766 lines
95 KiB
XML
766 lines
95 KiB
XML
<document ID-DOI="http://doi.org/10.5281/zenodo.3610545" ID-GBIF-Dataset="3269bae6-36d8-4c4e-a814-cda94b6aeece" ID-GBIF-Taxon="161746375" ID-Zenodo-Dep="3610545" checkinTime="1579089070375" checkinUser="plazi" docAuthor="Rheindt, Frank E., Prawiradilaga, Dewi M., Ashar, Hidayat, Lee, Geraldine W. X., Wu, Meng Yue & Ng, Nathaniel S. R." docDate="2020" docId="03F587A7FFBF8F31FF127026FE3BF869" docLanguage="en" docName="science.367.167-170_aax2146-Rheindt-SM.pdf" docOrigin="Science 36" docStyle="DocumentStyle{}" docTitle="Phylloscopus emilsalimi Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng 2020, species nova" docType="treatment" docVersion="9" lastPageId="46" lastPageNumber="47" masterDocId="FFCCFFDFFF9B8F1FFFD2714DFFBCFFEA" masterDocTitle="A lost world in Wallacea: Description of a montane archipelagic avifauna (supplement)" masterLastPageNumber="104" masterPageNumber="1" pageId="36" pageNumber="37" updateTime="1643451873296" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
|
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<mods:titleInfo>
|
||
<mods:title>A lost world in Wallacea: Description of a montane archipelagic avifauna (supplement)</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:name type="personal">
|
||
<mods:role>
|
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<mods:roleTerm>Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart>Rheindt, Frank E.</mods:namePart>
|
||
</mods:name>
|
||
<mods:name type="personal">
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||
<mods:role>
|
||
<mods:roleTerm>Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart>Prawiradilaga, Dewi M.</mods:namePart>
|
||
</mods:name>
|
||
<mods:name type="personal">
|
||
<mods:role>
|
||
<mods:roleTerm>Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart>Ashar, Hidayat</mods:namePart>
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||
</mods:name>
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<mods:name type="personal">
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<mods:role>
|
||
<mods:roleTerm>Author</mods:roleTerm>
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||
</mods:role>
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||
<mods:namePart>Lee, Geraldine W. X.</mods:namePart>
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||
</mods:name>
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||
<mods:name type="personal">
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||
<mods:role>
|
||
<mods:roleTerm>Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart>Wu, Meng Yue</mods:namePart>
|
||
</mods:name>
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||
<mods:name type="personal">
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||
<mods:role>
|
||
<mods:roleTerm>Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart>Ng, Nathaniel S. R.</mods:namePart>
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||
</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:relatedItem type="host">
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<mods:titleInfo>
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||
<mods:title>Science</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:part>
|
||
<mods:date>2020</mods:date>
|
||
<mods:detail type="pubDate">
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||
<mods:number>2020-01-10</mods:number>
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||
</mods:detail>
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||
<mods:detail type="volume">
|
||
<mods:number>36</mods:number>
|
||
</mods:detail>
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<mods:extent unit="page">
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<mods:start>1</mods:start>
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<mods:end>104</mods:end>
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</mods:extent>
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</mods:part>
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||
</mods:relatedItem>
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<mods:classification>journal article</mods:classification>
|
||
<mods:identifier type="DOI">http://doi.org/10.5281/zenodo.3608758</mods:identifier>
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<mods:identifier type="GBIF-Dataset">3269bae6-36d8-4c4e-a814-cda94b6aeece</mods:identifier>
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<mods:identifier type="Zenodo-Dep">3608758</mods:identifier>
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<mods:identifier type="ZooBank">8114B399-C68D-43C2-B6D3-B51AA898431E</mods:identifier>
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</mods:mods>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.3610545" ID-GBIF-Taxon="161746375" ID-Zenodo-Dep="3610545" LSID="urn:lsid:plazi:treatment:03F587A7FFBF8F31FF127026FE3BF869" httpUri="http://treatment.plazi.org/id/03F587A7FFBF8F31FF127026FE3BF869" lastPageId="46" lastPageNumber="47" pageId="36" pageNumber="37">
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<paragraph blockId="36.[192,1393,201,1946]" box="[192,291,363,401]" pageId="36" pageNumber="37">
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<emphasis bold="true" box="[192,291,363,401]" pageId="36" pageNumber="37">SM6:</emphasis>
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</paragraph>
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</subSubSection>
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<subSubSection box="[302,973,363,402]" pageId="36" pageNumber="37" type="nomenclature">
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<paragraph blockId="36.[192,1393,201,1946]" box="[302,973,363,402]" pageId="36" pageNumber="37">
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<heading bold="true" box="[302,973,363,402]" fontSize="16" level="5" pageId="36" pageNumber="37" reason="0">
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<emphasis bold="true" box="[302,973,363,402]" pageId="36" pageNumber="37">
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<taxonomicName authority="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng, 2020" authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[302,727,363,401]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="36" pageNumber="37" phylum="Chordata" rank="species" species="emilsalimi" status="species nova">
|
||
<emphasis bold="true" box="[302,727,363,401]" italics="true" pageId="36" pageNumber="37">Phylloscopus emilsalimi</emphasis>
|
||
</taxonomicName>
|
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,
|
||
<taxonomicNameLabel box="[749,973,363,402]" pageId="36" pageNumber="37" rank="species">species nova</taxonomicNameLabel>
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</emphasis>
|
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</heading>
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</paragraph>
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||
</subSubSection>
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||
<subSubSection pageId="36" pageNumber="37" type="vernacular_names">
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||
<paragraph blockId="36.[192,1393,201,1946]" pageId="36" pageNumber="37">
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||
<emphasis bold="true" pageId="36" pageNumber="37">
|
||
(
|
||
<vernacularName pageId="36" pageNumber="37">Taliabu Leaf-Warbler</vernacularName>
|
||
;
|
||
</emphasis>
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection pageId="36" pageNumber="37" type="nomenclature">
|
||
<paragraph blockId="36.[192,1393,201,1946]" pageId="36" pageNumber="37">
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<emphasis bold="true" pageId="36" pageNumber="37">urn:lsid:zoobank.org:act:E77116DC-D83F-4C3C-A472-519B99D2843F</emphasis>
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</paragraph>
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<paragraph blockId="36.[192,1393,201,1946]" pageId="36" pageNumber="37">
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||
<emphasis bold="true" box="[469,483,559,597]" pageId="36" pageNumber="37">)</emphasis>
|
||
Frank E. Rheindt, Dewi M. Prawiradilaga, Hidayat Ashari, Suparno, Nathaniel S. R. Ng
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection pageId="36" pageNumber="37" type="materials_examined">
|
||
<paragraph blockId="36.[192,1393,201,1946]" box="[192,316,807,835]" pageId="36" pageNumber="37">
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<heading bold="true" box="[192,316,807,835]" fontSize="12" level="7" pageId="36" pageNumber="37" reason="2">
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||
<materialsCitation ID-GBIF-Occurrence="2550489961" box="[192,316,807,835]" collectingDate="2013-12-09" collectionCode="MZB" collectorName="Rheindt & LIPI field party" country="Indonesia" elevation="1200" latitude="-1.0132262" location="Waiyo dinahana Camp" longLatPrecision="1" longitude="124.01339" pageId="36" pageNumber="37" specimenCode="MZB.Ornit.34.352" specimenCount="2" specimenCount-adult="1" specimenCount-male="1" typeStatus="holotype">
|
||
<emphasis bold="true" box="[192,316,807,835]" pageId="36" pageNumber="37">
|
||
<typeStatus box="[192,316,807,835]" pageId="36" pageNumber="37">Holotype</typeStatus>
|
||
</emphasis>
|
||
</materialsCitation>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="36.[192,1393,201,1946]" pageId="36" pageNumber="37">
|
||
<specimenCode box="[192,433,881,909]" pageId="36" pageNumber="37">MZB.Ornit.34.352</specimenCode>
|
||
(
|
||
<figureCitation box="[450,540,881,909]" captionStart="Fig" captionStartId="80.[192,239,1389,1417]" captionTargetBox="[200,1336,200,1336]" captionTargetId="figure@80.[192,1344,192,1344]" captionText="Fig. S8. Holotypes of Phylloscopus suaramerdu (MZB.Ornit.34.440) (top), and Phylloscopus emilsalimi (MZB.Ornit.34.352) (bottom)." figureDoi="http://doi.org/10.5281/zenodo.3608774" httpUri="https://zenodo.org/record/3608774/files/figure.png" pageId="36" pageNumber="37">fig. S8</figureCitation>
|
||
);
|
||
<specimenCount box="[564,628,881,909]" pageId="36" pageNumber="37" type="adult">adult</specimenCount>
|
||
<specimenCount box="[636,698,881,909]" pageId="36" pageNumber="37" type="male">male</specimenCount>
|
||
collected
|
||
<date box="[830,978,881,910]" pageId="36" pageNumber="37" value="2013-12-09">
|
||
<collectingDate box="[830,978,881,910]" pageId="36" pageNumber="37" value="2013-12-09">9 Dec 2013</collectingDate>
|
||
</date>
|
||
at
|
||
<location LSID="urn:lsid:plazi:treatment:03F587A7FFBF8F31FF127026FE3BF869:8E83606AFFBF8F3BFC2B723CFAA1FC67" box="[1017,1309,881,909]" latitude="-1.0132262" longLatPrecision="1" longitude="124.01339" name="Waiyo dinahana Camp" pageId="36" pageNumber="37">Waiyo dinahana Camp</location>
|
||
(~
|
||
<quantity box="[217,311,954,982]" metricMagnitude="3" metricUnit="m" metricValue="1.2" pageId="36" pageNumber="37" unit="m" value="1200.0">
|
||
<elevation box="[217,311,954,982]" metricMagnitude="3" metricUnit="m" metricValue="1.2" pageId="36" pageNumber="37" unit="m" value="1200.0">1200m</elevation>
|
||
</quantity>
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||
)
|
||
<location LSID="urn:lsid:plazi:treatment:03F587A7FFBF8F31FF127026FE3BF869:8E83606AFFBF8F3BFE9A72F7FCC3FC3C" box="[328,895,954,984]" latitude="-1.0132262" longLatPrecision="1" longitude="124.01339" name="above the village of Wahe on Taliabu Island" pageId="36" pageNumber="37">above the village of Wahe on Taliabu Island</location>
|
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(
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||
<geoCoordinate box="[914,1084,954,982]" degrees="01" direction="south" minutes="0" orientation="latitude" pageId="36" pageNumber="37" precision="1" seconds="47.614" value="-1.0132262">S 01⁰ 47.614</geoCoordinate>
|
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';
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||
<geoCoordinate box="[1100,1289,954,984]" degrees="124" direction="east" minutes="0" orientation="longitude" pageId="36" pageNumber="37" precision="1" seconds="48.216" value="124.01339">E 124⁰ 48.216</geoCoordinate>
|
||
'). Collected by the
|
||
<collectorName box="[410,511,1028,1056]" pageId="36" pageNumber="37">Rheindt</collectorName>
|
||
/
|
||
<collectorName box="[520,722,1028,1057]" pageId="36" pageNumber="37">LIPI field party</collectorName>
|
||
, including tissue samples from breast muscle and liver; skin prepared by Suparno; field number Tbu15; no molt; medium to high fat; weight
|
||
<quantity box="[192,243,1175,1203]" metricMagnitude="-2" metricUnit="kg" metricValue="1.0" pageId="36" pageNumber="37" unit="g" value="10.0">10g</quantity>
|
||
; wing length
|
||
<quantity box="[417,500,1175,1203]" metricMagnitude="-2" metricUnit="m" metricValue="6.8" pageId="36" pageNumber="37" unit="cm" value="6.8">6.8cm</quantity>
|
||
; wing spread
|
||
<quantity box="[676,775,1175,1203]" metricMagnitude="-1" metricUnit="m" metricValue="1.76" pageId="36" pageNumber="37" unit="cm" value="17.6">17.6cm</quantity>
|
||
; total length
|
||
<quantity box="[941,1040,1175,1203]" metricMagnitude="-1" metricUnit="m" metricValue="1.02" pageId="36" pageNumber="37" unit="cm" value="10.2">10.2cm</quantity>
|
||
; bill
|
||
<quantity box="[1104,1203,1175,1203]" metricMagnitude="-2" metricUnit="m" metricValue="1.35" pageId="36" pageNumber="37" unit="cm" value="1.35">1.35cm</quantity>
|
||
; tail
|
||
<quantity box="[1265,1348,1175,1203]" metricMagnitude="-2" metricUnit="m" metricValue="4.1" pageId="36" pageNumber="37" unit="cm" value="4.1">4.1cm</quantity>
|
||
; tarsus
|
||
<quantity box="[275,358,1249,1277]" metricMagnitude="-2" metricUnit="m" metricValue="2.5" pageId="36" pageNumber="37" unit="cm" value="2.5">2.5cm</quantity>
|
||
.
