="7" pageNumber="8">25 ± 2</td>
<td box="[890,1006,1757,1783]" gridcol="2" gridrow="22" pageId="7" pageNumber="8">
19 
<emphasis box="[926,945,1760,1783]" italics="true" pageId="7" pageNumber="8">±</emphasis>
1
</td>
<td box="[1087,1212,1757,1783]" gridcol="3" gridrow="22" pageId="7" pageNumber="8">11 ± 0,4</td>
</tr>
<tr box="[237,1212,1817,1842]" gridrow="23" pageId="7" pageNumber="8">
<th box="[237,601,1817,1842]" gridcol="0" gridrow="23" pageId="7" pageNumber="8">
Anterior end 
<emphasis box="[417,443,1817,1840]" italics="true" pageId="7" pageNumber="8">to</emphasis>
deirid
</th>
<td box="[677,816,1817,1842]" gridcol="1" gridrow="23" pageId="7" pageNumber="8">150 ± 8</td>
<td box="[890,1006,1817,1842]" gridcol="2" gridrow="23" pageId="7" pageNumber="8">150 ± 8.3</td>
<td box="[1087,1212,1817,1842]" gridcol="3" gridrow="23" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1872,1900]" gridrow="24" pageId="7" pageNumber="8">
<th box="[237,601,1872,1900]" gridcol="0" gridrow="24" pageId="7" pageNumber="8">
Postdeirid 
<emphasis box="[380,406,1875,1898]" italics="true" pageId="7" pageNumber="8">to</emphasis>
anus
</th>
<td box="[677,816,1872,1900]" gridcol="1" gridrow="24" pageId="7" pageNumber="8">1 70 ± 29.8</td>
<td box="[890,1006,1872,1900]" gridcol="2" gridrow="24" pageId="7" pageNumber="8">141 ± 1 4</td>
<td box="[1087,1212,1872,1900]" gridcol="3" gridrow="24" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1934,1959]" gridrow="25" pageId="7" pageNumber="8">
<th box="[237,601,1934,1959]" gridcol="0" gridrow="25" pageId="7" pageNumber="8">Length intestine</th>
<td box="[677,816,1934,1959]" gridcol="1" gridrow="25" pageId="7" pageNumber="8">651 ± 100</td>
<td box="[890,1006,1934,1959]" gridcol="2" gridrow="25" pageId="7" pageNumber="8">494 ± 32</td>
<td box="[1087,1212,1934,1959]" gridcol="3" gridrow="25" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,1992,2017]" gridrow="26" pageId="7" pageNumber="8">
<th box="[237,601,1992,2017]" gridcol="0" gridrow="26" pageId="7" pageNumber="8">Rectum length</th>
<td box="[677,816,1992,2017]" gridcol="1" gridrow="26" pageId="7" pageNumber="8">25 ± 2.6</td>
<td box="[890,1006,1992,2017]" gridcol="2" gridrow="26" pageId="7" pageNumber="8">24± 1.9</td>
<td box="[1087,1212,1992,2017]" gridcol="3" gridrow="26" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2047,2074]" gridrow="27" pageId="7" pageNumber="8">
<th box="[237,601,2047,2074]" gridcol="0" gridrow="27" pageId="7" pageNumber="8">
<emphasis box="[237,293,2050,2073]" italics="true" pageId="7" pageNumber="8">Anal</emphasis>
body width
</th>
<td box="[677,816,2047,2074]" gridcol="1" gridrow="27" pageId="7" pageNumber="8">22 ±2.1</td>
<td box="[890,1006,2047,2074]" gridcol="2" gridrow="27" pageId="7" pageNumber="8">1 7 ± 1.1</td>
<td box="[1087,1212,2047,2074]" gridcol="3" gridrow="27" pageId="7" pageNumber="8">
12 
<emphasis box="[1127,1146,2047,2074]" italics="true" pageId="7" pageNumber="8">±</emphasis>
0.6
</td>
</tr>
<tr box="[237,1212,2106,2133]" gridrow="28" pageId="7" pageNumber="8">
<th box="[237,601,2106,2133]" gridcol="0" gridrow="28" pageId="7" pageNumber="8">Tail length</th>
<td box="[677,816,2106,2133]" gridcol="1" gridrow="28" pageId="7" pageNumber="8">43 ± 4.3</td>
<td box="[890,1006,2106,2133]" gridcol="2" gridrow="28" pageId="7" pageNumber="8">32 ± 3.2</td>
<td box="[1087,1212,2106,2133]" gridcol="3" gridrow="28" pageId="7" pageNumber="8">
46 
<emphasis box="[1128,1147,2106,2133]" italics="true" pageId="7" pageNumber="8">±</emphasis>
2.4
</td>
</tr>
<tr box="[237,1212,2164,2193]" gridrow="29" pageId="7" pageNumber="8">
<th box="[237,601,2164,2193]" gridcol="0" gridrow="29" pageId="7" pageNumber="8">Anus to phasm id distance</th>
<td box="[677,816,2164,2193]" gridcol="1" gridrow="29" pageId="7" pageNumber="8">
26 
<emphasis box="[717,735,2164,2191]" italics="true" pageId="7" pageNumber="8">±</emphasis>
2.2
</td>
<td box="[890,1006,2164,2193]" gridcol="2" gridrow="29" pageId="7" pageNumber="8">-</td>
<td box="[1087,1212,2164,2193]" gridcol="3" gridrow="29" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2222,2252]" gridrow="30" pageId="7" pageNumber="8">
<th box="[237,601,2222,2252]" gridcol="0" gridrow="30" pageId="7" pageNumber="8">Gonad length3</th>
<td box="[677,816,2222,2252]" gridcol="1" gridrow="30" pageId="7" pageNumber="8">
<emphasis bold="true" box="[679,723,2222,2249]" pageId="7" pageNumber="8">303</emphasis>
<emphasis box="[732,751,2222,2249]" italics="true" pageId="7" pageNumber="8">±</emphasis>
68
</td>
<td box="[890,1006,2222,2252]" gridcol="2" gridrow="30" pageId="7" pageNumber="8">
342 
<emphasis box="[945,962,2225,2248]" italics="true" pageId="7" pageNumber="8">±</emphasis>
4 4
</td>
<td box="[1087,1212,2222,2252]" gridcol="3" gridrow="30" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2280,2310]" gridrow="31" pageId="7" pageNumber="8">
<th box="[237,601,2280,2310]" gridcol="0" gridrow="31" pageId="7" pageNumber="8">Gonad flexure length</th>
<td box="[677,816,2280,2310]" gridcol="1" gridrow="31" pageId="7" pageNumber="8">
226 
<emphasis box="[732,751,2280,2307]" italics="true" pageId="7" pageNumber="8">±</emphasis>
67
</td>
<td box="[890,1006,2280,2310]" gridcol="2" gridrow="31" pageId="7" pageNumber="8">
46 
<emphasis box="[929,948,2280,2307]" italics="true" pageId="7" pageNumber="8">±</emphasis>
6.8
</td>
<td box="[1087,1212,2280,2310]" gridcol="3" gridrow="31" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2339,2369]" gridrow="32" pageId="7" pageNumber="8">
<th box="[237,601,2339,2369]" gridcol="0" gridrow="32" pageId="7" pageNumber="8">Postuteiine sac</th>
<td box="[677,816,2339,2369]" gridcol="1" gridrow="32" pageId="7" pageNumber="8">45 ± 6.8</td>
<td box="[890,1006,2339,2369]" gridcol="2" gridrow="32" pageId="7" pageNumber="8">-</td>
<td box="[1087,1212,2339,2369]" gridcol="3" gridrow="32" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2397,2427]" gridrow="33" pageId="7" pageNumber="8">
<th box="[237,601,2397,2427]" gridcol="0" gridrow="33" pageId="7" pageNumber="8">
Sperm diam 
<emphasis box="[399,449,2401,2424]" italics="true" pageId="7" pageNumber="8">eter</emphasis>
</th>
<td box="[677,816,2397,2427]" gridcol="1" gridrow="33" pageId="7" pageNumber="8">-</td>
<td box="[890,1006,2397,2427]" gridcol="2" gridrow="33" pageId="7" pageNumber="8">9.8 ± 1.3</td>
<td box="[1087,1212,2397,2427]" gridcol="3" gridrow="33" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2456,2486]" gridrow="34" pageId="7" pageNumber="8">
<th box="[237,601,2456,2486]" gridcol="0" gridrow="34" pageId="7" pageNumber="8">Egg lengthb</th>
<td box="[677,816,2456,2486]" gridcol="1" gridrow="34" pageId="7" pageNumber="8">
53 ± 
<emphasis bold="true" box="[734,773,2456,2483]" pageId="7" pageNumber="8">3.1</emphasis>
</td>
<td box="[890,1006,2456,2486]" gridcol="2" gridrow="34" pageId="7" pageNumber="8">-</td>
<td box="[1087,1212,2456,2486]" gridcol="3" gridrow="34" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2514,2544]" gridrow="35" pageId="7" pageNumber="8">
<th box="[237,601,2514,2544]" gridcol="0" gridrow="35" pageId="7" pageNumber="8">Egg I liam eterb</th>
<td box="[677,816,2514,2544]" gridcol="1" gridrow="35" pageId="7" pageNumber="8">29 ±2.9</td>
<td box="[890,1006,2514,2544]" gridcol="2" gridrow="35" pageId="7" pageNumber="8">-</td>
<td box="[1087,1212,2514,2544]" gridcol="3" gridrow="35" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2572,2602]" gridrow="36" pageId="7" pageNumber="8">
<th box="[237,601,2572,2602]" gridcol="0" gridrow="36" pageId="7" pageNumber="8">
Spicule 
<emphasis box="[344,424,2576,2599]" italics="true" pageId="7" pageNumber="8">Length</emphasis>
</th>
<td box="[677,816,2572,2602]" gridcol="1" gridrow="36" pageId="7" pageNumber="8">-</td>
<td box="[890,1006,2572,2602]" gridcol="2" gridrow="36" pageId="7" pageNumber="8">25 ± 1</td>
<td box="[1087,1212,2572,2602]" gridcol="3" gridrow="36" pageId="7" pageNumber="8">-</td>
</tr>
<tr box="[237,1212,2631,2661]" gridrow="37" pageId="7" pageNumber="8">
<th box="[237,601,2631,2661]" gridcol="0" gridrow="37" pageId="7" pageNumber="8">
Gubernaculum 
<emphasis box="[446,525,2635,2658]" italics="true" pageId="7" pageNumber="8">length</emphasis>
</th>
<td box="[677,816,2631,2661]" gridcol="1" gridrow="37" pageId="7" pageNumber="8">-</td>
<td box="[890,1006,2631,2661]" gridcol="2" gridrow="37" pageId="7" pageNumber="8">
<emphasis bold="true" box="[894,921,2631,2658]" pageId="7" pageNumber="8">15</emphasis>
± 0.9
</td>
<td box="[1087,1212,2631,2661]" gridcol="3" gridrow="37" pageId="7" pageNumber="8">-</td>
</tr>
</table>
</paragraph>
<paragraph blockId="7.[1270,2246,365,1306]" pageId="7" pageNumber="8">
<taxonomicName box="[1306,1792,470,506]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1306,1792,470,506]" italics="true" pageId="7" pageNumber="8">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1809,1901,470,506]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
has until now only been found in 
<taxonomicName box="[1537,1735,518,554]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="7" pageNumber="8" phylum="Basidiomycota" rank="genus">
<emphasis box="[1537,1735,518,554]" italics="true" pageId="7" pageNumber="8">Ganoderma</emphasis>
</taxonomicName>
and 
<taxonomicName box="[1835,1940,518,554]" class="Agaricomycetes" family="Polyporaceae" genus="Fomes" kingdom="Fungi" order="Polyporales" pageId="7" pageNumber="8" phylum="Basidiomycota" rank="genus">
<emphasis box="[1835,1940,518,554]" italics="true" pageId="7" pageNumber="8">Fomes</emphasis>
</taxonomicName>
in Germany and Belgium in relation with the ciid beetle 
<emphasis box="[2001,2242,568,604]" italics="true" pageId="7" pageNumber="8">
<taxonomicName box="[2001,2237,568,604]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="7" pageNumber="8" phylum="Arthropoda" rank="species" species="castaneus">Cis castaneus</taxonomicName>
.
</emphasis>
The 
<taxonomicName box="[1351,1545,618,654]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="7" pageNumber="8" phylum="Basidiomycota" rank="genus">
<emphasis box="[1351,1545,618,654]" italics="true" pageId="7" pageNumber="8">Ganoderma</emphasis>
</taxonomicName>
carrying 
<taxonomicName box="[1708,1961,618,655]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1708,1734,619,655]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1754,1961,618,654]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1975,2062,619,655]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
from Oslo was not investigated for the presence of 
<taxonomicName box="[1974,2187,668,705]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="7" pageNumber="8" phylum="Arthropoda" rank="species" species="castaneus">
<emphasis box="[1974,2001,669,705]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[2024,2192,668,704]" italics="true" pageId="7" pageNumber="8">castaneus.</emphasis>
</taxonomicName>
In fungal fruiting bodies lacking the beetle C. 
<taxonomicName box="[2037,2243,718,754]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[2037,2243,718,754]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1271,1357,770,806]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
was not found. Dauers of C. 
<taxonomicName box="[1848,2054,770,806]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1848,2054,770,806]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[2068,2155,770,806]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
were found under the elytra of the beetle, but were not found internally when the beetle was further dissected. These findings indicate a phoretic association with the beetle. As only dauer larvae were isolated from beetles, while adults and larvae were present in the fruiting bodies, 
<emphasis box="[2103,2150,1020,1056]" italics="true" pageId="7" pageNumber="8">we</emphasis>
infer that 
<taxonomicName box="[1360,1623,1070,1106]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1360,1385,1070,1106]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1416,1623,1070,1106]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1645,1743,1070,1106]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
exit from dauer within the mushroom, develop to adulthood and start to reproduce. The food source of the species in natural conditions is not known, but they survive and reproduce easily on £ 
<taxonomicName box="[2187,2245,1218,1254]" pageId="7" pageNumber="8" rank="species" species="coli">
<emphasis box="[2187,2245,1218,1254]" italics="true" pageId="7" pageNumber="8">coli</emphasis>
</taxonomicName>
OP50 in 
<emphasis bold="true" box="[1420,1543,1270,1306]" pageId="7" pageNumber="8">culture.</emphasis>
</paragraph>
</subSubSection>
<subSubSection lastPageId="8" lastPageNumber="9" pageId="7" pageNumber="8" type="description">
<paragraph blockId="7.[1270,2247,1368,3057]" box="[1272,2174,1372,1403]" pageId="7" pageNumber="8">
<emphasis bold="true" box="[1272,1564,1372,1403]" italics="true" pageId="7" pageNumber="8">Genome sequence</emphasis>
of 
<emphasis box="[1619,1876,1372,1403]" italics="true" pageId="7" pageNumber="8">an inbred strain</emphasis>
of 
<taxonomicName box="[1934,2174,1372,1403]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="genus">
<emphasis box="[1934,2174,1372,1403]" italics="true" pageId="7" pageNumber="8">Caenorhabditis</emphasis>
</taxonomicName>
</paragraph>
<paragraph blockId="7.[1270,2247,1368,3057]" box="[1271,1574,1422,1453]" pageId="7" pageNumber="8">
<emphasis box="[1271,1574,1422,1453]" italics="true" pageId="7" pageNumber="8">
<taxonomicName box="[1271,1477,1422,1453]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[1489,1574,1422,1453]" pageId="7" pageNumber="8" rank="species">
<emphasis bold="true" box="[1489,1534,1422,1453]" italics="true" pageId="7" pageNumber="8">sp.</emphasis>
n.
</taxonomicNameLabel>
</emphasis>
</paragraph>
<paragraph blockId="7.[1270,2247,1368,3057]" pageId="7" pageNumber="8">
We sequenced the genome of an inbred strain (JU1677) of 
<taxonomicName box="[1319,1578,1520,1556]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1319,1344,1520,1556]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1366,1578,1520,1556]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1592,1682,1520,1556]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
using Illumina sequencing technology to ~110 
<emphasis bold="true" box="[1541,1563,1570,1606]" pageId="7" pageNumber="8">x</emphasis>
coverage. The genome was assembled into 6,864 scaffolds, spanning 115.1 Mb with a scaffold N50 of 49.4 kb (
<tableCitation box="[1546,1672,1670,1706]" captionStart="Table 2" captionStartId="8.[238,330,370,403]" captionTargetBox="[237,2243,433,1015]" captionTargetPageId="8" captionText="Table 2 Genome assembly statistics for C. monodelphis sp. n. and other Caenorhabditis species" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D9500084FE6A" pageId="7" pageNumber="8" tableUuid="DF0441CF2868FFCB3989D9500084FE6A">Table 2</tableCitation>
). CEGMA (Core Eukaryotic Gene Mapping Approach) [
<bibRefCitation author="Parra G &amp; Bradnam K" box="[1637,1678,1720,1756]" journalOrPublisher="Bioinformatics" pageId="7" pageNumber="8" pagination="1061 - 7" part="23" refString="40. Parra G, Bradnam K Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007; 23: 1061 - 7." title="Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes" type="journal article" year="2007">40</bibRefCitation>
] scores suggested the assembly is of high completeness. W e predicted 17,180 protein coding gene models using RNA-Seq evidence. These statistics, and the overall gene content and structure of the assembly were largely in keeping with those determined for other 
<taxonomicName box="[1273,1525,1970,2006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="genus">
<emphasis box="[1273,1525,1970,2006]" italics="true" pageId="7" pageNumber="8">Caenorhabditis</emphasis>
</taxonomicName>
species. The genome was larger than that of 
<taxonomicName box="[1323,1493,2020,2056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1323,1348,2020,2056]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1374,1493,2020,2056]" italics="true" pageId="7" pageNumber="8">elegans</emphasis>
</taxonomicName>
and 
<taxonomicName box="[1591,1777,2020,2056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="briggsae">
<emphasis box="[1591,1616,2020,2056]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1642,1783,2020,2056]" italics="true" pageId="7" pageNumber="8">briggsae,</emphasis>
</taxonomicName>
which are hermaphroditic species, but smaller than that of C. 
<emphasis box="[1861,2004,2070,2106]" italics="true" pageId="7" pageNumber="8">remanei,</emphasis>
a gonochoristic species.
</paragraph>
<paragraph blockId="7.[1270,2247,1368,3057]" lastBlockId="8.[238,1215,1117,1207]" lastPageId="8" lastPageNumber="9" pageId="7" pageNumber="8">
We carried out preliminary comparisons of the structure and 
<emphasis bold="true" box="[1353,1479,2220,2256]" pageId="7" pageNumber="8">content</emphasis>
of the 
<taxonomicName box="[1624,1886,2220,2256]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1624,1649,2220,2256]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1677,1886,2220,2256]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1905,2000,2220,2256]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
genome with those of other sequenced 
<taxonomicName box="[1753,2005,2270,2306]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="genus">
<emphasis box="[1753,2005,2270,2306]" italics="true" pageId="7" pageNumber="8">Caenorhabditis</emphasis>
</taxonomicName>
species. The number of genes identified was lower than estimates for most other 
<taxonomicName box="[1473,1725,2370,2406]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="genus">
<emphasis box="[1473,1725,2370,2406]" italics="true" pageId="7" pageNumber="8">Caenorhabditis</emphasis>
</taxonomicName>
species. To compare the gene structures of 
<taxonomicName box="[1503,1761,2420,2456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1503,1528,2420,2456]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1552,1761,2420,2456]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1777,1869,2420,2456]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
to that of 
<taxonomicName box="[2068,2236,2420,2456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[2068,2093,2420,2456]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[2117,2243,2420,2456]" italics="true" pageId="7" pageNumber="8">elegans,</emphasis>
</taxonomicName>
we identified 6,174 orthologous gene pairs and calculated gene structure statistics (
<tableCitation box="[1684,1806,2520,2556]" captionStart="Table 3" captionStartId="8.[238,329,2448,2481]" captionTargetBox="[238,1210,2554,2928]" captionText="Table 3 Gene structure comparison of orthologous gene pairs from C. monodelphis sp. N. and C. elegans" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D1B2055BF626" pageId="7" pageNumber="8" tableUuid="DF0441CF2868FFCB3989D1B2055BF626">Table 3</tableCitation>
, 
<figureCitation box="[1825,1917,2520,2556]" captionStart="Fig. 5" captionStartId="9.[264,311,2331,2358]" captionTargetBox="[237,2230,367,2308]" captionText="Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20 % longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log 2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count" httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="7" pageNumber="8">Fig. 5</figureCitation>
.). To minimize bias from erroneous gene predictions (such as merged or split genes), orthologous gene pairs which differed in CDS length by 20% were considered outliers. 
<taxonomicName box="[1984,2242,2670,2706]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1984,2009,2670,2706]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[2036,2242,2670,2706]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1271,1357,2720,2756]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
genes were typically longer than their orthologues in 
<taxonomicName box="[1273,1451,2770,2806]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1273,1298,2770,2806]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1326,1456,2770,2806]" italics="true" pageId="7" pageNumber="8">elegans.</emphasis>
</taxonomicName>
W e also found a clear trend toward more coding exons per gene in 
<taxonomicName box="[1730,1996,2820,2856]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1730,1756,2820,2856]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1780,1996,2820,2856]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[2011,2103,2820,2856]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
than in 
<taxonomicName box="[1273,1446,2870,2906]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1273,1298,2870,2906]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1323,1446,2870,2906]" italics="true" pageId="7" pageNumber="8">elegans</emphasis>
</taxonomicName>
(
<figureCitation box="[1475,1574,2870,2906]" captionStart="Fig. 5" captionStartId="9.[264,311,2331,2358]" captionTargetBox="[237,2230,367,2308]" captionText="Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20 % longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log 2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count" httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="7" pageNumber="8">Fig. 5</figureCitation>
a). A few examples of 
<taxonomicName box="[1977,2243,2870,2906]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1977,2003,2870,2906]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[2027,2243,2870,2906]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1271,1361,2920,2956]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
gene models compared to those of orthologues in 
<taxonomicName box="[1273,1443,2970,3006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1273,1298,2970,3006]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1320,1443,2970,3006]" italics="true" pageId="7" pageNumber="8">elegans</emphasis>
</taxonomicName>
are shown (
<figureCitation box="[1660,1756,2970,3006]" captionStart="Fig. 5" captionStartId="9.[264,311,2331,2358]" captionTargetBox="[237,2230,367,2308]" captionText="Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20 % longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log 2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count" httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="7" pageNumber="8">Fig. 5</figureCitation>
b). Although introns are, on average, shorter in 
<taxonomicName box="[1585,1835,3020,3056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1585,1610,3020,3056]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[1630,1835,3020,3056]" italics="true" pageId="7" pageNumber="8">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1847,1933,3020,3056]" pageId="7" pageNumber="8" rank="species">sp. n.</taxonomicNameLabel>
than in 
<taxonomicName box="[2076,2235,3020,3056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="7" pageNumber="8" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[2076,2100,3020,3056]" italics="true" pageId="7" pageNumber="8">C</emphasis>
. 
<emphasis box="[2120,2241,3020,3056]" italics="true" pageId="7" pageNumber="8">elegans,</emphasis>
</taxonomicName>
<taxonomicName box="[240,492,1120,1156]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis">
<emphasis box="[240,492,1120,1156]" italics="true" pageId="8" pageNumber="9">C. monodelphis</emphasis>
</taxonomicName>
genes typically have a longer total span of introns than C. 
<taxonomicName box="[495,612,1170,1206]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[495,612,1170,1206]" italics="true" pageId="8" pageNumber="9">elegans</emphasis>
</taxonomicName>
transcripts (
<tableCitation box="[816,937,1170,1206]" captionStart="Table 3" captionStartId="8.[238,329,2448,2481]" captionTargetBox="[238,1210,2554,2928]" captionText="Table 3 Gene structure comparison of orthologous gene pairs from C. monodelphis sp. N. and C. elegans" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D1B2055BF626" pageId="8" pageNumber="9" tableUuid="DF0441CF2868FFCB3989D1B2055BF626">Table 3</tableCitation>
, 
<figureCitation box="[957,1047,1170,1206]" captionStart="Fig. 5" captionStartId="9.[264,311,2331,2358]" captionTargetBox="[237,2230,367,2308]" captionText="Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20 % longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log 2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count" httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="8" pageNumber="9">Fig. 5</figureCitation>
.).
</paragraph>
<paragraph blockId="7.[237,1101,2164,2749]" pageId="7" pageNumber="8">
<tableNote pageId="7" pageNumber="8" targetBox="[237,1212,477,2661]" targetPageId="7">
afrom anus to flexure in the female; from 
<emphasis bold="true" box="[751,826,2687,2712]" pageId="7" pageNumber="8">cloaca</emphasis>
to flexure in the male bn = 7
</tableNote>
</paragraph>
<caption ID-Table-UUID="DF0441CF2868FFCB3989D9500084FE6A" box="[238,1666,370,403]" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D9500084FE6A" pageId="8" pageNumber="9" targetBox="[237,2243,433,1015]" targetIsTable="true" targetPageId="8">
<paragraph blockId="8.[237,2247,368,627]" box="[238,1666,370,403]" pageId="8" pageNumber="9">
<emphasis bold="true" box="[238,361,370,403]" pageId="8" pageNumber="9">Table 2</emphasis>
Genome assembly statistics for 
<taxonomicName box="[850,1073,372,403]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[850,870,372,403]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<taxonomicName box="[887,1073,372,403]" pageId="8" pageNumber="9" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[887,1073,372,403]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
</taxonomicName>
<taxonomicNameLabel box="[1085,1161,372,403]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
and other 
<taxonomicName box="[1333,1549,372,403]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[1333,1549,372,403]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
species
</paragraph>
</caption>
<paragraph blockId="8.[237,2247,368,627]" lastBlockId="8.[238,2198,662,1070]" pageId="8" pageNumber="9">
<table box="[237,2243,433,1015]" gridcols="9" gridrows="10" pageId="8" pageNumber="9">
<tr box="[237,2243,433,457]" gridrow="0" pageId="8" pageNumber="9">
<th box="[237,484,433,457]" gridcol="0" gridrow="0" pageId="8" pageNumber="9">
<emphasis box="[238,334,433,456]" italics="true" pageId="8" pageNumber="9">Species</emphasis>
</th>
<th box="[512,709,433,457]" gridcol="1" gridrow="0" pageId="8" pageNumber="9">
<taxonomicName box="[514,709,433,456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis">C monodelphis</taxonomicName>
</th>
<th box="[740,917,433,457]" gridcol="2" gridrow="0" pageId="8" pageNumber="9">
<taxonomicName box="[741,876,434,457]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="brenneri">C. brenneri</taxonomicName>
</th>
<th box="[949,1150,433,457]" gridcol="3" gridrow="0" pageId="8" pageNumber="9">
C. 
<taxonomicName box="[984,1089,434,457]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="briggsae">
<emphasis box="[984,1089,434,457]" italics="true" pageId="8" pageNumber="9">briggsae</emphasis>
</taxonomicName>
</th>
<th box="[1181,1383,433,457]" gridcol="4" gridrow="0" pageId="8" pageNumber="9">
C. 
<taxonomicName box="[1215,1308,433,456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1215,1308,433,456]" italics="true" pageId="8" pageNumber="9">elegans</emphasis>
</taxonomicName>
</th>
<th box="[1414,1593,433,457]" gridcol="5" gridrow="0" pageId="8" pageNumber="9">
<taxonomicName box="[1415,1553,433,456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="japonica">C. japonica</taxonomicName>
</th>
<th box="[1623,1801,433,457]" gridcol="6" gridrow="0" pageId="8" pageNumber="9">
C. 
<emphasis box="[1657,1760,433,456]" italics="true" pageId="8" pageNumber="9">remanei</emphasis>
</th>
<th box="[1832,2010,433,457]" gridcol="7" gridrow="0" pageId="8" pageNumber="9">
C. 