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="37" lastPageNumber="38" pageId="36" pageNumber="37" type="description">
|
||
<paragraph blockId="36.[192,1393,201,1946]" box="[192,510,1401,1429]" pageId="36" pageNumber="37">
|
||
<heading bold="true" box="[192,510,1401,1429]" fontSize="12" level="7" pageId="36" pageNumber="37" reason="2">
|
||
<emphasis bold="true" box="[192,510,1401,1429]" pageId="36" pageNumber="37">Description of holotype</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="36.[192,1393,201,1946]" lastBlockId="37.[192,1389,201,2002]" lastPageId="37" lastPageNumber="38" pageId="36" pageNumber="37">The crown (from forehead to nape) is dark brownish-olive (5Y 4/6), delimited below by a narrow long lemon supercilium (5Y 8/4) from bill base to nape side. Partial eye ring formed by small white feathers around the eye is broken by a dark brownish-olive eyestripe (5Y 3/3). Black rictal bristles. Lemon ear coverts down to malar and moustachial regions (5Y 9/10) grizzled with dusky-olive feather edging, making for a mottled facial appearance. Upperparts from mantle and scapulars to rump are mid-olive (7.5Y 4/6). Remiges are distinctly darker- olive (5Y 3/2) but have paler olive outer edging concolorous with mantle. Upperwing coverts have outer webs largely concolorous with mantle and inner webs concolorous with remiges. Rectrices are dark olive above (5Y 3/2) with brighter basal edging roughly concolorous with mantle, and have a more silvery sheen below (5Y 5/1). Underparts from chin to vent are largely lemon to sulphur yellow, with white feather bases creating a more lemon-yellow hue on throat, breast and belly (7.5Y 8/8) and olive feather tips (5Y 4/4) generating a more olive- mottled appearance on flanks, while the undertail coverts are largely uniform lemon (5Y 9/12).</paragraph>
|
||
<paragraph blockId="37.[192,1389,201,2002]" pageId="37" pageNumber="38">Iris brown; bill dark horn with base of lower mandible much paler pink-horn. Tarsus and toes on live bird reported as pink-horn with paler yellowish toepads.</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="38" lastPageNumber="39" pageId="37" pageNumber="38" type="diagnosis">
|
||
<paragraph blockId="37.[192,1389,201,2002]" box="[192,324,942,970]" pageId="37" pageNumber="38">
|
||
<heading bold="true" box="[192,324,942,970]" fontSize="12" level="7" pageId="37" pageNumber="38" reason="2">
|
||
<emphasis bold="true" box="[192,324,942,970]" pageId="37" pageNumber="38">Diagnosis</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="37.[192,1389,201,2002]" pageId="37" pageNumber="38">
|
||
Akin to the newly described species from Peleng,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[834,1003,1016,1045]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[834,1003,1016,1045]" italics="true" pageId="37" pageNumber="38">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
from Taliabu is a small
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[192,363,1089,1117]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="genus">
|
||
<emphasis box="[192,363,1089,1117]" italics="true" pageId="37" pageNumber="38">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
typical of the
|
||
<taxonomicName baseAuthorityName="Salvadori" baseAuthorityYear="1876" box="[547,763,1089,1119]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="poliocephalus">
|
||
<emphasis box="[547,763,1089,1119]" italics="true" pageId="37" pageNumber="38">P. poliocephalus</emphasis>
|
||
</taxonomicName>
|
||
leaf-warbler radiation from across Australo- Papua and Wallacea. It is most notable for its entirely lemon underparts (including throat), and the lack of a central crown stripe and wingbars. It differs from other members of the complex in bioacoustic traits in addition to a number of important plumage features:
|
||
</paragraph>
|
||
<paragraph blockId="37.[192,1389,201,2002]" pageId="37" pageNumber="38">
|
||
The new species
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[507,676,1384,1413]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[507,676,1384,1413]" italics="true" pageId="37" pageNumber="38">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
from Taliabu differs strikingly from the newly described species from Peleng (
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[599,790,1457,1487]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[599,790,1457,1487]" italics="true" pageId="37" pageNumber="38">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
, see SM5), which is the geographically most proximate member of the radiation, in its much yellower (versus white) supercilium, facial grizzling, and throat.
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[467,635,1604,1634]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[467,635,1604,1634]" italics="true" pageId="37" pageNumber="38">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
also has less of a mottled appearance on the breast, a greener crown, and paler bill and tarsus.
|
||
</paragraph>
|
||
<paragraph blockId="37.[192,1389,201,2002]" lastBlockId="38.[192,1393,201,1922]" lastPageId="38" lastPageNumber="39" pageId="37" pageNumber="38">
|
||
The new Taliabu species is most similar to
|
||
<taxonomicName box="[843,1015,1752,1781]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[843,1015,1752,1781]" italics="true" pageId="37" pageNumber="38">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
from large parts of montane Sulawesi, but differs in its paler bill and tarsus, its duller olive upperparts, and its less olive- mottled appearance on the breast. Specifically, it can be told from the geographically most proximate populations of
|
||
<taxonomicName box="[522,694,1972,2002]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="37" pageNumber="38" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[522,694,1972,2002]" italics="true" pageId="37" pageNumber="38">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
(from eastern, southeastern and central Sulawesi) by its paler yellow underparts coloration caused by an arrangement in which most feathers are predominantly white with strong yellow edging (versus all-yellow feathers, often with olive edges, in eastern Sulawesi birds). The new species is very distinct from
|
||
<taxonomicName baseAuthorityName="A. B. Meyer & Wiglesworth" baseAuthorityYear="1896" box="[1113,1310,350,378]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="sarasinorum">
|
||
<emphasis box="[1113,1310,350,378]" italics="true" pageId="38" pageNumber="39">P. sarasinorum</emphasis>
|
||
</taxonomicName>
|
||
in lacking both a pale central crown stripe and extensive white inner webs of outer rectrices.
|
||
</paragraph>
|
||
<paragraph blockId="38.[192,1393,201,1922]" pageId="38" pageNumber="39">
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[288,457,495,525]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[288,457,495,525]" italics="true" pageId="38" pageNumber="39">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
generally differs from remaining members of the
|
||
<taxonomicName baseAuthorityName="Salvadori" baseAuthorityYear="1876" box="[1098,1314,495,525]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="poliocephalus">
|
||
<emphasis box="[1098,1314,495,525]" italics="true" pageId="38" pageNumber="39">P. poliocephalus</emphasis>
|
||
</taxonomicName>
|
||
complex by a combination of features. In particular, it differs from
|
||
<taxonomicName class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="subSpecies" species="poliocephalus" subSpecies="giulianettii">
|
||
<emphasis box="[1053,1269,569,599]" italics="true" pageId="38" pageNumber="39">P. poliocephalus</emphasis>
|
||
<emphasis box="[192,332,642,670]" italics="true" pageId="38" pageNumber="39">giulianettii</emphasis>
|
||
</taxonomicName>
|
||
(Central Papua) in its lack of wingbars and lack of central crown stripe; from
|
||
<emphasis box="[1334,1361,644,672]" italics="true" pageId="38" pageNumber="39">P.</emphasis>
|
||
<taxonomicName baseAuthorityName="Salvadori" baseAuthorityYear="1876" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="45" phylum="Chordata" rank="species" species="poliocephalus">
|
||
<emphasis box="[1369,1393,644,672]" italics="true" pageId="38" pageNumber="39">p.</emphasis>
|
||
<emphasis box="[192,372,716,744]" italics="true" pageId="38" pageNumber="39">poliocephalus</emphasis>
|
||
</taxonomicName>
|
||
(West Papua) in its lack of wingbars, a yellower (versus more whitish) throat, a more olive (versus greyish) crown, and a much shorter, yellower (versus long and white) supercilium; from
|
||
<taxonomicName authority="(Seram)" authorityName="Seram" baseAuthorityName="Seram" box="[430,721,863,893]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="ceramensis">
|
||
<emphasis box="[430,610,865,893]" italics="true" pageId="38" pageNumber="39">P. ceramensis</emphasis>
|
||
(Seram)
|
||
</taxonomicName>
|
||
in its lack of well-defined wingbars, lack of central crown stripe, a yellower (versus white) supercilium, and a more olive tinge to the crown and auriculars (versus a darker grayish-brown head coloration); from
|
||
<taxonomicName authority="(Buru)" authorityName="Buru" baseAuthorityName="Buru" box="[1029,1254,1010,1040]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="everetti">
|
||
<emphasis box="[1029,1161,1012,1040]" italics="true" pageId="38" pageNumber="39">P. everetti</emphasis>
|
||
(Buru)
|
||
</taxonomicName>
|
||
in its lack of wingbars, slightly yellower throat, yellower (versus white) supercilium and olive (versus grayish) crown; from
|
||
<taxonomicName box="[472,663,1158,1187]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="waterstradti">
|
||
<emphasis box="[472,663,1158,1187]" italics="true" pageId="38" pageNumber="39">P. waterstradti</emphasis>
|
||
</taxonomicName>
|
||
(North Moluccas) in its yellower (versus white) throat, lack of wingbars (present in Obi population), an olive (versus grayish) head coloration and yellower supercilium; from
|
||
<taxonomicName box="[550,654,1305,1335]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="floris">
|
||
<emphasis box="[550,654,1305,1335]" italics="true" pageId="38" pageNumber="39">P. floris</emphasis>
|
||
</taxonomicName>
|
||
(Flores) in its non-contrasting olive (versus contrastingly grey) crown, a yellower (versus white) supercilium, and less intensely yellow underparts; and from
|
||
<taxonomicName authority="(Timor)" authorityName="Timor" baseAuthorityName="Timor" box="[262,528,1452,1482]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="38" pageNumber="39" phylum="Chordata" rank="species" species="presbytes">
|
||
<emphasis box="[262,419,1452,1482]" italics="true" pageId="38" pageNumber="39">P. presbytes</emphasis>
|
||
(Timor)
|
||
</taxonomicName>
|
||
in its lack of a central crown stripe, a yellower and shorter (versus long white) supercilium, and a yellower and less contrasting throat (versus a contrasting white throat).
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="39" lastPageNumber="40" pageId="38" pageNumber="39" type="etymology">
|
||
<paragraph blockId="38.[192,1393,201,1922]" box="[192,340,1746,1774]" pageId="38" pageNumber="39">
|
||
<heading bold="true" box="[192,340,1746,1774]" fontSize="12" level="7" pageId="38" pageNumber="39" reason="2">
|
||
<emphasis bold="true" box="[192,340,1746,1774]" pageId="38" pageNumber="39">Etymology</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="38.[192,1393,201,1922]" lastBlockId="39.[192,1394,201,1939]" lastPageId="39" lastPageNumber="40" pageId="38" pageNumber="39">We are pleased to name this new species after Prof Emil Salim, former Minister of Environment of the Republic of Indonesia and eminent environmentalist whose actions have contributed to more stringent international guidelines regulating extractive industries and mining, thereby benefitting many countries’ natural communities, including Indonesia.</paragraph>
|
||
</subSubSection>
|
||
<subSubSection pageId="39" pageNumber="40" type="discussion">
|
||
<paragraph blockId="39.[192,1394,201,1939]" box="[192,976,427,455]" pageId="39" pageNumber="40">
|
||
<heading bold="true" box="[192,976,427,455]" fontSize="12" level="7" pageId="39" pageNumber="40" reason="2">
|
||
<emphasis bold="true" box="[192,976,427,455]" pageId="39" pageNumber="40">Individual, sex and age-related variation within the taxon</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="39.[192,1394,201,1939]" pageId="39" pageNumber="40">A second specimen (MBZ.Ornit.34.387, an adult female) is very similar to the holotype, perhaps with a slightly darker crown, suggesting that this species may be sexually monomorphic.</paragraph>
|
||
<paragraph blockId="39.[192,1394,201,1939]" box="[192,468,800,828]" pageId="39" pageNumber="40">
|
||
<heading bold="true" box="[192,468,800,828]" fontSize="12" level="7" pageId="39" pageNumber="40" reason="2">
|
||
<emphasis bold="true" box="[192,468,800,828]" pageId="39" pageNumber="40">History of discovery</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="39.[192,1394,201,1939]" pageId="39" pageNumber="40">
|
||
A University of East Anglia expedition by Davidson et al. (
|
||
<bibRefCitation author="P. J. Davidson & T. Stones & R. S. Lucking" box="[954,986,874,902]" journalOrPublisher="Bird Conserv. Int." pageId="39" pageNumber="40" pagination="1 - 20" part="5" refId="ref30221" refString="64. P. J. Davidson, T. Stones, R. S. Lucking, The conservation status of key bird species on Taliabu and the Sula Islands, Indonesia. Bird Conserv. Int. 5, 1 - 20 (1995). doi: 10.1017 / S 0959270900002926" title="The conservation status of key bird species on Taliabu and the Sula Islands, Indonesia" type="journal article" year="1995">
|
||
<emphasis box="[954,986,874,902]" italics="true" pageId="39" pageNumber="40">64</emphasis>
|
||
</bibRefCitation>
|
||
) was the first to find a resident population of
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[372,543,948,976]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="39" pageNumber="40" phylum="Chordata" rank="genus">
|
||
<emphasis box="[372,543,948,976]" italics="true" pageId="39" pageNumber="40">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
leaf-warblers on Taliabu, which they encountered commonly in montane forest and which they considered to represent an undescribed taxon. Rheindt (
|
||
<bibRefCitation author="F. E. Rheindt" box="[1307,1339,1021,1049]" journalOrPublisher="Bull. Br. Ornithol. Club" pageId="39" pageNumber="40" pagination="33 - 51" part="130" refId="ref29294" refString="48. F. E. Rheindt, New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa. Bull. Br. Ornithol. Club 130, 33 - 51 (2010)." title="New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa" type="journal article" year="2010">
|
||
<emphasis box="[1307,1339,1021,1049]" italics="true" pageId="39" pageNumber="40">48</emphasis>
|
||
</bibRefCitation>
|
||
) then studied this leaf warbler during his visit between 4-18 April 2009, and we found them again during our expedition between 6-16 Dec 2 013 and collected two (
|
||
<bibRefCitation author="F. E. Rheindt & D. M. Prawiradilaga & S. Suparno & H. Ashari & P. R. Wilton" box="[1112,1144,1169,1197]" journalOrPublisher="Treubia" pageId="39" pageNumber="40" pagination="61 - 90" part="41" refId="ref27737" refString="19. F. E. Rheindt, D. M. Prawiradilaga, S. Suparno, H. Ashari, P. R. Wilton, New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate. Treubia 41, 61 - 90 (2014)." title="New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate" type="journal article" year="2014">
|
||
<emphasis box="[1112,1144,1169,1197]" italics="true" pageId="39" pageNumber="40">19</emphasis>
|
||
</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="40" lastPageNumber="41" pageId="39" pageNumber="40" type="distribution">
|
||
<paragraph blockId="39.[192,1394,201,1939]" box="[192,507,1321,1349]" pageId="39" pageNumber="40">
|
||
<heading bold="true" box="[192,507,1321,1349]" fontSize="12" level="7" pageId="39" pageNumber="40" reason="2">
|
||
<emphasis bold="true" box="[192,507,1321,1349]" pageId="39" pageNumber="40">Distribution and status</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="39.[192,1394,201,1939]" lastBlockId="40.[192,1390,201,2002]" lastPageId="40" lastPageNumber="41" pageId="39" pageNumber="40">
|
||
The new warbler inhabits disturbed and undisturbed montane forest on Taliabu from 700m up to probably the highest elevations above 1,400m (
|
||
<emphasis box="[832,960,1468,1496]" italics="true" pageId="39" pageNumber="40">
|
||
<bibRefCitation author="F. E. Rheindt & D. M. Prawiradilaga & S. Suparno & H. Ashari & P. R. Wilton" box="[832,867,1468,1496]" journalOrPublisher="Treubia" pageId="39" pageNumber="40" pagination="61 - 90" part="41" refId="ref27737" refString="19. F. E. Rheindt, D. M. Prawiradilaga, S. Suparno, H. Ashari, P. R. Wilton, New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate. Treubia 41, 61 - 90 (2014)." title="New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate" type="journal article" year="2014">19</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="F. E. Rheindt" box="[880,915,1468,1496]" journalOrPublisher="Bull. Br. Ornithol. Club" pageId="39" pageNumber="40" pagination="33 - 51" part="130" refId="ref29294" refString="48. F. E. Rheindt, New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa. Bull. Br. Ornithol. Club 130, 33 - 51 (2010)." title="New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa" type="journal article" year="2010">48</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="P. J. Davidson & T. Stones & R. S. Lucking" box="[928,960,1468,1496]" journalOrPublisher="Bird Conserv. Int." pageId="39" pageNumber="40" pagination="1 - 20" part="5" refId="ref30221" refString="64. P. J. Davidson, T. Stones, R. S. Lucking, The conservation status of key bird species on Taliabu and the Sula Islands, Indonesia. Bird Conserv. Int. 5, 1 - 20 (1995). doi: 10.1017 / S 0959270900002926" title="The conservation status of key bird species on Taliabu and the Sula Islands, Indonesia" type="journal article" year="1995">64</bibRefCitation>
|
||
</emphasis>
|
||
). It may also occur on the large neighboring island of Mangole, which rises to 1,127m and should harbor enough area of montane forest habitat above 700m to sustain a population. However, a lack of fieldwork in the mountains of Mangole means that there is no information available on its montane avifauna. The smallest main constituent of the Sula Archipelago, the densely populated island of Sanana, is unlikely to sustain any
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[661,832,1836,1864]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="39" pageNumber="40" phylum="Chordata" rank="genus">
|
||
<emphasis box="[661,832,1836,1864]" italics="true" pageId="39" pageNumber="40">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
leaf-warblers as it barely reaches above 600m, which seems to be too low for this species. The species is replaced on the Banggai Archipelago by the newly described
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[662,853,201,231]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[662,853,201,231]" italics="true" pageId="40" pageNumber="41">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
(see SM5), while
|
||
<taxonomicName baseAuthorityName="A. B. Meyer & Wiglesworth" baseAuthorityYear="1896" box="[1088,1285,203,231]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="sarasinorum">
|
||
<emphasis box="[1088,1285,203,231]" italics="true" pageId="40" pageNumber="41">P. sarasinorum</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[1347,1375,203,231]" italics="true" pageId="40" pageNumber="41">P.</emphasis>
|
||
<emphasis box="[192,329,274,302]" italics="true" pageId="40" pageNumber="41">nesophilus</emphasis>
|
||
</taxonomicName>
|
||
replace it in various parts of Sulawesi. Given its more relaxed elevational requirements and its tolerance for disturbed habitat, this species is probably not as immediately endangered as some of the other montane Taliabu avifauna.