<emphasis box="[1867,1934,433,456]" italics="true" pageId="8" pageNumber="9">sinica</emphasis>
</th>
<th box="[2042,2243,433,457]" gridcol="8" gridrow="0" pageId="8" pageNumber="9">
<taxonomicName authority="Version" authorityName="Version" box="[2043,2186,433,456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="tropicalis">C. tropicalis</taxonomicName>
</th>
</tr>
<tr box="[237,2243,487,511]" gridrow="1" pageId="8" pageNumber="9">
<th box="[237,484,487,511]" gridcol="0" gridrow="1" pageId="8" pageNumber="9">Version</th>
<td box="[512,709,487,511]" gridcol="1" gridrow="1" pageId="8" pageNumber="9">1.0</td>
<td box="[740,917,487,511]" gridcol="2" gridrow="1" pageId="8" pageNumber="9">
<emphasis box="[740,763,487,510]" italics="true" pageId="8" pageNumber="9">W</emphasis>
S254
</td>
<td box="[949,1150,487,511]" gridcol="3" gridrow="1" pageId="8" pageNumber="9">
<emphasis box="[949,972,487,510]" italics="true" pageId="8" pageNumber="9">W</emphasis>
S254
</td>
<td box="[1181,1383,487,511]" gridcol="4" gridrow="1" pageId="8" pageNumber="9">
<emphasis box="[1181,1204,487,510]" italics="true" pageId="8" pageNumber="9">W</emphasis>
S254
</td>
<td box="[1414,1593,487,511]" gridcol="5" gridrow="1" pageId="8" pageNumber="9">
<emphasis box="[1414,1437,487,510]" italics="true" pageId="8" pageNumber="9">W</emphasis>
S254
</td>
<td box="[1623,1801,487,511]" gridcol="6" gridrow="1" pageId="8" pageNumber="9">W S254</td>
<td box="[1832,2010,487,511]" gridcol="7" gridrow="1" pageId="8" pageNumber="9">
<emphasis box="[1832,1855,487,510]" italics="true" pageId="8" pageNumber="9">W</emphasis>
S254
</td>
<td box="[2042,2243,487,511]" gridcol="8" gridrow="1" pageId="8" pageNumber="9">
W 
<emphasis box="[2069,2083,488,511]" italics="true" pageId="8" pageNumber="9">S</emphasis>
254
</td>
</tr>
<tr box="[237,2243,545,570]" gridrow="2" pageId="8" pageNumber="9">
<th box="[237,484,545,570]" gridcol="0" gridrow="2" pageId="8" pageNumber="9">
Mating 
<emphasis box="[341,917,546,569]" italics="true" pageId="8" pageNumber="9">
<emphasis box="[341,396,546,569]" italics="true" pageId="8" pageNumber="9">type</emphasis>
<td box="[512,709,545,570]" gridcol="1" gridrow="2" pageId="8" pageNumber="9">
<emphasis box="[513,690,546,569]" italics="true" pageId="8" pageNumber="9">gonochoristic</emphasis>
</td>
<td box="[740,917,545,570]" gridcol="2" gridrow="2" pageId="8" pageNumber="9">
<emphasis box="[740,917,546,569]" italics="true" pageId="8" pageNumber="9">gonochoristic</emphasis>
</td>
</emphasis>
</th>
<td box="[949,1150,545,570]" gridcol="3" gridrow="2" pageId="8" pageNumber="9">
herm 
<emphasis box="[1020,1150,546,569]" italics="true" pageId="8" pageNumber="9">aphroditic</emphasis>
</td>
<td box="[1181,1383,545,570]" gridcol="4" gridrow="2" pageId="8" pageNumber="9">herm aphroditic</td>
<td box="[1414,1593,545,570]" gridcol="5" gridrow="2" pageId="8" pageNumber="9">gonochoristic</td>
<td box="[1623,1801,545,570]" gridcol="6" gridrow="2" pageId="8" pageNumber="9">gonochoristic</td>
<td box="[1832,2010,545,570]" gridcol="7" gridrow="2" pageId="8" pageNumber="9">gonochoristic</td>
<td box="[2042,2243,545,570]" gridcol="8" gridrow="2" pageId="8" pageNumber="9">
herm 
<emphasis italics="true" pageId="8" pageNumber="9">
<emphasis box="[2113,2243,547,570]" italics="true" pageId="8" pageNumber="9">aphroditic</emphasis>
<tr box="[237,2243,603,627]" gridrow="3" pageId="8" pageNumber="9">
<th box="[237,484,603,627]" gridcol="0" gridrow="3" pageId="8" pageNumber="9">
<emphasis box="[238,308,604,627]" italics="true" pageId="8" pageNumber="9">Strain</emphasis>
</th>
<td box="[512,709,603,627]" gridcol="1" gridrow="3" pageId="8" pageNumber="9">JU1667</td>
<td box="[740,917,603,627]" gridcol="2" gridrow="3" pageId="8" pageNumber="9">PB2801</td>
<td box="[949,1150,603,627]" gridcol="3" gridrow="3" pageId="8" pageNumber="9">
<emphasis box="[950,987,604,627]" italics="true" pageId="8" pageNumber="9">AF</emphasis>
16
</td>
<td box="[1181,1383,603,627]" gridcol="4" gridrow="3" pageId="8" pageNumber="9">N2</td>
<td box="[1414,1593,603,627]" gridcol="5" gridrow="3" pageId="8" pageNumber="9">DF5081</td>
<td box="[1623,1801,603,627]" gridcol="6" gridrow="3" pageId="8" pageNumber="9">PB4641</td>
<td box="[1832,2010,603,627]" gridcol="7" gridrow="3" pageId="8" pageNumber="9">JU800</td>
<td box="[2042,2243,603,627]" gridcol="8" gridrow="3" pageId="8" pageNumber="9">JU1373</td>
</tr>
</emphasis>
</td>
</tr>
<tr box="[237,2243,662,686]" gridrow="4" pageId="8" pageNumber="9">
<th box="[237,484,662,686]" gridcol="0" gridrow="4" pageId="8" pageNumber="9">
<emphasis box="[238,302,663,686]" italics="true" pageId="8" pageNumber="9">Span</emphasis>
(Mb)
</th>
<td box="[512,709,662,686]" gridcol="1" gridrow="4" pageId="8" pageNumber="9">115.12</td>
<td box="[740,917,662,686]" gridcol="2" gridrow="4" pageId="8" pageNumber="9">190.37</td>
<td box="[949,1150,662,686]" gridcol="3" gridrow="4" pageId="8" pageNumber="9">108.38</td>
<td box="[1181,1383,662,686]" gridcol="4" gridrow="4" pageId="8" pageNumber="9">100.29</td>
<td box="[1414,1593,662,686]" gridcol="5" gridrow="4" pageId="8" pageNumber="9">166.25</td>
<td box="[1623,1801,662,686]" gridcol="6" gridrow="4" pageId="8" pageNumber="9">118.55</td>
<td box="[1832,2010,662,686]" gridcol="7" gridrow="4" pageId="8" pageNumber="9">130.76</td>
<td box="[2042,2243,662,686]" gridcol="8" gridrow="4" pageId="8" pageNumber="9">79.32</td>
</tr>
<tr box="[237,2243,720,744]" gridrow="5" pageId="8" pageNumber="9">
<th box="[237,484,720,744]" gridcol="0" gridrow="5" pageId="8" pageNumber="9">Scaffolds (n)a</th>
<td box="[512,709,720,744]" gridcol="1" gridrow="5" pageId="8" pageNumber="9">6,864</td>
<td box="[740,917,720,744]" gridcol="2" gridrow="5" pageId="8" pageNumber="9">3,305</td>
<td box="[949,1150,720,744]" gridcol="3" gridrow="5" pageId="8" pageNumber="9">367</td>
<td box="[1181,1383,720,744]" gridcol="4" gridrow="5" pageId="8" pageNumber="9">7</td>
<td box="[1414,1593,720,744]" gridcol="5" gridrow="5" pageId="8" pageNumber="9">18,808</td>
<td box="[1623,1801,720,744]" gridcol="6" gridrow="5" pageId="8" pageNumber="9">1,591</td>
<td box="[1832,2010,720,744]" gridcol="7" gridrow="5" pageId="8" pageNumber="9">11,966</td>
<td box="[2042,2243,720,744]" gridcol="8" gridrow="5" pageId="8" pageNumber="9">660</td>
</tr>
<tr box="[237,2243,778,802]" gridrow="6" pageId="8" pageNumber="9">
<th box="[237,484,778,802]" gridcol="0" gridrow="6" pageId="8" pageNumber="9">
<emphasis box="[240,262,779,802]" italics="true" pageId="8" pageNumber="9">N</emphasis>
50 (
<emphasis box="[310,340,779,802]" italics="true" pageId="8" pageNumber="9">kb</emphasis>
)
</th>
<td box="[512,709,778,802]" gridcol="1" gridrow="6" pageId="8" pageNumber="9">49.4</td>
<td box="[740,917,778,802]" gridcol="2" gridrow="6" pageId="8" pageNumber="9">381.96</td>
<td box="[949,1150,778,802]" gridcol="3" gridrow="6" pageId="8" pageNumber="9">17,485.44</td>
<td box="[1181,1383,778,802]" gridcol="4" gridrow="6" pageId="8" pageNumber="9">17,493.82</td>
<td box="[1414,1593,778,802]" gridcol="5" gridrow="6" pageId="8" pageNumber="9">94.15</td>
<td box="[1623,1801,778,802]" gridcol="6" gridrow="6" pageId="8" pageNumber="9">1,522.09</td>
<td box="[1832,2010,778,802]" gridcol="7" gridrow="6" pageId="8" pageNumber="9">25,564</td>
<td box="[2042,2243,778,802]" gridcol="8" gridrow="6" pageId="8" pageNumber="9">20,921.87</td>
</tr>
<tr box="[237,2243,837,861]" gridrow="7" pageId="8" pageNumber="9">
<th box="[237,484,837,861]" gridcol="0" gridrow="7" pageId="8" pageNumber="9">Genes (n)</th>
<td box="[512,709,837,861]" gridcol="1" gridrow="7" pageId="8" pageNumber="9">17,180</td>
<td box="[740,917,837,861]" gridcol="2" gridrow="7" pageId="8" pageNumber="9">30,660</td>
<td box="[949,1150,837,861]" gridcol="3" gridrow="7" pageId="8" pageNumber="9">21,814</td>
<td box="[1181,1383,837,861]" gridcol="4" gridrow="7" pageId="8" pageNumber="9">20,362</td>
<td box="[1414,1593,837,861]" gridcol="5" gridrow="7" pageId="8" pageNumber="9">29,964</td>
<td box="[1623,1801,837,861]" gridcol="6" gridrow="7" pageId="8" pageNumber="9">26,226</td>
<td box="[1832,2010,837,861]" gridcol="7" gridrow="7" pageId="8" pageNumber="9">34,696</td>
<td box="[2042,2243,837,861]" gridcol="8" gridrow="7" pageId="8" pageNumber="9">22,326</td>
</tr>
<tr box="[237,2243,895,919]" gridrow="8" pageId="8" pageNumber="9">
<th box="[237,484,895,919]" gridcol="0" gridrow="8" pageId="8" pageNumber="9">G C (%)</th>
<td box="[512,709,895,919]" gridcol="1" gridrow="8" pageId="8" pageNumber="9">43.9</td>
<td box="[740,917,895,919]" gridcol="2" gridrow="8" pageId="8" pageNumber="9">38.6</td>
<td box="[949,1150,895,919]" gridcol="3" gridrow="8" pageId="8" pageNumber="9">37.4</td>
<td box="[1181,1383,895,919]" gridcol="4" gridrow="8" pageId="8" pageNumber="9">35.4</td>
<td box="[1414,1593,895,919]" gridcol="5" gridrow="8" pageId="8" pageNumber="9">39.2</td>
<td box="[1623,1801,895,919]" gridcol="6" gridrow="8" pageId="8" pageNumber="9">37.9</td>
<td box="[1832,2010,895,919]" gridcol="7" gridrow="8" pageId="8" pageNumber="9">39.5</td>
<td box="[2042,2243,895,919]" gridcol="8" gridrow="8" pageId="8" pageNumber="9">37.7</td>
</tr>
<tr box="[237,2243,954,1015]" gridrow="9" pageId="8" pageNumber="9">
<th box="[237,484,954,1015]" gridcol="0" gridrow="9" pageId="8" pageNumber="9">
CEGM 
<emphasis box="[319,338,955,978]" italics="true" pageId="8" pageNumber="9">A</emphasis>
com plete/ partial (%)
</th>
<td box="[512,709,954,1015]" gridcol="1" gridrow="9" pageId="8" pageNumber="9">89.11/ 97.98</td>
<td box="[740,917,954,1015]" gridcol="2" gridrow="9" pageId="8" pageNumber="9">98.39/ 99.60</td>
<td box="[949,1150,954,1015]" gridcol="3" gridrow="9" pageId="8" pageNumber="9">97.98/99.19</td>
<td box="[1181,1383,954,1015]" gridcol="4" gridrow="9" pageId="8" pageNumber="9">96.77/99.19</td>
<td box="[1414,1593,954,1015]" gridcol="5" gridrow="9" pageId="8" pageNumber="9">78.63/ 97.18</td>
<td box="[1623,1801,954,1015]" gridcol="6" gridrow="9" pageId="8" pageNumber="9">94.35/ 98.79</td>
<td box="[1832,2010,954,1015]" gridcol="7" gridrow="9" pageId="8" pageNumber="9">95.56/ 99.60</td>
<td box="[2042,2243,954,1015]" gridcol="8" gridrow="9" pageId="8" pageNumber="9">97.18/98.79</td>
</tr>
</table>
</paragraph>
<paragraph blockId="8.[238,2198,662,1070]" box="[238,872,1045,1070]" pageId="8" pageNumber="9">
<tableNote box="[238,872,1045,1070]" pageId="8" pageNumber="9" targetBox="[237,2243,433,1015]" targetPageId="8">“Scaffolds shorter than 500 bp were not considered</tableNote>
</paragraph>
<paragraph blockId="8.[237,1212,1269,2407]" pageId="8" pageNumber="9">
<emphasis box="[239,261,1271,1304]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[280,717,1273,1304]" italics="true" pageId="8" pageNumber="9">
<taxonomicName box="[280,486,1273,1304]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis bold="true" box="[280,486,1273,1304]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[498,582,1273,1304]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
is sister
</emphasis>
to 
<emphasis bold="true" box="[772,858,1273,1304]" pageId="8" pageNumber="9">other</emphasis>
<emphasis box="[868,975,1273,1304]" italics="true" pageId="8" pageNumber="9">known</emphasis>
<taxonomicName box="[239,479,1323,1354]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis bold="true" box="[239,479,1323,1354]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
</paragraph>
<paragraph blockId="8.[237,1212,1269,2407]" pageId="8" pageNumber="9">
We clustered a total of 634,564 protein sequences from 
<taxonomicName box="[240,502,1420,1456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[240,502,1420,1456]" italics="true" pageId="8" pageNumber="9">C. monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[520,613,1420,1456]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
, twenty-two other 
<taxonomicName box="[954,1210,1420,1456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[954,1210,1420,1456]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
species, and two rhabditomorph outgroup species (
<emphasis italics="true" pageId="8" pageNumber="9">
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Oscheius" higherTaxonomySource="GBIF" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="tipulae">Oscheius tipulae</taxonomicName>
;
</emphasis>
data courtesy of M. A. Félix, and 
<taxonomicName class="Secernentea" family="Heterorhabditidae" genus="Heterorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="bacteriophora">
<emphasis italics="true" pageId="8" pageNumber="9">Heterorhabditis bacteriophora</emphasis>
</taxonomicName>
) to define putative orthologues. We identified 34,425 putatively orthologous groups containing at least two members, 303 of which were either single copy or absent across all 25 species. These single copy orthologues were aligned, and the alignments concatenated and used to perform maximum-likelihood and Bayesian inference analysis using RAxML and PhyloBayes, respectively. Both analysis methods resulted in an identical topology, with the placement of 
<taxonomicName box="[479,736,1970,2006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[479,503,1970,2006]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[531,736,1970,2006]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[755,847,1970,2006]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
arising basally to all other 
<taxonomicName box="[350,597,2020,2056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[350,597,2020,2056]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
species (
<figureCitation box="[769,870,2020,2056]" captionStart="Fig. 6" captionStartId="10.[264,311,1264,1291]" captionTargetBox="[531,1952,370,1235]" captionText="Fig. 6 Phylogenetic relationships o f Caenorhabditis species and tw o outgroup species. M aximum - likelihood based tree from RAxML. Bootstrap support values (1000 replicates) w ere 100 all branches, unless noted otherw ise as num bers on branches. Bayesian Posterior Probabilities w ere 1 for all branches and are not show n. Coloured boxes indicate supergroups, as defined in [3], Strain names from w hich protein sequence w ere derived are noted" httpUri="https://zenodo.org/record/322322/files/figure.png" pageId="8" pageNumber="9">Fig. 6</figureCitation>
). All branches had maximal support except for three nodes within the 
<taxonomicName box="[1088,1212,2070,2106]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="15" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1088,1212,2070,2106]" italics="true" pageId="8" pageNumber="9">Elegans</emphasis>
</taxonomicName>
super-group. Our analysis included data from several new and currently undescribed putative species of 
<emphasis italics="true" pageId="8" pageNumber="9">
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
,
</emphasis>
including 
<emphasis box="[463,488,2220,2256]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. sp. 21 which is the sister taxon to the 
<emphasis italics="true" pageId="8" pageNumber="9">Drosophilae</emphasis>
plus 
<taxonomicName box="[476,600,2270,2306]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="15" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[476,600,2270,2306]" italics="true" pageId="8" pageNumber="9">Elegans</emphasis>
</taxonomicName>
super-groups and 
<emphasis box="[937,961,2270,2306]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. sp. 31 which forms the first branch in the 
<taxonomicName box="[714,838,2320,2356]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="15" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[714,838,2320,2356]" italics="true" pageId="8" pageNumber="9">Elegans</emphasis>
</taxonomicName>
super-group. 
<emphasis box="[1071,1096,2320,2356]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. sp. 38 is placed within the 
<emphasis box="[582,779,2370,2406]" italics="true" pageId="8" pageNumber="9">Drosophilae</emphasis>
super-group, while 
<emphasis box="[1120,1144,2370,2406]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. sp.
</paragraph>
<paragraph blockId="8.[1271,2246,1116,1306]" pageId="8" pageNumber="9">
26, 
<emphasis box="[1336,1361,1120,1156]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. sp. 32 (sister to C. 
<emphasis box="[1712,1788,1120,1156]" italics="true" pageId="8" pageNumber="9">afin)</emphasis>
and C. sp. 40 (sister to C. 
<emphasis box="[1271,1366,1170,1206]" italics="true" pageId="8" pageNumber="9">sinica</emphasis>
) are all members of the 
<taxonomicName box="[1796,1918,1170,1206]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="15" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1796,1918,1170,1206]" italics="true" pageId="8" pageNumber="9">Elegans</emphasis>
</taxonomicName>
super-group. From these analyses we conclude that 
<taxonomicName box="[1800,2048,1220,1256]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1800,1826,1220,1256]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[1845,2048,1220,1256]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[2060,2144,1220,1256]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
is sister to all other known 
<emphasis box="[1641,1895,1270,1306]" italics="true" pageId="8" pageNumber="9">
<taxonomicName box="[1641,1890,1270,1306]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
.
</emphasis>
</paragraph>
</subSubSection>
<subSubSection lastPageId="10" lastPageNumber="11" pageId="8" pageNumber="9" type="discussion">
<paragraph blockId="8.[1270,2249,1370,3056]" box="[1272,1833,1372,1403]" pageId="8" pageNumber="9">
<heading bold="true" box="[1272,1833,1372,1403]" fontSize="9" level="5" pageId="8" pageNumber="9" reason="6">
<emphasis bold="true" box="[1272,1833,1372,1403]" italics="true" pageId="8" pageNumber="9">Stemspecies pattern reconstruction</emphasis>
</heading>
</paragraph>
<paragraph blockId="8.[1270,2249,1370,3056]" pageId="8" pageNumber="9">
Our phylogenetic analyses were based on species with whole genome data available, and thus did not include the full known diversity of the genus. The stemspecies pattern was reconstructed based on ingroup and outgroup comparison. Previous molecular phylogenetic analyses of 
<taxonomicName box="[1415,1672,1670,1706]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[1415,1672,1670,1706]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
species using a small num ber of marker genes [
<bibRefCitation author="Kiontke K &amp; Sudhaus W." box="[1537,1577,1720,1756]" journalOrPublisher="Worm Book" pageId="8" pageNumber="9" refString="10. Kiontke K, Sudhaus W. Ecology of Caenorhabditis species. In: Community TCeR: WormBook, editor. Worm Book 2006." title="10" type="book" volumeTitle="Community TCeR: WormBook, editor" year="2006">10</bibRefCitation>
] placed 
<taxonomicName box="[1735,2000,1720,1756]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1735,1761,1720,1756]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[1787,2000,1720,1756]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[2018,2112,1720,1756]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
and 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="sonorae">
<emphasis box="[2212,2237,1720,1756]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[1271,1400,1770,1806]" italics="true" pageId="8" pageNumber="9">sonorae</emphasis>
</taxonomicName>
[
<bibRefCitation author="Kiontke K." box="[1427,1467,1770,1806]" journalOrPublisher="Fundam Appl Nematol" pageId="8" pageNumber="9" pagination="305 - 15" part="20" refString="41. Kiontke K. Description of Rhabditis (Caenorhabditis) drosophiiae n. sp. and R. (CJ sonorae n. sp. (Nematoda: Rhabditida) from saguaro cactus rot in Arizona. Fundam Appl Nematol. 1997; 20: 305 - 15." title="Description of Rhabditis (Caenorhabditis) drosophiiae n. sp. and R. (CJ sonorae n. sp. (Nematoda: Rhabditida) from saguaro cactus rot in Arizona" type="journal article" year="1997">41</bibRefCitation>
] as sister species, again arising at the 
<emphasis bold="true" box="[2126,2199,1770,1806]" pageId="8" pageNumber="9">base</emphasis>
of the genus.
</paragraph>
<paragraph blockId="8.[1270,2249,1370,3056]" pageId="8" pageNumber="9">
The following morphological synapomorphies can 
<emphasis bold="true" box="[2206,2244,1870,1906]" pageId="8" pageNumber="9">be</emphasis>
hypothesised to support a 
<taxonomicName box="[1758,2024,1920,1956]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1758,1783,1920,1956]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[1813,2024,1920,1956]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[2046,2143,1920,1956]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
- 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="sonorae">
<emphasis box="[2212,2236,1920,1956]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<emphasis box="[1271,1400,1970,2006]" italics="true" pageId="8" pageNumber="9">sonorae</emphasis>
</taxonomicName>
clade: m outh opening triangular (
<figureCitation box="[2008,2106,1970,2006]" captionStart="Fig. 4" captionStartId="6.[264,311,2504,2531]" captionTargetBox="[268,2215,393,2476]" captionText="Fig. 4 Scanning electron m icrographs o f Caenorhabditis monodelphis sp. n. a, d Anterior end of fem ale; b, c Anterior end o f male; e Fem ale vulva; f. g Lateral field o f fem ale and male, respectively; h Fem ale anus and tail; ij Male bursa with genital papillae indicated; k Detail of cloaca region with postcloacal sensillae; I Detail o f male spiculum" httpUri="https://zenodo.org/record/322320/files/figure.png" pageId="8" pageNumber="9">Fig. 4</figureCitation>
b), spicule having a complicated tip (notched or dentated) and a longish thin walled “window” in the blade (Figs, li, 41), postcloacal sensilla being filiform (
<figureCitation box="[1888,1987,2120,2156]" captionStart="Fig. 4" captionStartId="6.[264,311,2504,2531]" captionTargetBox="[268,2215,393,2476]" captionText="Fig. 4 Scanning electron m icrographs o f Caenorhabditis monodelphis sp. n. a, d Anterior end of fem ale; b, c Anterior end o f male; e Fem ale vulva; f. g Lateral field o f fem ale and male, respectively; h Fem ale anus and tail; ij Male bursa with genital papillae indicated; k Detail of cloaca region with postcloacal sensillae; I Detail o f male spiculum" httpUri="https://zenodo.org/record/322320/files/figure.png" pageId="8" pageNumber="9">Fig. 4</figureCitation>
k), and the female tail shortened to less than three times anal body width. Other similarities between both these species are plesiomorphic.
</paragraph>
<paragraph blockId="8.[1270,2249,1370,3056]" lastBlockId="9.[237,1212,2617,3056]" lastPageId="9" lastPageNumber="10" pageId="8" pageNumber="9">
<taxonomicName box="[1307,1564,2320,2356]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[1307,1564,2320,2356]" italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
and its sister group constitute the monophylum Anarhabditis within the 
<taxonomicName box="[1972,2158,2370,2406]" class="Secernentea" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="subOrder" subOrder="Rhabditina">Rhabditina</taxonomicName>
. For convenience, we will call the sister clade of 
<taxonomicName authority="Protoscapter" authorityName="Protoscapter" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
Protoscapter
</taxonomicName>
(
<figureCitation box="[1604,1703,2470,2506]" captionStart="Fig. 7" captionStartId="11.[264,311,1151,1178]" captionTargetBox="[240,1199,370,1120]" captionText="Fig. 7 Stemspecies pattern reconstruction. Legend for the cladogram: Black squares indicate the following apomorphies: 1) Glottoid apparatus transformed, sectors of metastegostom not spherically protruding; - median bulb prominent oval; - GP 3 shifted posterior of cloaca level (only two precloacal papillae present); - GP 7 - 9 clustered; - spiculum blade dorsally velum-like. 2) GPs 3 - 6 clustered, but with small gaps in betw een; - GP 6 thickened, its tip em bedded w ithin the bursa velum; - posterior part o f bursa velum w ith &quot; wash-board pattern &quot; (transverse striae); - spiculum shaft with transverse seam; - dauerlarvae unsheathed. 3) Stoma triangular in cross section; - spiculum terminally notched or dentated and w ith an oval &quot; w indow &quot; in the blade; - postcloacal sensilla filiform; - shortening o f the fem ale tail. 4) Adult cuticle lateral with 3 longitudinal ridges; - sexual dimorphism in cephalic sensilla: they are lost in the female (not projecting to the exterior); - each sector of metastegostom with a triangular flap projecting into the buccal cavity; - precloacal lip anteriorly framed. 5) Gymnostom extended and stegostom shortened, so that only a remnant of the pharyngeal sleeve is present; - gubernaculum distally forked (only presumed for P. friste)" httpUri="https://zenodo.org/record/322324/files/figure.png" pageId="8" pageNumber="9">Fig. 7</figureCitation>
): it comprises 
<emphasis box="[1965,2230,2470,2506]" italics="true" pageId="8" pageNumber="9">
“ 
<taxonomicName box="[1976,2230,2470,2506]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
</emphasis>
”, 
<emphasis box="[1270,1813,2520,2556]" italics="true" pageId="8" pageNumber="9">
<taxonomicName box="[1270,1580,2520,2556]" class="Secernentea" family="Rhabditidae" genus="Prodontorhabditis" higherTaxonomySource="GBIF" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Prodontorhabditis</taxonomicName>
, 
<taxonomicName box="[1599,1813,2520,2556]" class="Secernentea" family="Rhabditidae" genus="Diploscapter" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Diploscapter</taxonomicName>
</emphasis>
and 
<taxonomicName box="[1903,2155,2520,2556]" class="Chromadorea" family="Rhabditidae" genus="Sclerorhabditis" higherTaxonomySource="GBIF" kingdom="Metazoa" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[1903,2155,2520,2556]" italics="true" pageId="8" pageNumber="9">Sclerorhabditis</emphasis>
</taxonomicName>
[
<bibRefCitation author="Sudhaus W." box="[2184,2228,2520,2556]" journalOrPublisher="J Nematode Morphol Syst" pageId="8" pageNumber="9" pagination="113 - 78" part="14" refString="42. Sudhaus W. Phylogenetic systematisation and catalogue of paraphyletic &quot; Rhabditidae &quot; (Secementea, Nematoda). J Nematode Morphol Syst. 2011; 14: 113 - 78." title="Phylogenetic systematisation and catalogue of paraphyletic &quot; Rhabditidae &quot; (Secementea, Nematoda)" type="journal article" year="2011">42</bibRefCitation>
]. To reconstruct the characters of the stemspecies of 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis italics="true" pageId="8" pageNumber="9">Caenorhabditis</emphasis>
</taxonomicName>
it is necessary to consider the morphologies of all these taxa, and not only the taxa for which we have molecular data. 