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection lastPageId="46" lastPageNumber="47" pageId="40" pageNumber="41" type="discussion">
|
||
<paragraph blockId="40.[192,1390,201,2002]" box="[192,1131,574,603]" pageId="40" pageNumber="41">
|
||
<heading bold="true" box="[192,1131,574,603]" fontSize="12" level="7" pageId="40" pageNumber="41" reason="2">
|
||
<emphasis bold="true" box="[192,1131,574,603]" pageId="40" pageNumber="41">
|
||
Taxonomic rationale (combined for
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[684,880,574,603]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis bold="true" box="[684,880,574,603]" italics="true" pageId="40" pageNumber="41">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[948,1120,574,603]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis bold="true" box="[948,1120,574,603]" italics="true" pageId="40" pageNumber="41">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
)
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="40.[192,1390,201,2002]" pageId="40" pageNumber="41">
|
||
The leaf-warbler genus
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[497,668,648,676]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[497,668,648,676]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
constitutes a large Old World radiation of small passerines that is exceptionally well-studied in phylogenetic terms (
|
||
<emphasis box="[1059,1166,721,751]" italics="true" pageId="40" pageNumber="41">10 6-1 09</emphasis>
|
||
). Recent demonstrations of genus paraphyly in combination with
|
||
<taxonomicName authorityName="Swainson" authorityYear="1837" box="[915,1038,796,824]" class="Aves" family="Phylloscopidae" genus="Seicercus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[915,1038,796,824]" italics="true" pageId="40" pageNumber="41">Seicercus</emphasis>
|
||
</taxonomicName>
|
||
[summarized in (
|
||
<emphasis box="[1264,1312,795,823]" italics="true" pageId="40" pageNumber="41">10 8</emphasis>
|
||
)] have prompted a variety of new generic treatments, including a division into two re-defined genera [
|
||
<taxonomicName authorityName="Swainson" authorityYear="1837" box="[296,419,943,971]" class="Aves" family="Phylloscopidae" genus="Seicercus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[296,419,943,971]" italics="true" pageId="40" pageNumber="41">Seicercus</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[481,652,942,970]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[481,652,942,970]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
; see (
|
||
<bibRefCitation author="J. A. Eaton & S. van Balen & N. W. Brickle & F. E. Rheindt" box="[728,760,943,971]" journalOrPublisher="Lynx Edicions" pageId="40" pageNumber="41" refId="ref29850" refString="57. J. A. Eaton, S. van Balen, N. W. Brickle, F. E. Rheindt, Birds of the Indonesian Archipelago: Greater Sundas and Wallacea. (Lynx Edicions, 2016)." title="Birds of the Indonesian Archipelago: Greater Sundas and Wallacea" type="book" year="2016">
|
||
<emphasis box="[728,760,943,971]" italics="true" pageId="40" pageNumber="41">57</emphasis>
|
||
</bibRefCitation>
|
||
)], but we here follow the latest phylogenetic treatise that suggests a merger of all
|
||
<taxonomicName authorityName="Swainson" authorityYear="1837" box="[660,783,1017,1045]" class="Aves" family="Phylloscopidae" genus="Seicercus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[660,783,1017,1045]" italics="true" pageId="40" pageNumber="41">Seicercus</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[845,1016,1016,1044]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[845,1016,1016,1044]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
into a single genus
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[192,363,1089,1117]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[192,363,1089,1117]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<emphasis box="[381,429,1089,1117]" italics="true" pageId="40" pageNumber="41">10 8</emphasis>
|
||
).
|
||
</paragraph>
|
||
<paragraph blockId="40.[192,1390,201,2002]" lastBlockId="41.[192,1392,201,1922]" lastPageId="41" lastPageNumber="42" pageId="40" pageNumber="41">
|
||
Despite the genus’s well-known evolutionary history, a sizeable sub-clade of
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[192,363,1236,1264]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[192,363,1236,1264]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
from the Australasian (including Indonesian) Archipelago has largely been omitted from modern molecular insights. Notable exceptions include the first-ever example of a new avian species description (
|
||
<taxonomicName authorityName="Ng, N.g.Prawiradilaga, Suparno, Ashari, Trainor, Verbelen & Rheindt" authorityYear="2018" box="[649,794,1385,1413]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="rotiensis">
|
||
<emphasis box="[649,794,1385,1413]" italics="true" pageId="40" pageNumber="41">P. rotiensis</emphasis>
|
||
</taxonomicName>
|
||
) partly based on genome-wide DNA data from the Timor region (
|
||
<emphasis box="[498,546,1457,1485]" italics="true" pageId="40" pageNumber="41">11 0</emphasis>
|
||
). However, most island populations of
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[1052,1223,1457,1485]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[1052,1223,1457,1485]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
in this region have been merged into a limited number of ‘wastebasket species’, e.g. Mountain Leaf Warbler
|
||
<taxonomicName authorityName="Strickland" authorityYear="1849" box="[305,475,1606,1634]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="trivirgatus">
|
||
<emphasis box="[305,475,1606,1634]" italics="true" pageId="40" pageNumber="41">P. trivirgatus</emphasis>
|
||
</taxonomicName>
|
||
and Island Leaf Warbler
|
||
<taxonomicName baseAuthorityName="Salvadori" baseAuthorityYear="1876" box="[803,1019,1604,1634]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="species" species="poliocephalus">
|
||
<emphasis box="[803,1019,1604,1634]" italics="true" pageId="40" pageNumber="41">P. poliocephalus</emphasis>
|
||
</taxonomicName>
|
||
, although vocal and plumage differences among them often far exceed those documented among the better- studied continental groups of
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[572,743,1752,1780]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="40" pageNumber="41" phylum="Chordata" rank="genus">
|
||
<emphasis box="[572,743,1752,1780]" italics="true" pageId="40" pageNumber="41">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<emphasis box="[762,794,1752,1780]" italics="true" pageId="40" pageNumber="41">8 0</emphasis>
|
||
). As a consequence, some modern treatments [e.g. (
|
||
<bibRefCitation author="J. A. Eaton & S. van Balen & N. W. Brickle & F. E. Rheindt" box="[268,300,1827,1855]" journalOrPublisher="Lynx Edicions" pageId="40" pageNumber="41" refId="ref29850" refString="57. J. A. Eaton, S. van Balen, N. W. Brickle, F. E. Rheindt, Birds of the Indonesian Archipelago: Greater Sundas and Wallacea. (Lynx Edicions, 2016)." title="Birds of the Indonesian Archipelago: Greater Sundas and Wallacea" type="book" year="2016">
|
||
<emphasis box="[268,300,1827,1855]" italics="true" pageId="40" pageNumber="41">57</emphasis>
|
||
</bibRefCitation>
|
||
)] have adopted a ‘yardstick approach’ (
|
||
<bibRefCitation author="E. Mayr & P. Ashlock" box="[811,843,1825,1853]" journalOrPublisher="McGraw-Hill, ed" pageId="40" pageNumber="41" refId="ref30411" refString="70. E. Mayr, P. Ashlock, Principles of Systematic Zoology. (McGraw-Hill, ed. 2, 1991)." title="Principles of Systematic Zoology" type="book" year="1991">
|
||
<emphasis box="[811,843,1825,1853]" italics="true" pageId="40" pageNumber="41">70</emphasis>
|
||
</bibRefCitation>
|
||
) in which pairwise plumage and vocal differences between archipelagic taxa that are comparable in magnitude to those between better-studied continental species pairs (or exceed them) are interpreted as being indicative of species status. In this way, a number of highly distinct island taxa have been elevated to species level, such as Buru Leaf Warbler
|
||
<taxonomicName authority=", Seram Leaf Warbler" authorityName="Seram Leaf Warbler" box="[723,1132,274,304]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="everetti">
|
||
<emphasis box="[723,855,276,304]" italics="true" pageId="41" pageNumber="42">P. everetti</emphasis>
|
||
, Seram Leaf Warbler
|
||
</taxonomicName>
|
||
<taxonomicName box="[1140,1320,276,304]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="ceramensis">
|
||
<emphasis box="[1140,1320,276,304]" italics="true" pageId="41" pageNumber="42">P. ceramensis</emphasis>
|
||
</taxonomicName>
|
||
[a treatment that had previously been suggested on the basis of vocal and plumage comparisons; see (
|
||
<bibRefCitation author="F. E. Rheindt & R. O. Hutchinson" box="[252,284,422,450]" journalOrPublisher="BirdingASIA" pageId="41" pageNumber="42" pagination="18 - 38" part="7" refId="ref30942" refString="80. F. E. Rheindt, R. O. Hutchinson, A photoshot odyssey through the confused avian taxonomy of Seram and Buru (southern Moluccas). BirdingASIA 7, 18 - 38 (2007)." title="A photoshot odyssey through the confused avian taxonomy of Seram and Buru (southern Moluccas)" type="journal article" year="2007">
|
||
<emphasis box="[252,284,422,450]" italics="true" pageId="41" pageNumber="42">80</emphasis>
|
||
</bibRefCitation>
|
||
)], and a number of additional Wallacean taxa. Our description of
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[1129,1319,422,451]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[1129,1319,422,451]" italics="true" pageId="41" pageNumber="42">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[192,361,495,525]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[192,361,495,525]" italics="true" pageId="41" pageNumber="42">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
follows this framework of affording species rank to taxa when vocal and plumage characters indicate deeper divisions. We also bring genome-wide DNA data to bear on the taxonomic classification of these two new species. However, following the yardstick approach as applied under the Biological Species Concept, we believe that biological characters, especially bioacoustic ones, will be the most important indicators when conferring species status in
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[406,577,863,891]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="genus">
|
||
<emphasis box="[406,577,863,891]" italics="true" pageId="41" pageNumber="42">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
leaf-warblers.
|
||
</paragraph>
|
||
<paragraph blockId="41.[192,1392,201,1922]" pageId="41" pageNumber="42">
|
||
<emphasis bold="true" box="[288,532,937,965]" pageId="41" pageNumber="42">Plumage evidence</emphasis>
|
||
: As for plumage characters,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[902,1093,937,967]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[902,1093,937,967]" italics="true" pageId="41" pageNumber="42">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[1154,1323,937,967]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[1154,1323,937,967]" italics="true" pageId="41" pageNumber="42">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
differ from each other and from surrounding taxa in a number of important traits (see Diagnosis for each taxon) which are far more salient than the plumage differences of often identical-looking species pairs on the Asian continent that are otherwise vocally and phylogenetically deeply diverged [e.g. the three members of the Arctic Warbler
|
||
<taxonomicName baseAuthorityName="J. H. Blasius" baseAuthorityYear="1858" box="[1218,1359,1231,1261]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="borealis">
|
||
<emphasis box="[1218,1359,1231,1261]" italics="true" pageId="41" pageNumber="42">P. borealis</emphasis>
|
||
</taxonomicName>
|
||
trio; (
|
||
<emphasis box="[264,312,1305,1333]" italics="true" pageId="41" pageNumber="42">11 1</emphasis>
|
||
)]. Most importantly,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[588,779,1305,1335]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[588,779,1305,1335]" italics="true" pageId="41" pageNumber="42">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
has a contrastingly white throat and supercilium and a grey-and-white grizzled auricular patch where all other surrounding taxa are much more yellowish, rendering it instantly recognizable in large series of specimens. In contrast,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[309,478,1526,1555]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[309,478,1526,1555]" italics="true" pageId="41" pageNumber="42">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
is superficially reminiscent of Sulawesi Leaf Warbler
|
||
<taxonomicName box="[1178,1351,1526,1555]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="41" pageNumber="42" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[1178,1351,1526,1555]" italics="true" pageId="41" pageNumber="42">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
in its overall more yellowish coloration, displaying a phenotypic leapfrog pattern that has been documented from the Taliabu-Peleng-Sulawesi island trio on multiple previous occasions (
|
||
<emphasis box="[203,283,1746,1776]" italics="true" pageId="41" pageNumber="42">50, 7 2</emphasis>
|
||
). However, this superficial resemblance notwithstanding, it has important distinctions in bare-parts coloration and overall pigmentation (see Diagnosis), apart from obvious vocal differences.
|
||
</paragraph>
|
||
<paragraph blockId="42.[192,1391,201,1997]" pageId="42" pageNumber="43">
|
||
<emphasis bold="true" box="[288,569,201,229]" pageId="42" pageNumber="43">Bioacoustic evidence</emphasis>
|
||
: In bioacoustic terms, the song of
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[1012,1203,201,231]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[1012,1203,201,231]" italics="true" pageId="42" pageNumber="43">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
is characterized by melodious jumbles of 1–1.5sec, mostly at 2000–6000 Hz, with short individual high notes between 5000–7000 Hz occasionally interspersed. Song motifs generally lack repetitive element sequences or trills (
|
||
<figureCitation box="[867,957,422,450]" captionStart="Fig" captionStartId="81.[192,239,947,975]" captionTargetBox="[233,1297,232,852]" captionTargetId="figure@81.[192,1344,192,900]" captionTargetPageId="81" captionText="Fig. S9. Sample spectrograms of the Taliabu Phylloscopus emilsalimi, Peleng P. suaramerdu, and Sulawesi P. nesophilus Leaf-Warblers. P. suaramerdu is characterized by a song with melodious jumbles of elements, lasting around 1.5 sec at between 2-6 kHz, that lack any repetitive element sequences or trills, but with short individual high notes between 5-7 kHz occasionally interspersed. While similar in general structure, the song of P. emilsalimi usually features multiple repetitive elements at the end. The song of P. nesophilus is typically longer, consisting of simple introductory elements followed by a short nasal note at ~2 kHz, and ending with a series of repetitive elements. Xeno-Canto Sound Library (www.xeno-canto.org) accession numbers for the three recordings are: XC497894, XC497899 and XC497903 from top to bottom." figureDoi="http://doi.org/10.5281/zenodo.3608776" httpUri="https://zenodo.org/record/3608776/files/figure.png" pageId="42" pageNumber="43">fig. S9</figureCitation>
|
||
). In contrast, the song of
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[1282,1310,423,451]" italics="true" pageId="42" pageNumber="43">P.</emphasis>
|
||
<emphasis box="[192,325,495,523]" italics="true" pageId="42" pageNumber="43">emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
is characterized by 1.5–3sec strophes mostly between 2000–6500 Hz (typically of a wider frequency range than
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[573,764,569,599]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[573,764,569,599]" italics="true" pageId="42" pageNumber="43">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
) that constitute a melodious jumble often followed by a final repetitive phrase, which can sometimes be omitted (
|
||
<figureCitation box="[1108,1198,642,670]" captionStart="Fig" captionStartId="81.[192,239,947,975]" captionTargetBox="[233,1297,232,852]" captionTargetId="figure@81.[192,1344,192,900]" captionTargetPageId="81" captionText="Fig. S9. Sample spectrograms of the Taliabu Phylloscopus emilsalimi, Peleng P. suaramerdu, and Sulawesi P. nesophilus Leaf-Warblers. P. suaramerdu is characterized by a song with melodious jumbles of elements, lasting around 1.5 sec at between 2-6 kHz, that lack any repetitive element sequences or trills, but with short individual high notes between 5-7 kHz occasionally interspersed. While similar in general structure, the song of P. emilsalimi usually features multiple repetitive elements at the end. The song of P. nesophilus is typically longer, consisting of simple introductory elements followed by a short nasal note at ~2 kHz, and ending with a series of repetitive elements. Xeno-Canto Sound Library (www.xeno-canto.org) accession numbers for the three recordings are: XC497894, XC497899 and XC497903 from top to bottom." figureDoi="http://doi.org/10.5281/zenodo.3608776" httpUri="https://zenodo.org/record/3608776/files/figure.png" pageId="42" pageNumber="43">fig. S9</figureCitation>
|
||
). In this respect,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[299,467,716,746]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[299,467,716,746]" italics="true" pageId="42" pageNumber="43">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
is slightly more reminiscent of the East Sulawesi population of
|
||
<taxonomicName class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[1288,1315,718,746]" italics="true" pageId="42" pageNumber="43">P.</emphasis>
|
||
<emphasis box="[192,329,790,818]" italics="true" pageId="42" pageNumber="43">nesophilus</emphasis>
|
||
</taxonomicName>
|
||
than
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[400,591,790,819]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[400,591,790,819]" italics="true" pageId="42" pageNumber="43">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
from Peleng (despite the geographic proximity of the latter two). The
|
||
<taxonomicName box="[324,497,863,893]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[324,497,863,893]" italics="true" pageId="42" pageNumber="43">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
population on Gunung Tumpu (East Sulawesi) is often characterized by strong repetitive series at a very broad frequency range (2500–7000 Hz), mostly preceded by a variable but simple melodious series of elements between 2000–5000 Hz and a brief nasal note separating this variable series from the repetitive series (
|
||
<figureCitation box="[1051,1141,1084,1112]" captionStart="Fig" captionStartId="81.[192,239,947,975]" captionTargetBox="[233,1297,232,852]" captionTargetId="figure@81.[192,1344,192,900]" captionTargetPageId="81" captionText="Fig. S9. Sample spectrograms of the Taliabu Phylloscopus emilsalimi, Peleng P. suaramerdu, and Sulawesi P. nesophilus Leaf-Warblers. P. suaramerdu is characterized by a song with melodious jumbles of elements, lasting around 1.5 sec at between 2-6 kHz, that lack any repetitive element sequences or trills, but with short individual high notes between 5-7 kHz occasionally interspersed. While similar in general structure, the song of P. emilsalimi usually features multiple repetitive elements at the end. The song of P. nesophilus is typically longer, consisting of simple introductory elements followed by a short nasal note at ~2 kHz, and ending with a series of repetitive elements. Xeno-Canto Sound Library (www.xeno-canto.org) accession numbers for the three recordings are: XC497894, XC497899 and XC497903 from top to bottom." figureDoi="http://doi.org/10.5281/zenodo.3608776" httpUri="https://zenodo.org/record/3608776/files/figure.png" pageId="42" pageNumber="43">fig. S9</figureCitation>
|
||
). Depending on the presence or absence of components, the song rendition (=motif) can be 1.5–4sec long. In summary, the songs of these three forms (
|
||
<emphasis box="[729,1104,1231,1261]" italics="true" pageId="42" pageNumber="43">
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[729,922,1231,1261]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="suaramerdu">P. suaramerdu</taxonomicName>
|
||
,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[935,1104,1231,1261]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="emilsalimi">P. emilsalimi</taxonomicName>
|
||
</emphasis>
|
||
and
|
||
<taxonomicName box="[1166,1339,1231,1261]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[1166,1339,1231,1261]" italics="true" pageId="42" pageNumber="43">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
), while highly variable, are predictably different and strongly indicative of species status when put into the context of song differences among other
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[870,1041,1378,1406]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="genus">
|
||
<emphasis box="[870,1041,1378,1406]" italics="true" pageId="42" pageNumber="43">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
species (
|
||
<emphasis box="[1160,1208,1378,1408]" italics="true" pageId="42" pageNumber="43">10 7</emphasis>
|
||
).