<emphasis box="[1579,1858,2720,2756]" italics="true" pageId="8" pageNumber="9">
“ 
<taxonomicName box="[1590,1847,2720,2756]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
”
</emphasis>
is paraphyletic. The 
<emphasis box="[1274,1460,2770,2806]" italics="true" pageId="8" pageNumber="9">Oxyuroides</emphasis>
group is sister taxon of 
<taxonomicName box="[1938,2243,2770,2806]" class="Secernentea" family="Rhabditidae" genus="Prodontorhabditis" higherTaxonomySource="GBIF" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">
<emphasis box="[1938,2243,2770,2806]" italics="true" pageId="8" pageNumber="9">Prodontorhabditis</emphasis>
</taxonomicName>
[
<bibRefCitation author="Sudhaus W." box="[1286,1327,2820,2856]" journalOrPublisher="Systematik, Okologie, Biologie und Ethologie der Rhabditidae (Nematoda). Zodogica" pageId="8" pageNumber="9" pagination="1 - 229" part="43" refString="43. Sudhaus W. Vergleichende Untersuchungen zur Phylogenie, Systematik, Okologie, Biologie und Ethologie der Rhabditidae (Nematoda). Zodogica. 1976; 43: 1 - 229." title="Vergleichende Untersuchungen zur Phylogenie" type="journal article" year="1976">43</bibRefCitation>
, 
<bibRefCitation author="Sudhaus W &amp; Fitch D." box="[1350,1396,2820,2856]" journalOrPublisher="J Nematol" pageId="8" pageNumber="9" pagination="1 - 70" part="33" refString="44. Sudhaus W, Fitch D. Comparative studies on the phylogeny and systematics of the Rhabditidae (Nematoda). J Nematol. 2001; 33: 1 - 70." title="Comparative studies on the phylogeny and systematics of the Rhabditidae (Nematoda)" type="journal article" year="2001">44</bibRefCitation>
], and the 
<emphasis box="[1577,1719,2820,2856]" italics="true" pageId="8" pageNumber="9">Xylocola</emphasis>
group may be sister taxon of 
<emphasis box="[1270,1759,2870,2906]" italics="true" pageId="8" pageNumber="9">
<taxonomicName box="[1270,1486,2870,2906]" class="Secernentea" family="Rhabditidae" genus="Diploscapter" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Diploscapter</taxonomicName>
! 
<taxonomicName box="[1498,1754,2870,2906]" class="Chromadorea" family="Rhabditidae" genus="Sclerorhabditis" higherTaxonomySource="GBIF" kingdom="Metazoa" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="genus">Sclerorhabditis</taxonomicName>
.
</emphasis>
However, the two species 
<taxonomicName authority="Hirschmann in Osche, 1952" authorityName="Hirschmann in Osche" authorityYear="1952" box="[1270,2167,2920,2956]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="elaphri">
<emphasis box="[1270,1647,2920,2956]" italics="true" pageId="8" pageNumber="9">
Protorhabditis 
<taxonomicName authority="Hirschmann in Osche, 1952" authorityName="Hirschmann in Osche" authorityYear="1952" box="[1528,2167,2920,2956]" pageId="8" pageNumber="9" rank="species" species="elaphri">
<taxonomicName box="[1528,1647,2920,2956]" pageId="8" pageNumber="9" rank="species" species="elaphri">elaphri</taxonomicName>
(Hirschmann in Osche, 1952)
</taxonomicName>
</emphasis>
</taxonomicName>
and 
<taxonomicName box="[1270,1412,2970,3006]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="tristis">
<emphasis box="[1270,1412,2970,3006]" italics="true" pageId="8" pageNumber="9">
P. 
<taxonomicName box="[1319,1412,2970,3006]" pageId="8" pageNumber="9" rank="species" species="tristis">tristis</taxonomicName>
</emphasis>
</taxonomicName>
[
<bibRefCitation author="Hirschmann H." box="[1440,1480,2970,3006]" journalOrPublisher="Zoologische Jahrbucher (Systematik" pageId="8" pageNumber="9" pagination="313 - 407" part="81" refString="45. Hirschmann H. Die Nematoden der Wassergrenze mittelfrankischer Gewasser. Zoologische Jahrbucher (Systematik. 1952; 81: 313 - 407." title="Die Nematoden der Wassergrenze mittelfrankischer Gewasser" type="journal article" year="1952">45</bibRefCitation>
] appear to represent basal branches in Protoscapter (compare [
<bibRefCitation author="Sudhaus W." box="[1629,1674,3020,3056]" journalOrPublisher="Systematik, Okologie, Biologie und Ethologie der Rhabditidae (Nematoda). Zodogica" pageId="8" pageNumber="9" pagination="1 - 229" part="43" refString="43. Sudhaus W. Vergleichende Untersuchungen zur Phylogenie, Systematik, Okologie, Biologie und Ethologie der Rhabditidae (Nematoda). Zodogica. 1976; 43: 1 - 229." title="Vergleichende Untersuchungen zur Phylogenie" type="journal article" year="1976">43</bibRefCitation>
]). These last two species, despite the paucity of 
<emphasis bold="true" box="[488,689,2620,2656]" pageId="9" pageNumber="10">information</emphasis>
available for them, are crucial for comparisons that will illuminate the stemspecies patterns of Anarhabditis, Protoscapter and 
<emphasis box="[926,1190,2720,2756]" italics="true" pageId="9" pageNumber="10">
<taxonomicName box="[926,1186,2720,2756]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
.
</emphasis>
</paragraph>
<caption ID-Table-UUID="DF0441CF2868FFCB3989D1B2055BF626" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D1B2055BF626" pageId="8" pageNumber="9" targetBox="[238,1210,2554,2928]" targetIsTable="true" targetPageId="8">
<paragraph blockId="8.[238,1183,2448,2527]" pageId="8" pageNumber="9">
<emphasis bold="true" box="[238,360,2448,2481]" pageId="8" pageNumber="9">Table 3</emphasis>
Gene structure comparison of orthologous gene 
<emphasis italics="true" pageId="8" pageNumber="9">pairs from</emphasis>
C. 
<taxonomicName box="[358,544,2496,2527]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. N.">
<emphasis box="[358,544,2496,2527]" italics="true" pageId="8" pageNumber="9">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[557,636,2496,2527]" pageId="8" pageNumber="9" rank="species">sp. N.</taxonomicNameLabel>
and 
<taxonomicName box="[718,861,2496,2527]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[718,737,2496,2527]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. elegans
</taxonomicName>
</paragraph>
</caption>
<paragraph pageId="8" pageNumber="9">
<table box="[238,1210,2554,2928]" gridcols="3" gridrows="7" pageId="8" pageNumber="9">
<tr box="[238,1210,2554,2581]" gridrow="0" pageId="8" pageNumber="9" rowspan-0="1">
<th box="[733,1010,2554,2581]" gridcol="1" gridrow="0" pageId="8" pageNumber="9">
<emphasis box="[734,750,2554,2581]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<taxonomicName box="[766,931,2554,2581]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[941,1010,2554,2581]" pageId="8" pageNumber="9" rank="species">sp. n.</taxonomicNameLabel>
</th>
<th box="[1083,1210,2554,2581]" gridcol="2" gridrow="0" pageId="8" pageNumber="9">
<emphasis box="[1084,1101,2554,2581]" italics="true" pageId="8" pageNumber="9">C</emphasis>
. 
<taxonomicName box="[1117,1210,2554,2581]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="8" pageNumber="9" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
</th>
</tr>
<tr box="[238,1210,2609,2636]" gridrow="1" pageId="8" pageNumber="9">
<th box="[238,657,2609,2636]" gridcol="0" gridrow="1" pageId="8" pageNumber="9">Gene length (bp)</th>
<td box="[733,1010,2609,2636]" gridcol="1" gridrow="1" pageId="8" pageNumber="9">3359</td>
<td box="[1083,1210,2609,2636]" gridcol="2" gridrow="1" pageId="8" pageNumber="9">2854</td>
</tr>
<tr box="[238,1210,2667,2694]" gridrow="2" pageId="8" pageNumber="9">
<th box="[238,657,2667,2694]" gridcol="0" gridrow="2" pageId="8" pageNumber="9">
<emphasis box="[238,333,2670,2693]" italics="true" pageId="8" pageNumber="9">Coding</emphasis>
exon length (bp)
</th>
<td box="[733,1010,2667,2694]" gridcol="1" gridrow="2" pageId="8" pageNumber="9">
<emphasis bold="true" box="[736,780,2667,2694]" pageId="8" pageNumber="9">109</emphasis>
</td>
<td box="[1083,1210,2667,2694]" gridcol="2" gridrow="2" pageId="8" pageNumber="9">144</td>
</tr>
<tr box="[238,1210,2726,2753]" gridrow="3" pageId="8" pageNumber="9">
<th box="[238,657,2726,2753]" gridcol="0" gridrow="3" pageId="8" pageNumber="9">Coding exon count (n)</th>
<td box="[733,1010,2726,2753]" gridcol="1" gridrow="3" pageId="8" pageNumber="9">10</td>
<td box="[1083,1210,2726,2753]" gridcol="2" gridrow="3" pageId="8" pageNumber="9">6</td>
</tr>
<tr box="[238,1210,2784,2811]" gridrow="4" pageId="8" pageNumber="9">
<th box="[238,657,2784,2811]" gridcol="0" gridrow="4" pageId="8" pageNumber="9">CDS span (bp)a</th>
<td box="[733,1010,2784,2811]" gridcol="1" gridrow="4" pageId="8" pageNumber="9">
<emphasis bold="true" box="[736,796,2784,2811]" pageId="8" pageNumber="9">1167</emphasis>
</td>
<td box="[1083,1210,2784,2811]" gridcol="2" gridrow="4" pageId="8" pageNumber="9">
<emphasis bold="true" box="[1086,1145,2784,2811]" pageId="8" pageNumber="9">1182</emphasis>
</td>
</tr>
<tr box="[238,1210,2842,2869]" gridrow="5" pageId="8" pageNumber="9">
<th box="[238,657,2842,2869]" gridcol="0" gridrow="5" pageId="8" pageNumber="9">Utron length (bp)</th>
<td box="[733,1010,2842,2869]" gridcol="1" gridrow="5" pageId="8" pageNumber="9">69</td>
<td box="[1083,1210,2842,2869]" gridcol="2" gridrow="5" pageId="8" pageNumber="9">76</td>
</tr>
<tr box="[238,1210,2901,2928]" gridrow="6" pageId="8" pageNumber="9">
<th box="[238,657,2901,2928]" gridcol="0" gridrow="6" pageId="8" pageNumber="9">lotal intron span per gene (bp)</th>
<td box="[733,1010,2901,2928]" gridcol="1" gridrow="6" pageId="8" pageNumber="9">
<emphasis bold="true" box="[736,796,2901,2928]" pageId="8" pageNumber="9">1918</emphasis>
</td>
<td box="[1083,1210,2901,2928]" gridcol="2" gridrow="6" pageId="8" pageNumber="9">
<emphasis bold="true" box="[1086,1146,2901,2928]" pageId="8" pageNumber="9">1187</emphasis>
</td>
</tr>
</table>
</paragraph>
<tableNote pageId="8" pageNumber="9" targetBox="[238,1210,2554,2928]" targetPageId="8">
<paragraph blockId="8.[237,1065,2955,3051]" box="[238,512,2955,2980]" pageId="8" pageNumber="9">All values are medians</paragraph>
<paragraph blockId="8.[237,1065,2955,3051]" pageId="8" pageNumber="9">
aorthologous gene pairs which differed in CDS 
<emphasis bold="true" box="[820,897,2991,3016]" pageId="8" pageNumber="9">length</emphasis>
by 20% were not included
</paragraph>
</tableNote>
<caption httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="9" pageNumber="10" targetBox="[237,2230,367,2308]" targetPageId="9">
<paragraph pageId="9" pageNumber="10">
Fig. 5 Comparison of exon counts in single-copy orthologues between C 
<taxonomicName box="[1265,1430,2331,2358]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[1440,1508,2334,2357]" pageId="9" pageNumber="10" rank="species">sp. n.</taxonomicNameLabel>
and C 
<taxonomicName box="[1613,1708,2334,2357]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
. a Exon counts in 6,174 single-copy orthologous gene pairs. C. 
<taxonomicName box="[625,788,2372,2399]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[799,867,2375,2398]" pageId="9" pageNumber="10" rank="species">sp. n.</taxonomicNameLabel>
genes w hich had transcripts with CDS lengths 20% longer (orange) or shorter (black) than C. 
<taxonomicName box="[2123,2218,2372,2399]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log2 ratio of C. 
<taxonomicName box="[1641,1800,2417,2440]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
<taxonomicNameLabel box="[1810,1876,2417,2440]" pageId="9" pageNumber="10" rank="species">sp. n.</taxonomicNameLabel>
exon counts to C. 
<taxonomicName box="[2121,2213,2414,2441]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="9" pageNumber="10" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count
</paragraph>
</caption>
<paragraph blockId="9.[237,1212,2617,3056]" pageId="9" pageNumber="10">
By ingroup comparison we reconstruct the following characters of the 
<emphasis bold="true" box="[563,763,2820,2856]" pageId="9" pageNumber="10">stemspecies</emphasis>
of Anarhabditis without differentiating 
<emphasis bold="true" box="[503,590,2870,2906]" pageId="9" pageNumber="10">them</emphasis>
into apo- or plesiomorphies (on apomorphies 
<emphasis bold="true" box="[471,522,2920,2956]" pageId="9" pageNumber="10">see</emphasis>
the legend of 
<figureCitation box="[772,866,2920,2956]" captionStart="Fig. 7" captionStartId="11.[264,311,1151,1178]" captionTargetBox="[240,1199,370,1120]" captionText="Fig. 7 Stemspecies pattern reconstruction. Legend for the cladogram: Black squares indicate the following apomorphies: 1) Glottoid apparatus transformed, sectors of metastegostom not spherically protruding; - median bulb prominent oval; - GP 3 shifted posterior of cloaca level (only two precloacal papillae present); - GP 7 - 9 clustered; - spiculum blade dorsally velum-like. 2) GPs 3 - 6 clustered, but with small gaps in betw een; - GP 6 thickened, its tip em bedded w ithin the bursa velum; - posterior part o f bursa velum w ith &quot; wash-board pattern &quot; (transverse striae); - spiculum shaft with transverse seam; - dauerlarvae unsheathed. 3) Stoma triangular in cross section; - spiculum terminally notched or dentated and w ith an oval &quot; w indow &quot; in the blade; - postcloacal sensilla filiform; - shortening o f the fem ale tail. 4) Adult cuticle lateral with 3 longitudinal ridges; - sexual dimorphism in cephalic sensilla: they are lost in the female (not projecting to the exterior); - each sector of metastegostom with a triangular flap projecting into the buccal cavity; - precloacal lip anteriorly framed. 5) Gymnostom extended and stegostom shortened, so that only a remnant of the pharyngeal sleeve is present; - gubernaculum distally forked (only presumed for P. friste)" httpUri="https://zenodo.org/record/322324/files/figure.png" pageId="9" pageNumber="10">Fig. 7</figureCitation>
):
</paragraph>
<paragraph blockId="9.[237,1212,2617,3056]" lastBlockId="10.[237,1212,1515,2206]" lastPageId="10" lastPageNumber="11" pageId="9" pageNumber="10">
<emphasis bold="true" box="[273,412,2970,3006]" pageId="9" pageNumber="10">- adults</emphasis>
of small size (less than 1 mm); - lips not offset from 
<emphasis bold="true" box="[397,530,3020,3056]" pageId="9" pageNumber="10">anterior</emphasis>
end; - four cephalic sensilla present in male and female; - stoma with pharyngeal sleeve (
<emphasis bold="true" box="[2184,2243,2620,2656]" pageId="9" pageNumber="10">stegostom</emphasis>
length nearly that of gymnostom); - median bulb of pharynx strongly developed, corpus intima with transverse ridging, terminal bulb with double haustrulum; - gonochoristic; - female tail elongate conoid; - gonads amphidelphic, the anterior branch right and the posterior left of intestine; - vulva at midbody, a transverse slit; - oviparous, usually only one egg at a time in the uteri; - male gonad on the right side, reflexed to the ventral; - bursa peloderan and anteriorly open, oval-shaped in ventral view, with smooth margin, terminally not notched; - 9 pairs of even genital papillae, two precloacal largely spaced, GP 
<emphasis bold="true" box="[432,451,1670,1706]" pageId="10" pageNumber="11">3</emphasis>
-6 evenly spaced, the last three GPs forming a tight cluster; GP1, GP5 and GP7 terminate on the dorsal surface of the bursa velum; - phasmids open behind GP9, inconspicuous; - bursa formula thus vl, 
<emphasis box="[971,992,1820,1856]" italics="true" pageId="10" pageNumber="11">v</emphasis>
2/v3,v4,ad,v5 (pd,v6,v7)ph; - male tail tip present; - 1 + 2 circumcloacal sensilla inconspicuous, precloacal lip simple; - spicules separate, stout, head not rounded, behind the shaft a slight ventral projection, dorsal part of blade weakly 
<emphasis bold="true" box="[1096,1210,2020,2056]" pageId="10" pageNumber="11">cuticularised</emphasis>
(velum), its tip possibly not even (argued below); - gubernaculum simple spatulate; - dauerlarvae with double cuticle (ensheathed), not waving.
</paragraph>
<caption httpUri="https://zenodo.org/record/322322/files/figure.png" pageId="10" pageNumber="11" targetBox="[531,1952,370,1235]" targetPageId="10">
<paragraph pageId="10" pageNumber="11">
Fig. 6 Phylogenetic relationships of 
<taxonomicName box="[752,942,1264,1291]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
species and two outgroup species. M aximum -likelihood based tree from RAxML. Bootstrap support values (1000 replicates) were 100 all branches, unless noted otherw ise as numbers on branches. Bayesian Posterior Probabilities were 1 for all branches and are not shown. Coloured boxes indicate supergroups, as defined in [3], Strain names from which protein sequence were derived are noted
</paragraph>
</caption>
<paragraph blockId="10.[237,1216,2265,3058]" box="[240,436,2267,2304]" pageId="10" pageNumber="11">
<heading bold="true" box="[240,436,2267,2304]" fontSize="12" level="2" pageId="10" pageNumber="11" reason="0">
<emphasis bold="true" box="[240,436,2267,2304]" pageId="10" pageNumber="11">Discussion</emphasis>
</heading>
</paragraph>
<paragraph blockId="10.[237,1216,2265,3058]" box="[237,1031,2321,2354]" pageId="10" pageNumber="11">
<emphasis bold="true" box="[237,711,2321,2354]" pageId="10" pageNumber="11">
Taxonomy of 
<emphasis box="[470,929,2323,2354]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[470,711,2323,2354]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
<taxonomicName box="[724,929,2323,2354]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
</emphasis>
</emphasis>
<taxonomicNameLabel box="[943,1031,2321,2354]" pageId="10" pageNumber="11" rank="species">
<emphasis bold="true" box="[943,989,2321,2354]" pageId="10" pageNumber="11">sp.</emphasis>
n.
</taxonomicNameLabel>
</paragraph>
<paragraph blockId="10.[237,1216,2265,3058]" pageId="10" pageNumber="11">
<taxonomicName box="[240,730,2370,2406]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[240,730,2370,2406]" italics="true" pageId="10" pageNumber="11">
Caenorhabditis 
<taxonomicName box="[518,730,2370,2406]" pageId="10" pageNumber="11" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[751,847,2370,2406]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
is a new species of 
<taxonomicName box="[240,497,2420,2456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">
<emphasis box="[240,497,2420,2456]" italics="true" pageId="10" pageNumber="11">Caenorhabditis</emphasis>
</taxonomicName>
supported by its phylogenetic position as inferred from 303 molecular markers, morphology, 
<emphasis bold="true" box="[1100,1211,2470,2506]" pageId="10" pageNumber="11">habitat</emphasis>
and specific association with 
<taxonomicName box="[752,980,2520,2556]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="10" pageNumber="11" phylum="Arthropoda" rank="species" species="castaneus">
<emphasis box="[752,980,2520,2556]" italics="true" pageId="10" pageNumber="11">
Cis 
<taxonomicName box="[822,980,2520,2556]" pageId="10" pageNumber="11" rank="species" species="castaneus">castaneus</taxonomicName>
</emphasis>
</taxonomicName>
(
<taxonomicName box="[1013,1195,2520,2556]" class="Insecta" kingdom="Animalia" order="Coleoptera" pageId="10" pageNumber="11" phylum="Arthropoda" rank="order">Coleoptera</taxonomicName>
). Morphologically, it could 
<emphasis bold="true" box="[661,698,2570,2606]" pageId="10" pageNumber="11">be</emphasis>
confused with 
<emphasis box="[953,1213,2570,2606]" italics="true" pageId="10" pageNumber="11">
“ 
<taxonomicName box="[963,1201,2570,2606]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
&quot;
</emphasis>
species because of the 
<emphasis bold="true" box="[610,736,2620,2656]" pageId="10" pageNumber="11">absence</emphasis>
of a clear glottoid apparatus. A glottoid apparatus has 
<emphasis bold="true" box="[649,727,2670,2706]" pageId="10" pageNumber="11">been</emphasis>
lost 5-6 
<emphasis bold="true" box="[882,970,2670,2706]" pageId="10" pageNumber="11">times</emphasis>
independently within “ 
<taxonomicName box="[368,562,2720,2756]" class="Secernentea" family="Rhabditidae" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="family">Rhabditidae</taxonomicName>
” [
<bibRefCitation author="Sudhaus W." box="[601,640,2720,2756]" editor="Schmidt-Rhaesa A" journalOrPublisher="Nematodath ed. Berlin, Boston: Walter De Gruyter" pageId="10" pageNumber="11" pagination="537 - 55" part="2" refString="46. Sudhaus W. Order Rhabditina: &quot; Rhabditidae'. In: Schmidt-Rhaesa A, editor. Handbook of zoology gastrotricha, cycloneuralia and gnathifera, vol. 2. Nematodath ed. Berlin, Boston: Walter De Gruyter; 2014. p. 537 - 55." title="46" type="book chapter" volumeTitle="Handbook of zoology gastrotricha, cycloneuralia and gnathifera" year="2014">46</bibRefCitation>
] and, 
<emphasis bold="true" box="[747,779,2720,2756]" pageId="10" pageNumber="11">as</emphasis>
illustrated 
<emphasis bold="true" box="[965,1037,2720,2756]" pageId="10" pageNumber="11">here</emphasis>
, also in 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis italics="true" pageId="10" pageNumber="11">
C. 
<taxonomicName box="[238,443,2770,2806]" pageId="10" pageNumber="11" rank="species" species="monodelphis" status="sp. n.">monodelphis</taxonomicName>
</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[465,561,2770,2806]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
This 
<emphasis bold="true" box="[677,791,2770,2806]" pageId="10" pageNumber="11">species</emphasis>
resembles 
<emphasis bold="true" box="[996,1110,2770,2806]" pageId="10" pageNumber="11">species</emphasis>
from 
<emphasis box="[238,501,2820,2856]" italics="true" pageId="10" pageNumber="11">
“ 
<taxonomicName authority="With" authorityName="With" box="[248,488,2820,2856]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
&quot;
</emphasis>
With a 
<emphasis box="[617,687,2820,2856]" italics="true" pageId="10" pageNumber="11">very</emphasis>
long stoma without glottoid 
<emphasis bold="true" box="[238,359,2870,2906]" pageId="10" pageNumber="11">apparatus</emphasis>
, but differs from the 
<emphasis box="[712,907,2870,2906]" italics="true" pageId="10" pageNumber="11">Oxyuroides-</emphasis>
group within 
<emphasis italics="true" pageId="10" pageNumber="11">
‘ 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
&quot;
</emphasis>
in having an open bursa and GP1 not anterior of the bursa. 
<emphasis bold="true" box="[475,501,2970,3006]" pageId="10" pageNumber="11">It</emphasis>
is differentiated from the 
<emphasis box="[964,1116,2970,3006]" italics="true" pageId="10" pageNumber="11">Xylocola-</emphasis>
group within 
<emphasis box="[352,615,3020,3056]" italics="true" pageId="10" pageNumber="11">
“ 
<taxonomicName box="[362,602,3020,3056]" class="Secernentea" family="Rhabditidae" genus="Protorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Protorhabditis</taxonomicName>
&quot;
</emphasis>
in having nine genital papillae.
</paragraph>
<paragraph blockId="10.[1271,2246,1516,1958]" pageId="10" pageNumber="11">
<emphasis bold="true" box="[1306,1481,1520,1556]" pageId="10" pageNumber="11">Previously</emphasis>
, 
<taxonomicName box="[1510,1768,1520,1556]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">
<emphasis box="[1510,1768,1520,1556]" italics="true" pageId="10" pageNumber="11">Caenorhabditis</emphasis>
</taxonomicName>
<emphasis bold="true" box="[1789,1946,1520,1556]" pageId="10" pageNumber="11">has been</emphasis>
characterised 
<emphasis bold="true" box="[2213,2244,1520,1556]" pageId="10" pageNumber="11">as</emphasis>
having the following apomorphic 
<emphasis bold="true" box="[1914,2245,1570,1606]" pageId="10" pageNumber="11">characteristics: the</emphasis>
presence of a dorsal 
<emphasis bold="true" box="[1633,1738,1620,1656]" pageId="10" pageNumber="11">velum</emphasis>
on the spicule, 
<emphasis bold="true" box="[2021,2039,1620,1656]" pageId="10" pageNumber="11">a</emphasis>
lateral field 
<emphasis bold="true" box="[1271,1346,1670,1706]" pageId="10" pageNumber="11">with</emphasis>
three ridges, an unsheathed dauer juvenile 
<emphasis bold="true" pageId="10" pageNumber="11">and a slightly thickened</emphasis>
GP6 [
<bibRefCitation author="Sudhaus W." box="[1691,1736,1720,1756]" journalOrPublisher="J Nematode Morphol Syst" pageId="10" pageNumber="11" pagination="113 - 78" part="14" refString="42. Sudhaus W. Phylogenetic systematisation and catalogue of paraphyletic &quot; Rhabditidae &quot; (Secementea, Nematoda). J Nematode Morphol Syst. 2011; 14: 113 - 78." title="Phylogenetic systematisation and catalogue of paraphyletic &quot; Rhabditidae &quot; (Secementea, Nematoda)" type="journal article" year="2011">42</bibRefCitation>
], W ith the discovery 
<emphasis bold="true" box="[2114,2175,1720,1756]" pageId="10" pageNumber="11">and</emphasis>
description of 
<taxonomicName box="[1487,1749,1770,1806]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1487,1512,1770,1806]" italics="true" pageId="10" pageNumber="11">C</emphasis>
. 
<taxonomicName box="[1538,1749,1770,1806]" pageId="10" pageNumber="11" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1538,1749,1770,1806]" italics="true" pageId="10" pageNumber="11">monodelphis</emphasis>
</taxonomicName>
</taxonomicName>
<taxonomicNameLabel box="[1766,1858,1770,1806]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
the num 
<emphasis bold="true" box="[2022,2078,1770,1806]" pageId="10" pageNumber="11">ber</emphasis>
of 
<emphasis bold="true" box="[2142,2245,1770,1806]" pageId="10" pageNumber="11">lateral</emphasis>
ridges is no longer an apomorphic character of 
<emphasis italics="true" pageId="10" pageNumber="11">
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">
<emphasis bold="true" italics="true" pageId="10" pageNumber="11">Caenorhabditis</emphasis>
</taxonomicName>
,
</emphasis>
since 
<taxonomicName box="[1532,1793,1870,1906]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1532,1558,1870,1906]" italics="true" pageId="10" pageNumber="11">C</emphasis>
. 
<taxonomicName box="[1580,1793,1870,1906]" pageId="10" pageNumber="11" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1580,1793,1870,1906]" italics="true" pageId="10" pageNumber="11">monodelphis</emphasis>
</taxonomicName>
</taxonomicName>
<taxonomicNameLabel box="[1806,1896,1870,1906]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
<emphasis bold="true" box="[1911,2052,1870,1906]" pageId="10" pageNumber="11">only has</emphasis>
one 
<emphasis bold="true" box="[2142,2245,1870,1906]" pageId="10" pageNumber="11">lateral</emphasis>
ridge.