|
||
</paragraph>
|
||
<paragraph blockId="42.[192,1391,201,1997]" pageId="42" pageNumber="43">
|
||
<emphasis bold="true" box="[288,536,1452,1480]" pageId="42" pageNumber="43">Genomic evidence</emphasis>
|
||
: We generated a set of ~4,100 SNPs and a genome-wide sequence alignment spanning almost 3 million base pairs (bp), along with an alignment of mitochondrial cytochrome-
|
||
<emphasis box="[541,557,1599,1627]" italics="true" pageId="42" pageNumber="43">b</emphasis>
|
||
(cyt-
|
||
<emphasis box="[626,642,1599,1627]" italics="true" pageId="42" pageNumber="43">b</emphasis>
|
||
) sequences, to shed light on the differentiation of
|
||
<taxonomicName authorityName="F.Boie" authorityYear="1826" box="[192,363,1673,1701]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="genus">
|
||
<emphasis box="[192,363,1673,1701]" italics="true" pageId="42" pageNumber="43">Phylloscopus</emphasis>
|
||
</taxonomicName>
|
||
leaf-warblers from Sulawesi, Peleng and Taliabu. Details on laboratory and analytical methods are given in separate Methods paragraphs below.
|
||
</paragraph>
|
||
<paragraph blockId="42.[192,1391,201,1997]" lastBlockId="43.[192,1393,201,1997]" lastPageId="43" lastPageNumber="44" pageId="42" pageNumber="43">
|
||
Each of the three taxa (
|
||
<taxonomicName box="[586,758,1820,1850]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[586,758,1820,1850]" italics="true" pageId="42" pageNumber="43">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
from East Sulawesi,
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[1031,1221,1820,1850]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[1031,1221,1820,1850]" italics="true" pageId="42" pageNumber="43">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
from Peleng and
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[246,415,1894,1923]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="42" pageNumber="43" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[246,415,1894,1923]" italics="true" pageId="42" pageNumber="43">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
from Taliabu) formed a spatially separate cluster in population-genomic space based on ~4100 genome-wide SNPs (
|
||
<figureCitation box="[752,858,1967,1995]" captionStart="Fig" captionStartId="82.[192,239,1053,1081]" captionTargetBox="[253,1338,249,947]" captionTargetId="figure@82.[192,1395,192,1008]" captionTargetPageId="82" captionText="Fig. S10. Map of Sulawesi, Peleng, and Taliabu; principal component analysis (PCA) plots of genome-wide marker sets for Phyllergates leaftoilers and Phylloscopus leaf- warblers. Grey areas represent modern-day land extent; black lines off the coasts depict - 120m isobaths, indicating land extent during Quaternary glacial maxima. The triangle, circle and square symbols indicate collection localities on each of the islands (Sulawesi = A, Peleng = B, and Taliabu = C). The two PCA plots on the inset are based on genome-wide sets of 8515 and 4104 SNPs for the leaftoilers and leaf-warblers, respectively. Drawings of the birds are modified from Eaton et al. (57). PC1 and 2 account for more than 50% of observed variation in both taxa, and each island population occupies its own cluster in genomic space." figureDoi="http://doi.org/10.5281/zenodo.3608778" httpUri="https://zenodo.org/record/3608778/files/figure.png" pageId="42" pageNumber="43">fig. S10</figureCitation>
|
||
). The main division according to genomic PCA occurred between
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[615,784,201,231]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[615,784,201,231]" italics="true" pageId="43" pageNumber="44">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
versus the other two taxa (PC1 in
|
||
<figureCitation box="[1226,1331,201,229]" captionStart="Fig" captionStartId="82.[192,239,1053,1081]" captionTargetBox="[253,1338,249,947]" captionTargetId="figure@82.[192,1395,192,1008]" captionTargetPageId="82" captionText="Fig. S10. Map of Sulawesi, Peleng, and Taliabu; principal component analysis (PCA) plots of genome-wide marker sets for Phyllergates leaftoilers and Phylloscopus leaf- warblers. Grey areas represent modern-day land extent; black lines off the coasts depict - 120m isobaths, indicating land extent during Quaternary glacial maxima. The triangle, circle and square symbols indicate collection localities on each of the islands (Sulawesi = A, Peleng = B, and Taliabu = C). The two PCA plots on the inset are based on genome-wide sets of 8515 and 4104 SNPs for the leaftoilers and leaf-warblers, respectively. Drawings of the birds are modified from Eaton et al. (57). PC1 and 2 account for more than 50% of observed variation in both taxa, and each island population occupies its own cluster in genomic space." figureDoi="http://doi.org/10.5281/zenodo.3608778" httpUri="https://zenodo.org/record/3608778/files/figure.png" pageId="43" pageNumber="44">fig. S10</figureCitation>
|
||
). The same relationship was strongly reflected in maximum-likelihood (ML) analysis of concatenated genome-wide sequence alignments of almost 3 million base pairs length as well as in maximum-parsimony (MP) analysis of a concatenated set of ~4100 genome-wide SNPs (topology 1 in
|
||
<figureCitation box="[381,486,495,523]" captionStart="Fig" captionStartId="83.[192,239,1206,1234]" captionTargetBox="[201,1390,201,1157]" captionTargetId="figure@83.[192,1395,192,1159]" captionTargetPageId="83" captionText="Fig. S11. Cladograms comparing different phylogenetic analyses for Phyllergates leaftoilers and Phylloscopus leaf-warblers. Topologies are depicted for trees resulting from the application of (1) mitochondrial tree inference (=mtDNA), (2) a coalescent species tree method based on genomic SNPs (=species tree), and (3) concatenation methods applied to genomic SNPs and sequence-based data (=concatenation). Outgroups used (not shown) were Cettia parens for the leaftoilers and Phylloscopus poliocephalus pallescens for the leaf warblers. Branch support values <75 not shown. In the mtDNA and species tree topologies, branch support values sequentially represent mitochondrial maximum likelihood (ML) bootstrap, mitochondrial maximum parsimony (MP) bootstrap, and coalescent species tree posterior probability (multiplied by 100). In the concatenation topologies, branch support values sequentially represent bootstrap from ML analysis on the concatenated read supermatrix and bootstrap from MP analysis on concatenated SNPs. Percentage values between clades denote mitochondrial raw pairwise p-divergences for the coding gene used." figureDoi="http://doi.org/10.5281/zenodo.3608780" httpUri="https://zenodo.org/record/3608780/files/figure.png" pageId="43" pageNumber="44">fig. S11</figureCitation>
|
||
). In contrast, mitochondrial cyt-
|
||
<emphasis box="[899,915,495,523]" italics="true" pageId="43" pageNumber="44">b</emphasis>
|
||
gene analysis and species-tree inference of genome-wide SNPs recovered a topology in which
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[1012,1181,569,599]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[1012,1181,569,599]" italics="true" pageId="43" pageNumber="44">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[1243,1271,571,599]" italics="true" pageId="43" pageNumber="44">P.</emphasis>
|
||
<emphasis box="[192,347,642,670]" italics="true" pageId="43" pageNumber="44">suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
were strongly supported sister lineages, with
|
||
<taxonomicName box="[933,1106,642,672]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[933,1106,642,672]" italics="true" pageId="43" pageNumber="44">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
being more basal (topology 2 in
|
||
<figureCitation box="[381,486,716,744]" captionStart="Fig" captionStartId="83.[192,239,1206,1234]" captionTargetBox="[201,1390,201,1157]" captionTargetId="figure@83.[192,1395,192,1159]" captionTargetPageId="83" captionText="Fig. S11. Cladograms comparing different phylogenetic analyses for Phyllergates leaftoilers and Phylloscopus leaf-warblers. Topologies are depicted for trees resulting from the application of (1) mitochondrial tree inference (=mtDNA), (2) a coalescent species tree method based on genomic SNPs (=species tree), and (3) concatenation methods applied to genomic SNPs and sequence-based data (=concatenation). Outgroups used (not shown) were Cettia parens for the leaftoilers and Phylloscopus poliocephalus pallescens for the leaf warblers. Branch support values <75 not shown. In the mtDNA and species tree topologies, branch support values sequentially represent mitochondrial maximum likelihood (ML) bootstrap, mitochondrial maximum parsimony (MP) bootstrap, and coalescent species tree posterior probability (multiplied by 100). In the concatenation topologies, branch support values sequentially represent bootstrap from ML analysis on the concatenated read supermatrix and bootstrap from MP analysis on concatenated SNPs. Percentage values between clades denote mitochondrial raw pairwise p-divergences for the coding gene used." figureDoi="http://doi.org/10.5281/zenodo.3608780" httpUri="https://zenodo.org/record/3608780/files/figure.png" pageId="43" pageNumber="44">fig. S11</figureCitation>
|
||
). Depths of uncorrected pairwise sequence divergence (as determined by cyt-
|
||
<emphasis box="[282,298,790,818]" italics="true" pageId="43" pageNumber="44">b</emphasis>
|
||
distances) were comparatively low across all three leaf-warblers (0.7-1.6%;
|
||