</paragraph>
</subSubSection>
<subSubSection lastPageId="11" lastPageNumber="12" pageId="10" pageNumber="11" type="biology_ecology">
<paragraph blockId="10.[1271,2250,2018,3056]" box="[1272,1888,2021,2054]" pageId="10" pageNumber="11">
<heading bold="true" box="[1272,1888,2021,2054]" fontSize="10" level="5" pageId="10" pageNumber="11" reason="6">
<emphasis bold="true" box="[1272,1888,2021,2054]" pageId="10" pageNumber="11">Association with fungivorous beetles</emphasis>
</heading>
</paragraph>
<paragraph blockId="10.[1271,2250,2018,3056]" pageId="10" pageNumber="11">
Species of 
<taxonomicName box="[1471,1729,2070,2106]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">
<emphasis box="[1471,1729,2070,2106]" italics="true" pageId="10" pageNumber="11">Caenorhabditis</emphasis>
</taxonomicName>
<emphasis bold="true" box="[1750,1801,2070,2106]" pageId="10" pageNumber="11">are</emphasis>
known 
<emphasis bold="true" box="[1956,2107,2070,2106]" pageId="10" pageNumber="11">to occur</emphasis>
in 
<emphasis bold="true" box="[2180,2238,2070,2106]" pageId="10" pageNumber="11">soil</emphasis>
, compost, cadavers of insects, some 
<emphasis bold="true" box="[1918,2163,2120,2156]" pageId="10" pageNumber="11">plant material</emphasis>
and the intestine of 
<emphasis bold="true" box="[1559,1643,2170,2206]" pageId="10" pageNumber="11">birds</emphasis>
[
<bibRefCitation author="Kiontke K &amp; Sudhaus W." box="[1676,1720,2170,2206]" journalOrPublisher="Worm Book" pageId="10" pageNumber="11" refString="10. Kiontke K, Sudhaus W. Ecology of Caenorhabditis species. In: Community TCeR: WormBook, editor. Worm Book 2006." title="10" type="book" volumeTitle="Community TCeR: WormBook, editor" year="2006">10</bibRefCitation>
], and 
<emphasis bold="true" box="[1837,2165,2170,2206]" pageId="10" pageNumber="11">can most easily be</emphasis>
<emphasis bold="true" box="[1272,1353,2220,2256]" pageId="10" pageNumber="11">isolated</emphasis>
from rotting fruits, flowers and 
<emphasis bold="true" pageId="10" pageNumber="11">
stems [
<bibRefCitation author="Kiontke K &amp; Felix M-A &amp; Ailion M &amp; Rockman M &amp; Braendle C &amp; Penigault J-B" box="[2053,2074,2220,2256]" journalOrPublisher="BMC Evol Biol" pageId="10" pageNumber="11" pagination="339" part="11" refString="3. Kiontke K, Felix M-A, Ailion M, Rockman M, Braendle C, Penigault J-B, et al. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol. 2011; 11: 339." title="A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits" type="journal article" year="2011">3</bibRefCitation>
], 
<emphasis italics="true" pageId="10" pageNumber="11">
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
<taxonomicName box="[1421,1541,2270,2306]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
</emphasis>
</emphasis>
has also 
<emphasis bold="true" box="[1702,1783,2270,2306]" pageId="10" pageNumber="11">been</emphasis>
found 
<emphasis bold="true" box="[1907,2199,2270,2306]" pageId="10" pageNumber="11">infesting cultures</emphasis>
of the m ushroom 
<taxonomicName box="[1537,1841,2320,2356]" class="Agaricomycetes" family="Agaricaceae" genus="Agaricus" kingdom="Fungi" order="Agaricales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="species" species="bisporus">
<emphasis box="[1537,1841,2320,2356]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[1537,1686,2320,2356]" class="Agaricomycetes" family="Agaricaceae" genus="Agaricus" higherTaxonomySource="CoL" kingdom="Fungi" order="Agaricales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="genus">Agaricus</taxonomicName>
bisporus
</emphasis>
</taxonomicName>
[
<bibRefCitation author="Grewal PS &amp; Richardson PN." box="[1869,1914,2320,2356]" journalOrPublisher="Ann Appl Biol" pageId="10" pageNumber="11" pagination="381 - 94" part="118" refString="47. Grewal PS, Richardson PN. Effects of Caenorhabditis eiegans (Nematoda: Rhabditidae) on yield and quality of the cultivated mushroom Agaricus bisporus. Ann Appl Biol. 1991; 118: 381 - 94." title="Effects of Caenorhabditis eiegans (Nematoda: Rhabditidae) on yield and quality of the cultivated mushroom Agaricus bisporus" type="journal article" year="1991">47</bibRefCitation>
]. Wild mushrooms are an under-explored habitat 
<emphasis bold="true" box="[1828,2246,2370,2406]" pageId="10" pageNumber="11">for this genus, but our</emphasis>
limited geographical sampling 
<emphasis bold="true" box="[1811,2244,2420,2456]" pageId="10" pageNumber="11">indicates that they could</emphasis>
be an important habitat. 
<taxonomicName box="[1707,2184,2470,2506]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis bold="true" box="[1707,2184,2470,2506]" italics="true" pageId="10" pageNumber="11">Caenorhabditis monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
<emphasis bold="true" box="[1318,1381,2520,2556]" pageId="10" pageNumber="11">was</emphasis>
present in galleries 
<emphasis bold="true" pageId="10" pageNumber="11">
made by 
<taxonomicName box="[1903,2132,2520,2556]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="10" pageNumber="11" phylum="Arthropoda" rank="species" species="castaneus">
<emphasis bold="true" box="[1903,2132,2520,2556]" italics="true" pageId="10" pageNumber="11">Cis castaneus</emphasis>
</taxonomicName>
inside 
<emphasis box="[1274,1692,2570,2606]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[1274,1469,2570,2606]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="genus">Ganoderma</taxonomicName>
<taxonomicName box="[1489,1692,2570,2606]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="species" species="applanatum">applanatum</taxonomicName>
</emphasis>
</emphasis>
in 
<emphasis bold="true" box="[1769,2247,2570,2606]" pageId="10" pageNumber="11">Belgium, Norway, Germany</emphasis>
and in an old fruiting body of 
<taxonomicName box="[1863,2188,2620,2656]" class="Agaricomycetes" family="Polyporaceae" genus="Fomes" kingdom="Fungi" order="Polyporales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="species" species="fomentarius">
<emphasis box="[1863,2188,2620,2656]" italics="true" pageId="10" pageNumber="11">Fomes fomentarius</emphasis>
</taxonomicName>
in 
<emphasis bold="true" box="[1273,1411,2670,2706]" pageId="10" pageNumber="11">Belgium</emphasis>
. Although the true 
<emphasis bold="true" box="[1741,1935,2670,2706]" pageId="10" pageNumber="11">distribution</emphasis>
of 
<emphasis box="[1992,2017,2670,2706]" italics="true" pageId="10" pageNumber="11">C</emphasis>
. 
<taxonomicName box="[2037,2246,2670,2706]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis bold="true" box="[2037,2246,2670,2706]" italics="true" pageId="10" pageNumber="11">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1272,1359,2720,2756]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
is not yet known, it is expected that 
<emphasis bold="true" box="[1985,2175,2720,2756]" pageId="10" pageNumber="11">this species</emphasis>
will 
<emphasis bold="true" box="[1272,1309,2770,2806]" pageId="10" pageNumber="11">be</emphasis>
found throughout Europe where 
<taxonomicName box="[1922,2124,2770,2806]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="genus">
<emphasis bold="true" box="[1922,2124,2770,2806]" italics="true" pageId="10" pageNumber="11">Ganoderma</emphasis>
</taxonomicName>
(or in 
<emphasis bold="true" box="[1272,1494,2820,2856]" pageId="10" pageNumber="11">lesser extent</emphasis>
<emphasis box="[1513,1632,2820,2856]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[1513,1620,2820,2856]" class="Agaricomycetes" family="Polyporaceae" genus="Fomes" kingdom="Fungi" order="Polyporales" pageId="10" pageNumber="11" phylum="Basidiomycota" rank="genus">Fomes</taxonomicName>
)
</emphasis>
co-occurs 
<emphasis bold="true" box="[1840,1990,2820,2856]" pageId="10" pageNumber="11">with the</emphasis>
mycophagous beetle 
<emphasis box="[1388,1627,2870,2906]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[1388,1440,2870,2906]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="10" pageNumber="11" phylum="Arthropoda" rank="genus">Cis</taxonomicName>
<emphasis bold="true" box="[1453,1627,2870,2906]" italics="true" pageId="10" pageNumber="11">
<taxonomicName box="[1453,1622,2870,2906]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="10" pageNumber="11" phylum="Arthropoda" rank="species" species="castaneus">castaneus</taxonomicName>
.
</emphasis>
</emphasis>
</paragraph>
<paragraph blockId="10.[1271,2250,2018,3056]" lastBlockId="11.[1272,2248,366,606]" lastPageId="11" lastPageNumber="12" pageId="10" pageNumber="11">
That 
<taxonomicName box="[1411,1668,2920,2956]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="genus">
<emphasis box="[1411,1668,2920,2956]" italics="true" pageId="10" pageNumber="11">Caenorhabditis</emphasis>
</taxonomicName>
<emphasis bold="true" box="[1693,1913,2920,2956]" pageId="10" pageNumber="11">species have</emphasis>
phoretic relationships 
<emphasis bold="true" box="[1371,1576,2970,3006]" pageId="10" pageNumber="11">with insects</emphasis>
and 
<emphasis bold="true" box="[1669,1993,2970,3006]" pageId="10" pageNumber="11">other invertebrates</emphasis>
is well known [
<bibRefCitation author="Kiontke K &amp; Sudhaus W." box="[1287,1330,3020,3056]" journalOrPublisher="Worm Book" pageId="10" pageNumber="11" refString="10. Kiontke K, Sudhaus W. Ecology of Caenorhabditis species. In: Community TCeR: WormBook, editor. Worm Book 2006." title="10" type="book" volumeTitle="Community TCeR: WormBook, editor" year="2006">10</bibRefCitation>
]. For 
<taxonomicName box="[1453,1722,3020,3056]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="10" pageNumber="11" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1453,1478,3020,3056]" italics="true" pageId="10" pageNumber="11">C</emphasis>
. 
<emphasis box="[1510,1722,3020,3056]" italics="true" pageId="10" pageNumber="11">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1746,1847,3020,3056]" pageId="10" pageNumber="11" rank="species">sp. n.</taxonomicNameLabel>
, 
<emphasis bold="true" box="[1879,2141,3020,3056]" pageId="10" pageNumber="11">all records are</emphasis>
from m ushroom fruiting bodies that are also inhabited by different insect groups, and dauer larvae were found under the elytra of 
<emphasis box="[474,714,2070,2106]" italics="true" pageId="11" pageNumber="12">
<taxonomicName box="[474,710,2070,2106]" class="Insecta" family="Ciidae" genus="Cis" kingdom="Animalia" order="Coleoptera" pageId="11" pageNumber="12" phylum="Arthropoda" rank="species" species="castaneus">Cis castaneus</taxonomicName>
.
</emphasis>
Based on this evidence, we propose that C. 
<taxonomicName box="[516,719,2120,2156]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[516,719,2120,2156]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[737,825,2120,2156]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
propagates in galleries generated by 
<taxonomicName box="[466,583,2170,2206]" class="Insecta" family="Cisidae" higherTaxonomySource="GBIF" kingdom="Animalia" order="Coleoptera" pageId="11" pageNumber="12" phylum="Arthropoda" rank="family">Cisidae</taxonomicName>
and the dauer larvae are transported by these beetles to uninfested mushrooms. Records of 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1179,1204,2220,2256]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[239,442,2270,2306]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[456,541,2270,2306]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
in both 
<taxonomicName box="[684,876,2270,2306]" class="Agaricomycetes" family="Ganodermataceae" genus="Ganoderma" kingdom="Fungi" order="Polyporales" pageId="11" pageNumber="12" phylum="Basidiomycota" rank="genus">
<emphasis box="[684,876,2270,2306]" italics="true" pageId="11" pageNumber="12">Ganoderma</emphasis>
</taxonomicName>
and 
<emphasis box="[960,1072,2270,2306]" italics="true" pageId="11" pageNumber="12">
<taxonomicName box="[960,1066,2270,2306]" class="Agaricomycetes" family="Polyporaceae" genus="Fomes" kingdom="Fungi" order="Polyporales" pageId="11" pageNumber="12" phylum="Basidiomycota" rank="genus">Fomes</taxonomicName>
,
</emphasis>
respectively the preferred [
<bibRefCitation author="Guevara R &amp; Rayner ADM &amp; Reynolds SE." box="[572,591,2320,2356]" journalOrPublisher="Physiol Entomol" pageId="11" pageNumber="12" pagination="288 - 95" part="25" refString="9. Guevara R, Rayner ADM, Reynolds SE. Orientation of specialist and generalist fungivorous ciid beetles to host and non-host odours. Physiol Entomol. 2000; 25: 288 - 95." title="Orientation of specialist and generalist fungivorous ciid beetles to host and non-host odours" type="journal article" year="2000">9</bibRefCitation>
] and the known [
<bibRefCitation author="0 kland B." box="[900,940,2320,2356]" journalOrPublisher="Fauna Norv Ser B" pageId="11" pageNumber="12" pagination="21 - 6" part="42" refString="48. 0 kland B. Insect fauna compared between six polypore species in a southern Norwegian spruce forest. Fauna Norv Ser B. 1995; 42: 21 - 6." title="Insect fauna compared between six polypore species in a southern Norwegian spruce forest" type="journal article" year="1995">48</bibRefCitation>
] host indicate a beede-specific rather than a mushroom-specific relationship. The only other known 
<taxonomicName box="[723,971,2420,2456]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">
<emphasis box="[723,971,2420,2456]" italics="true" pageId="11" pageNumber="12">Caenorhabditis</emphasis>
</taxonomicName>
species which appears to be phoretically associated with fimgivorous organisms, most likely insects, is C. 