<figureCitation captionStart="Fig" captionStartId="83.[192,239,1206,1234]" captionTargetBox="[201,1390,201,1157]" captionTargetId="figure@83.[192,1395,192,1159]" captionTargetPageId="83" captionText="Fig. S11. Cladograms comparing different phylogenetic analyses for Phyllergates leaftoilers and Phylloscopus leaf-warblers. Topologies are depicted for trees resulting from the application of (1) mitochondrial tree inference (=mtDNA), (2) a coalescent species tree method based on genomic SNPs (=species tree), and (3) concatenation methods applied to genomic SNPs and sequence-based data (=concatenation). Outgroups used (not shown) were Cettia parens for the leaftoilers and Phylloscopus poliocephalus pallescens for the leaf warblers. Branch support values <75 not shown. In the mtDNA and species tree topologies, branch support values sequentially represent mitochondrial maximum likelihood (ML) bootstrap, mitochondrial maximum parsimony (MP) bootstrap, and coalescent species tree posterior probability (multiplied by 100). In the concatenation topologies, branch support values sequentially represent bootstrap from ML analysis on the concatenated read supermatrix and bootstrap from MP analysis on concatenated SNPs. Percentage values between clades denote mitochondrial raw pairwise p-divergences for the coding gene used." figureDoi="http://doi.org/10.5281/zenodo.3608780" httpUri="https://zenodo.org/record/3608780/files/figure.png" pageId="43" pageNumber="44">fig. S11</figureCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph blockId="43.[192,1393,201,1997]" lastBlockId="44.[192,1392,201,1928]" lastPageId="44" lastPageNumber="45" pageId="43" pageNumber="44">
|
||
In summary, our phylogenomic analyses demonstrated considerable incongruence among tree topologies, including a strong mito-nuclear discordance that calls into doubt the reliability of mitochondrial divergence values in this dataset. For instance, the deepest genomic divergence was detected between
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[746,914,1158,1187]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[746,914,1158,1187]" italics="true" pageId="43" pageNumber="44">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
and the other two species (PC1 in
|
||
<figureCitation box="[192,294,1231,1259]" captionStart="Fig" captionStartId="82.[192,239,1053,1081]" captionTargetBox="[253,1338,249,947]" captionTargetId="figure@82.[192,1395,192,1008]" captionTargetPageId="82" captionText="Fig. S10. Map of Sulawesi, Peleng, and Taliabu; principal component analysis (PCA) plots of genome-wide marker sets for Phyllergates leaftoilers and Phylloscopus leaf- warblers. Grey areas represent modern-day land extent; black lines off the coasts depict - 120m isobaths, indicating land extent during Quaternary glacial maxima. The triangle, circle and square symbols indicate collection localities on each of the islands (Sulawesi = A, Peleng = B, and Taliabu = C). The two PCA plots on the inset are based on genome-wide sets of 8515 and 4104 SNPs for the leaftoilers and leaf-warblers, respectively. Drawings of the birds are modified from Eaton et al. (57). PC1 and 2 account for more than 50% of observed variation in both taxa, and each island population occupies its own cluster in genomic space." figureDoi="http://doi.org/10.5281/zenodo.3608778" httpUri="https://zenodo.org/record/3608778/files/figure.png" pageId="43" pageNumber="44">fig. S10</figureCitation>
|
||
), whereas on mitochondrial cyt-
|
||
<emphasis box="[710,726,1231,1259]" italics="true" pageId="43" pageNumber="44">b</emphasis>
|
||
evidence
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[856,1024,1231,1261]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="43" pageNumber="44" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[856,1024,1231,1261]" italics="true" pageId="43" pageNumber="44">P. emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
displayed some of the most shallow divergences from the other taxa (
|
||
<figureCitation box="[722,828,1305,1333]" captionStart="Fig" captionStartId="83.[192,239,1206,1234]" captionTargetBox="[201,1390,201,1157]" captionTargetId="figure@83.[192,1395,192,1159]" captionTargetPageId="83" captionText="Fig. S11. Cladograms comparing different phylogenetic analyses for Phyllergates leaftoilers and Phylloscopus leaf-warblers. Topologies are depicted for trees resulting from the application of (1) mitochondrial tree inference (=mtDNA), (2) a coalescent species tree method based on genomic SNPs (=species tree), and (3) concatenation methods applied to genomic SNPs and sequence-based data (=concatenation). Outgroups used (not shown) were Cettia parens for the leaftoilers and Phylloscopus poliocephalus pallescens for the leaf warblers. Branch support values <75 not shown. In the mtDNA and species tree topologies, branch support values sequentially represent mitochondrial maximum likelihood (ML) bootstrap, mitochondrial maximum parsimony (MP) bootstrap, and coalescent species tree posterior probability (multiplied by 100). In the concatenation topologies, branch support values sequentially represent bootstrap from ML analysis on the concatenated read supermatrix and bootstrap from MP analysis on concatenated SNPs. Percentage values between clades denote mitochondrial raw pairwise p-divergences for the coding gene used." figureDoi="http://doi.org/10.5281/zenodo.3608780" httpUri="https://zenodo.org/record/3608780/files/figure.png" pageId="43" pageNumber="44">fig. S11</figureCitation>
|
||
). The use of mitochondrial divergences in species delimitation suffers from multiple confounding biases (
|
||
<emphasis box="[1002,1162,1378,1408]" italics="true" pageId="43" pageNumber="44">79, 10 0, 10 1</emphasis>
|
||
), especially when dealing with complexes containing closely-allied allopatric taxa that have a propensity for secondary gene flow (
|
||
<emphasis box="[475,582,1526,1555]" italics="true" pageId="43" pageNumber="44">11 2-11 4</emphasis>
|
||
). The best explanatory hypothesis for the pronounced mito- nuclear discordance in this dataset is that occasional overwater dispersal followed by hybridization and gene flow may have led to the introgression of foreign alleles in one or the other species, obfuscating clean branching patterns. Gene flow during sporadic hybridization is known to artifactually reduce mitochondrial divergences, masking deeper levels of genomic differentiation (
|
||
<bibRefCitation author="F. E. Rheindt & S. V. Edwards" box="[512,544,1894,1922]" journalOrPublisher="Auk" pageId="43" pageNumber="44" pagination="620 - 632" part="128" refId="ref30898" refString="79. F. E. Rheindt, S. V. Edwards, Genetic introgression: An integral but neglected component of speciation in birds. Auk 128, 620 - 632 (2011). doi: 10.1525 / auk. 2011.128.4.620" title="Genetic introgression: An integral but neglected component of speciation in birds" type="journal article" year="2011">
|
||
<emphasis box="[512,544,1894,1922]" italics="true" pageId="43" pageNumber="44">79</emphasis>
|
||
</bibRefCitation>
|
||
). Hence, introgression can account for the presence of relatively low mitochondrial divergences in a group of species characterized by comparatively deep genomic divergences and pronounced levels of bioacoustic differentiation [(
|
||
<emphasis box="[1168,1248,201,231]" italics="true" pageId="44" pageNumber="45">
|
||
<bibRefCitation author="F. E. Rheindt" box="[1168,1200,201,229]" journalOrPublisher="Bull. Br. Ornithol. Club" pageId="44" pageNumber="45" pagination="33 - 51" part="130" refId="ref29294" refString="48. F. E. Rheindt, New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa. Bull. Br. Ornithol. Club 130, 33 - 51 (2010)." title="New biogeographic records for the avifauna of Taliabu (Sula Islands, Indonesia), with the preliminary documentation of two previously undiscovered taxa" type="journal article" year="2010">48</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="F. E. Rheindt & F. Verbelen & D. D. Putra & A. Rahman & M. Indrawan" box="[1216,1248,201,229]" journalOrPublisher="Bull. Br. Ornithol. Club" pageId="44" pageNumber="45" pagination="181 - 207" part="130" refId="ref29343" refString="49. F. E. Rheindt, F. Verbelen, D. D. Putra, A. Rahman, M. Indrawan, New biogeographic records in the avifauna of Peleng Island (Sulawesi, Indonesia), with taxonomic notes on some endemic taxa. Bull. Br. Ornithol. Club 130, 181 - 207 (2010)." title="New biogeographic records in the avifauna of Peleng Island (Sulawesi, Indonesia), with taxonomic notes on some endemic taxa" type="journal article" year="2010">49</bibRefCitation>
|
||
</emphasis>
|
||
), see data above and
|
||
<figureCitation box="[331,421,274,302]" captionStart="Fig" captionStartId="81.[192,239,947,975]" captionTargetBox="[233,1297,232,852]" captionTargetId="figure@81.[192,1344,192,900]" captionTargetPageId="81" captionText="Fig. S9. Sample spectrograms of the Taliabu Phylloscopus emilsalimi, Peleng P. suaramerdu, and Sulawesi P. nesophilus Leaf-Warblers. P. suaramerdu is characterized by a song with melodious jumbles of elements, lasting around 1.5 sec at between 2-6 kHz, that lack any repetitive element sequences or trills, but with short individual high notes between 5-7 kHz occasionally interspersed. While similar in general structure, the song of P. emilsalimi usually features multiple repetitive elements at the end. The song of P. nesophilus is typically longer, consisting of simple introductory elements followed by a short nasal note at ~2 kHz, and ending with a series of repetitive elements. Xeno-Canto Sound Library (www.xeno-canto.org) accession numbers for the three recordings are: XC497894, XC497899 and XC497903 from top to bottom." figureDoi="http://doi.org/10.5281/zenodo.3608776" httpUri="https://zenodo.org/record/3608776/files/figure.png" pageId="44" pageNumber="45">fig. S9</figureCitation>
|
||
].