<emphasis box="[846,1047,2520,2556]" italics="true" pageId="11" pageNumber="12">auriculariae</emphasis>
Tsuda &amp; Futai, [
<bibRefCitation author="Tsuda K &amp; Futai K." box="[361,401,2570,2606]" journalOrPublisher="Jpn J Nematol" pageId="11" pageNumber="12" pagination="18 - 23" part="29" refString="49. Tsuda K, Futai K. Description of Caenorhabditis auricuiariae n. sp. (Nematoda: Rhabditida) from fruiting bodies of Auricuiaria poiytricha. Jpn J Nematol. 1999; 29: 18 - 23." title="Description of Caenorhabditis auricuiariae n. sp. (Nematoda: Rhabditida) from fruiting bodies of Auricuiaria poiytricha" type="journal article" year="1999">49</bibRefCitation>
] of the 
<taxonomicName box="[556,678,2570,2606]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="15" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[556,678,2570,2606]" italics="true" pageId="11" pageNumber="12">Elegans</emphasis>
</taxonomicName>
super-group. This species was found only once in the fruit bodies of 
<taxonomicName class="Agaricomycetes" family="Auriculariaceae" genus="Auricularia" kingdom="Animalia" order="Auriculariales" pageId="11" pageNumber="12" phylum="Basidiomycota" rank="species" species="polytricha">
<emphasis italics="true" pageId="11" pageNumber="12">Auricularia polytricha</emphasis>
</taxonomicName>
(Agaricomycetes) in Japan, but the vector needed to infest the mushroom is unknown [
<bibRefCitation author="Tsuda K &amp; Futai K." box="[808,851,2720,2756]" journalOrPublisher="Jpn J Nematol" pageId="11" pageNumber="12" pagination="18 - 23" part="29" refString="49. Tsuda K, Futai K. Description of Caenorhabditis auricuiariae n. sp. (Nematoda: Rhabditida) from fruiting bodies of Auricuiaria poiytricha. Jpn J Nematol. 1999; 29: 18 - 23." title="Description of Caenorhabditis auricuiariae n. sp. (Nematoda: Rhabditida) from fruiting bodies of Auricuiaria poiytricha" type="journal article" year="1999">49</bibRefCitation>
], 
<taxonomicName box="[887,1053,2720,2756]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[887,1053,2720,2756]" italics="true" pageId="11" pageNumber="12">C. elegans</emphasis>
</taxonomicName>
was also found to infest cultures of the champignon mushroom 
<taxonomicName box="[236,535,2820,2856]" class="Agaricomycetes" family="Agaricaceae" genus="Agaricus" kingdom="Fungi" order="Agaricales" pageId="11" pageNumber="12" phylum="Basidiomycota" rank="species" species="bisporus">
<emphasis box="[236,535,2820,2856]" italics="true" pageId="11" pageNumber="12">Agaricus bisporus</emphasis>
</taxonomicName>
[
<bibRefCitation author="Grewal PS &amp; Richardson PN." box="[573,616,2820,2856]" journalOrPublisher="Ann Appl Biol" pageId="11" pageNumber="12" pagination="381 - 94" part="118" refString="47. Grewal PS, Richardson PN. Effects of Caenorhabditis eiegans (Nematoda: Rhabditidae) on yield and quality of the cultivated mushroom Agaricus bisporus. Ann Appl Biol. 1991; 118: 381 - 94." title="Effects of Caenorhabditis eiegans (Nematoda: Rhabditidae) on yield and quality of the cultivated mushroom Agaricus bisporus" type="journal article" year="1991">47</bibRefCitation>
], but most likely originated from mushroom compost where it can be frequently found. Several samples of different mushrooms on wood in Europe, USA and Japan did not yield other 
<taxonomicName box="[879,1127,2970,3006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">
<emphasis box="[879,1127,2970,3006]" italics="true" pageId="11" pageNumber="12">Caenorhabditis</emphasis>
</taxonomicName>
spp. However, given that many more insect species are known to feed and reproduce on mushrooms [
<bibRefCitation author="Hammond PM &amp; Lawrence JF." box="[1930,1969,370,406]" editor="Wilding N" journalOrPublisher="London: Academic Press" pageId="11" pageNumber="12" pagination="275 - 324" part="14" refString="50. Hammond PM, Lawrence JF. Appendix - Mycophagy in Insects: a Summary. In: Insect-fungus Interactions. Wilding N, Collins NM, Hammond PM, Webber JF, editors, vol. 14. London: Academic Press; 1989. p. 275 - 324." title="50" type="book chapter" volumeTitle="Insect-fungus Interactions" year="1989">50</bibRefCitation>
] and 
<taxonomicName box="[2070,2245,370,406]" class="Secernentea" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="order">Rhabditida</taxonomicName>
are known to use insects as a phoretic transport carrier [
<bibRefCitation author="Timper P &amp; Davies KG." box="[1286,1327,470,506]" editor="Gaugler R" journalOrPublisher="Wallingford, UK: CABI" pageId="11" pageNumber="12" pagination="277 - 308" refString="51. Timper P, Davies KG. Biotic interactions. In: Nematode Behaviour. Gaugler R, Bilgrami AL, editors. Wallingford, UK: CABI; 2004. p. 277 - 308." title="51" type="book chapter" volumeTitle="Nematode Behaviour" year="2004">51</bibRefCitation>
], it is possible that mushroom species are habitats for many other rhabditid species, including new species of 
<emphasis box="[1274,1528,570,606]" italics="true" pageId="11" pageNumber="12">
<taxonomicName box="[1274,1523,570,606]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
.
</emphasis>
</paragraph>
</subSubSection>
<subSubSection pageId="11" pageNumber="12" type="discussion">
<paragraph blockId="11.[1267,2246,668,2407]" pageId="11" pageNumber="12">
Genome 
<emphasis bold="true" box="[1423,1925,670,703]" pageId="11" pageNumber="12">sequence and gene structures</emphasis>
of 
<taxonomicName box="[1983,2229,672,703]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis bold="true" box="[1983,2229,672,703]" italics="true" pageId="11" pageNumber="12">C. monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1272,1360,721,754]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
</paragraph>
<paragraph blockId="11.[1267,2246,668,2407]" pageId="11" pageNumber="12">
Using next generation sequencing technologies and advanced bioinformatics toolkits, we have generated a good first-draft genome sequence for an inbred line derived from the type strain of 
<taxonomicName box="[1658,1911,920,956]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n">
<emphasis box="[1658,1683,920,956]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1703,1911,920,956]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1922,2000,920,956]" pageId="11" pageNumber="12" rank="species">sp. n</taxonomicNameLabel>
.. Although assembly metrics and CEGMA scores indicate the assembly is relatively contiguous and complete, it is likely that a proportion of 
<taxonomicName box="[1518,1776,1070,1106]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1518,1543,1070,1106]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1567,1776,1070,1106]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1792,1883,1070,1106]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
genes are assembled only partially. This may have affected gene prediction, with the number of predicted gene models (17,180) being lower than estimates from most other 
<taxonomicName box="[1856,2108,1220,1256]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">
<emphasis box="[1856,2108,1220,1256]" italics="true" pageId="11" pageNumber="12">Caenorhabditis</emphasis>
</taxonomicName>
species with available sequence data [
<bibRefCitation author="Howe KL &amp; Bolt BJ &amp; Cain S &amp; Chan J &amp; Chen WJ &amp; Davis P" box="[1765,1808,1270,1306]" journalOrPublisher="Nucleic Acids Res" pageId="11" pageNumber="12" pagination="774 - 80" part="44" refString="25. Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, et al. WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 2016; 44 D 774 - 80." title="WormBase 2016: expanding to enable helminth genomic research" type="journal article" year="2016">25</bibRefCitation>
]. Comparisons of orthologous gene pairs revealed a significant divergence in gene structure between 
<taxonomicName box="[1585,1839,1370,1406]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1585,1610,1370,1406]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1630,1839,1370,1406]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1851,1939,1370,1406]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
and 
<taxonomicName box="[2027,2190,1370,1406]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[2027,2051,1370,1406]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis italics="true" pageId="11" pageNumber="12">
elegans. 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">C. monodelphis</taxonomicName>
</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1491,1578,1420,1456]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
genes are typically longer, contain more coding exons and a longer span of introns than 
<taxonomicName box="[2082,2245,1470,1506]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[2082,2108,1470,1506]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[2128,2245,1470,1506]" italics="true" pageId="11" pageNumber="12">elegans</emphasis>
</taxonomicName>
genes (
<tableCitation box="[1390,1514,1520,1556]" captionStart="Table 3" captionStartId="8.[238,329,2448,2481]" captionTargetBox="[238,1210,2554,2928]" captionText="Table 3 Gene structure comparison of orthologous gene pairs from C. monodelphis sp. N. and C. elegans" httpUri="http://table.plazi.org/id/DF0441CF2868FFCB3989D1B2055BF626" pageId="11" pageNumber="12" tableUuid="DF0441CF2868FFCB3989D1B2055BF626">Table 3</tableCitation>
). This increase in gene length may, in part, account for the difference in genome span between 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[2212,2237,1570,1606]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1273,1481,1620,1656]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1492,1579,1620,1656]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
and C. 
<emphasis box="[1709,1833,1620,1656]" italics="true" pageId="11" pageNumber="12">
<taxonomicName box="[1709,1828,1620,1656]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">elegans</taxonomicName>
.
</emphasis>
The clear trend towards more coding-exons in C. 
<taxonomicName box="[1705,1911,1670,1706]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1705,1911,1670,1706]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1927,2016,1670,1706]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
relative to 
<taxonomicName class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[2212,2237,1670,1706]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1272,1391,1720,1756]" italics="true" pageId="11" pageNumber="12">elegans</emphasis>
</taxonomicName>
(
<figureCitation box="[1415,1504,1720,1756]" captionStart="Fig. 5" captionStartId="9.[264,311,2331,2358]" captionTargetBox="[237,2230,367,2308]" captionText="Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20 % longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log 2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count" httpUri="https://zenodo.org/record/322321/files/figure.png" pageId="11" pageNumber="12">Fig. 5</figureCitation>
) could be explained by extensive intron loss or gain in either species. Previous studies using a small number of genes have shown that intron losses have been far m ore common in 
<taxonomicName box="[1653,1915,1870,1906]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">
<emphasis box="[1653,1915,1870,1906]" italics="true" pageId="11" pageNumber="12">Caenorhabditis</emphasis>
</taxonomicName>
evolution than intron gains [
<bibRefCitation author="Kiontke K &amp; Gavin NP &amp; Raynes Y &amp; Roehrig C &amp; Piano F &amp; Fitch DHA." box="[1479,1500,1920,1956]" journalOrPublisher="Proc Natl Acad Sei U S A" pageId="11" pageNumber="12" pagination="9003 - 8" part="101" refString="7. Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DHA. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sei U S A. 2004; 101: 9003 - 8." title="Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss" type="journal article" year="2004">7</bibRefCitation>
, 
<bibRefCitation author="Cho S &amp; Jin S-W &amp; Cohen A &amp; Ellis RE. A" box="[1523,1566,1920,1956]" journalOrPublisher="Genome Res" pageId="11" pageNumber="12" pagination="1207 - 20" part="14" refString="52. Cho S, Jin S-W, Cohen A, Ellis RE. A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res. 2004; 14: 1207 - 20." title="phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution" type="journal article" year="2004">52</bibRefCitation>
, 
<bibRefCitation author="Hoogewijs D &amp; De Henau S &amp; Dewilde S &amp; Moens L &amp; Couvreur M &amp; Borgonie G" box="[1588,1633,1920,1956]" journalOrPublisher="BMC Evol Biol" pageId="11" pageNumber="12" pagination="1" part="8" refString="53. Hoogewijs D, De Henau S, Dewilde S, Moens L, Couvreur M, Borgonie G, et al. The Caenorhabditis globin gene family reveals extensive nematodespecific radiation and diversification. BMC Evol Biol. 2008; 8: 1." title="The Caenorhabditis globin gene family reveals extensive nematodespecific radiation and diversification" type="journal article" year="2008">53</bibRefCitation>
], Thus, it 
<emphasis box="[1820,1845,1920,1956]" italics="true" pageId="11" pageNumber="12">is</emphasis>
possible that the gene structures seen in C. 
<taxonomicName box="[1696,1911,1970,2006]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="monodelphis" status="sp. n.">
<emphasis box="[1696,1911,1970,2006]" italics="true" pageId="11" pageNumber="12">monodelphis</emphasis>
</taxonomicName>
<taxonomicNameLabel box="[1940,2043,1970,2006]" pageId="11" pageNumber="12" rank="species">sp. n.</taxonomicNameLabel>
reflect an intron-rich ancestral state, and intron loss has predominated during the evolution of 
<taxonomicName box="[1799,1970,2070,2106]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1799,1825,2070,2106]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1849,1975,2070,2106]" italics="true" pageId="11" pageNumber="12">elegans.</emphasis>
</taxonomicName>
In 
<emphasis italics="true" pageId="11" pageNumber="12">
<taxonomicName class="Secernentea" family="Neodiplogastridae" genus="Pristionchus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="pacifions">Pristionchus pacifions</taxonomicName>
,
</emphasis>
which is distantly related to 
<emphasis box="[1984,2244,2120,2156]" italics="true" pageId="11" pageNumber="12">
<taxonomicName box="[1984,2237,2120,2156]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">Caenorhabditis</taxonomicName>
,
</emphasis>
genes typically have roughly twice as many introns as their orthologues in 
<taxonomicName box="[1534,1702,2220,2256]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="species" species="elegans">
<emphasis box="[1534,1560,2220,2256]" italics="true" pageId="11" pageNumber="12">C</emphasis>
. 
<emphasis box="[1583,1702,2220,2256]" italics="true" pageId="11" pageNumber="12">elegans</emphasis>
</taxonomicName>
[
<bibRefCitation author="Dieterich C &amp; Clifton SW &amp; Schuster LN &amp; Chinwalla A &amp; Delehaunty K" box="[1731,1775,2220,2256]" journalOrPublisher="Nat Genet" pageId="11" pageNumber="12" pagination="1193 - 8" part="40" refString="54. Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K Dinkelacker I, et al. The Pistionchus pacifiais genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008; 40: 1193 - 8." title="Dinkelacker I, et al. The Pistionchus pacifiais genome provides a unique perspective on nematode lifestyle and parasitism" type="journal article" year="2008">54</bibRefCitation>
], Further analysis using genomes from more closely related outgroup species and other 
<taxonomicName box="[1380,1632,2320,2356]" class="Secernentea" family="Rhabditidae" genus="Caenorhabditis" kingdom="Animalia" order="Rhabditida" pageId="11" pageNumber="12" phylum="Nematoda" rank="genus">
<emphasis box="[1380,1632,2320,2356]" italics="true" pageId="11" pageNumber="12">Caenorhabditis</emphasis>
</taxonomicName>
species is necessary before we can infer the dynamics of intron evolution in the genus.
</paragraph>
</subSubSection>
</treatment>
</document>