|
||
</paragraph>
|
||
<paragraph blockId="44.[192,1392,201,1928]" box="[192,372,427,455]" pageId="44" pageNumber="45">
|
||
<heading bold="true" box="[192,372,427,455]" fontSize="12" level="7" pageId="44" pageNumber="45" reason="2">
|
||
<emphasis bold="true" box="[192,372,427,455]" pageId="44" pageNumber="45">Methodology</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph blockId="44.[192,1392,201,1928]" pageId="44" pageNumber="45">
|
||
<emphasis bold="true" box="[192,522,500,528]" pageId="44" pageNumber="45">Laboratory procedures:</emphasis>
|
||
We extracted DNA from the fresh muscle tissue of the holotype of
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" box="[192,383,574,604]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="44" pageNumber="45" phylum="Chordata" rank="species" species="suaramerdu">
|
||
<emphasis box="[192,383,574,604]" italics="true" pageId="44" pageNumber="45">P. suaramerdu</emphasis>
|
||
</taxonomicName>
|
||
and the three specimens collected by us (including the holotype) of
|
||
<taxonomicName authorityName="Rheindt & Prawiradilaga & Ashar & Lee & Wu & Ng" authorityYear="2020" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="44" pageNumber="45" phylum="Chordata" rank="species" species="emilsalimi">
|
||
<emphasis box="[1257,1284,576,604]" italics="true" pageId="44" pageNumber="45">P.</emphasis>
|
||
<emphasis box="[192,325,648,676]" italics="true" pageId="44" pageNumber="45">emilsalimi</emphasis>
|
||
</taxonomicName>
|
||
, along with one individual of
|
||
<taxonomicName box="[712,884,648,677]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="44" pageNumber="45" phylum="Chordata" rank="species" species="nesophilus">
|
||
<emphasis box="[712,884,648,677]" italics="true" pageId="44" pageNumber="45">P. nesophilus</emphasis>
|
||
</taxonomicName>
|
||
that we had collected on Mt Tumpu on the eastern peninsula of Sulawesi (
|
||
<bibRefCitation author="F. E. Rheindt & D. M. Prawiradilaga & S. Suparno & H. Ashari & P. R. Wilton" box="[637,669,721,749]" journalOrPublisher="Treubia" pageId="44" pageNumber="45" pagination="61 - 90" part="41" refId="ref27737" refString="19. F. E. Rheindt, D. M. Prawiradilaga, S. Suparno, H. Ashari, P. R. Wilton, New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate. Treubia 41, 61 - 90 (2014)." title="New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate" type="journal article" year="2014">
|
||
<emphasis box="[637,669,721,749]" italics="true" pageId="44" pageNumber="45">19</emphasis>
|
||
</bibRefCitation>
|
||
). Additional tissue samples were obtained from the American Museum of Natural History, New York (AMNH): three samples of
|
||
<taxonomicName baseAuthorityName="A. B. Meyer & Wiglesworth" baseAuthorityYear="1896" box="[1193,1390,797,825]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="44" pageNumber="45" phylum="Chordata" rank="species" species="sarasinorum">
|
||
<emphasis box="[1193,1390,797,825]" italics="true" pageId="44" pageNumber="45">P. sarasinorum</emphasis>
|
||
</taxonomicName>
|
||
from South Sulawesi and an outgroup sample of
|
||
<taxonomicName box="[818,1174,868,898]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="44" pageNumber="45" phylum="Chordata" rank="subSpecies" species="poliocephalus" subSpecies="pallescens">
|
||
<emphasis box="[818,1174,868,898]" italics="true" pageId="44" pageNumber="45">P. poliocephalus pallescens</emphasis>
|
||
</taxonomicName>
|
||
from the Solomon Islands. The AMNH samples were only used for phylogenomic rooting. DNA extraction was performed using the Exgene Clinic SV kit (GeneAll Biotechnology, Seoul) following the manufacturer’s instructions. We eluted the DNA in two consecutive rounds of 100μl molecular grade water. We prepared double-digest restriction enzyme associated DNA sequencing (ddRADSeq) libraries using the same protocol as Garg et al. (
|
||
<emphasis box="[1134,1182,1236,1266]" italics="true" pageId="44" pageNumber="45">11 5</emphasis>
|
||
) with EcoRI and MspI as restriction enzymes. We quantified DNA and library product concentrations using the Qubit 2.0 Broad Range DNA Assay (Invitrogen, California), and used a Fragment Analyzer (Advanced Analytical Technologies, Iowa) to perform final quality checks on the library product. The genomic libraries were sequenced on an Illumina HiSeq 3000 platform at the Singapore Center for Environmental Life Science Engineering. Filtering and demultiplexing of the genomic data in STACKS 1.34 followed the same general procedures as detailed by Ng et al. (
|
||
<emphasis box="[504,536,1752,1781]" italics="true" pageId="44" pageNumber="45">7 2</emphasis>
|
||
), and are the result of comprehensive trials using a wide variety of different parameters and settings at each step of the analysis. DNA data is deposited with Genbank at BioProject accession number PRJNA566263.
|
||
</paragraph>
|
||
<paragraph blockId="45.[192,1389,201,1923]" pageId="45" pageNumber="46">
|
||
<emphasis bold="true" box="[288,970,201,229]" pageId="45" pageNumber="46">SNP calling and genomic supermatrix generation:</emphasis>
|
||
Reference genome alignment was performed using BWA 0.7.12 (
|
||
<emphasis box="[650,682,274,302]" italics="true" pageId="45" pageNumber="46">9 1</emphasis>
|
||
) and samtools 0.1.19 (http://samtools.sourceforge.net) (
|
||
<emphasis box="[203,283,348,378]" italics="true" pageId="45" pageNumber="46">9 2, 9 3</emphasis>
|
||
) on the Greenish Warbler (
|
||
<taxonomicName authorityName="Blyth" authorityYear="1843" box="[635,1096,348,376]" class="Aves" family="Phylloscopidae" genus="Phylloscopus" kingdom="Animalia" order="Passeriformes" pageId="45" pageNumber="46" phylum="Chordata" rank="subSpecies" species="trochiloides" subSpecies="viridanus">
|
||
<emphasis box="[635,1096,348,376]" italics="true" pageId="45" pageNumber="46">Phylloscopus trochiloides viridanus</emphasis>
|
||
</taxonomicName>
|
||
) genome (
|
||
<emphasis box="[1234,1282,348,376]" italics="true" pageId="45" pageNumber="46">11 6</emphasis>
|
||
), the most closely related available full genome. We performed SNP calling in STACKS 1.34 as per Ng et al. (
|
||
<emphasis box="[369,401,495,525]" italics="true" pageId="45" pageNumber="46">7 2</emphasis>
|
||
). We required loci to be present across all individuals, and retained one random SNP per locus to exclude obviously linked SNP loci. Subsequently, we used PLINK 1.9 (
|
||
<emphasis box="[251,299,642,672]" italics="true" pageId="45" pageNumber="46">11 7</emphasis>
|
||
) and Bayescan 2.1 (
|
||
<emphasis box="[561,609,642,670]" italics="true" pageId="45" pageNumber="46">11 8</emphasis>
|
||
) to filter SNPs for linkage disequilibrium and signs of selection. Data format manipulation and conversions were performed with PGDSpider (
|
||
<emphasis box="[1318,1366,716,744]" italics="true" pageId="45" pageNumber="46">1 19</emphasis>
|
||
). The final filtered dataset totaled 4,104 SNPs. In addition, we created concatenated SNP datasets for each group for use in downstream maximum parsimony analysis.
|
||
</paragraph>
|
||
<paragraph blockId="45.[192,1389,201,1923]" pageId="45" pageNumber="46">
|
||
Following the procedures used by Ng et al. (
|
||
<emphasis box="[858,890,937,966]" italics="true" pageId="45" pageNumber="46">7 2</emphasis>
|
||
), we generated a concatenated read supermatrix without missing data using pyRAD (
|
||
<emphasis box="[823,871,1010,1038]" italics="true" pageId="45" pageNumber="46">12 0</emphasis>
|
||
). We stipulated a minimum required locus coverage of 20, and kept the clustering threshold within and between reads at the default of 0.88. The final concatenated read supermatrix amounted to 2,861,661 bp in length, generated from 19,985 loci.
|
||
</paragraph>
|
||
<paragraph blockId="45.[192,1389,201,1923]" pageId="45" pageNumber="46">
|
||
<emphasis bold="true" box="[288,781,1305,1333]" pageId="45" pageNumber="46">Mitochondrial sequence generation:</emphasis>
|
||
We sequenced cyt-
|
||
<emphasis box="[1032,1048,1305,1333]" italics="true" pageId="45" pageNumber="46">b</emphasis>
|
||
using the primers H16065 (
|
||
<emphasis box="[203,251,1378,1406]" italics="true" pageId="45" pageNumber="46">12 1</emphasis>
|
||
) and L14995 (
|
||
<emphasis box="[442,490,1378,1406]" italics="true" pageId="45" pageNumber="46">12 2</emphasis>
|
||
), with 40 cycles of PCR performed at an annealing temperature of 72°C. We conducted PCR product cleanup with ExoSAP-IT
|
||
<superScript attach="left" box="[964,980,1448,1467]" fontSize="8" pageId="45" pageNumber="46">®</superScript>
|
||
and used the BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems Inc., Foster City, CA) for cycle- sequencing. Sequencing was carried out on an Applied Biosystems 3130xl Genetic Analyzer using capillary electrophoresis. We assembled cyt-
|
||
<emphasis box="[842,858,1673,1701]" italics="true" pageId="45" pageNumber="46">b</emphasis>
|
||
sequences with CodonCode Aligner 4.1 and aligned them with ClustalW (
|
||
<emphasis box="[625,673,1746,1774]" italics="true" pageId="45" pageNumber="46">12 3</emphasis>
|
||
). The final cyt-
|
||
<emphasis box="[874,890,1746,1774]" italics="true" pageId="45" pageNumber="46">b</emphasis>
|
||
alignment was 1,100bp long, indel- free and fully translatable. Mitochondrial sequences have been deposited with Genbank at accession numbers MN518858-MN518862.
|
||
</paragraph>
|
||
<paragraph blockId="46.[192,1389,201,1923]" pageId="46" pageNumber="47">
|
||
<emphasis bold="true" box="[288,717,201,229]" pageId="46" pageNumber="47">Population structure inference:</emphasis>
|
||
In order to test for the presence of geographic structuring across East Sulawesi, Peleng, and Taliabu, we applied principal component analysis (PCA) to the genomic SNP data. PCA was performed using ade4 (
|
||
<emphasis box="[1155,1203,348,376]" italics="true" pageId="46" pageNumber="47">12 4</emphasis>
|
||
) and factoextra (
|
||
<emphasis box="[339,387,422,451]" italics="true" pageId="46" pageNumber="47">12 5</emphasis>
|
||
), both available as R packages (
|
||
<emphasis box="[802,850,422,450]" italics="true" pageId="46" pageNumber="47">12 6</emphasis>
|
||
).
|
||
</paragraph>
|
||
<paragraph blockId="46.[192,1389,201,1923]" pageId="46" pageNumber="47">
|
||
<emphasis bold="true" box="[288,692,495,523]" pageId="46" pageNumber="47">Mitochondrial tree inference:</emphasis>
|
||
We constructed phylogenetic cyt-
|
||
<emphasis box="[1130,1146,495,523]" italics="true" pageId="46" pageNumber="47">b</emphasis>
|
||
trees using two methods: maximum parsimony (MP) and maximum likelihood (ML). We ran MP analyses using the seqboot, dnapars, and consense algorithms in PHYLIP v3.695 (
|
||
<emphasis box="[1130,1178,642,672]" italics="true" pageId="46" pageNumber="47">12 7</emphasis>
|
||
), performing 10,000 bootstrap replicates. For ML analyses, we first used jModelTest v2.1.6 (
|
||
<bibRefCitation author="D. Darriba & G. L. Taboada & R. Doallo & D. Posada" box="[1212,1244,716,744]" pageId="46" pageNumber="47" pagination="772" refId="ref31959" refString="97. D. Darriba, G. L. Taboada, R. Doallo, D. Posada, jModelTest 2: More models, new heuristics and parallel computing. Nat. Methods 9, 772 (2012). doi: 10.1038 / nmeth. 2109 Medline" type="journal article" year="2012">
|
||
<emphasis box="[1212,1244,716,744]" italics="true" pageId="46" pageNumber="47">97</emphasis>
|
||
</bibRefCitation>
|
||
) and determined that the Jukes-Cantor model (
|
||
<emphasis box="[723,771,790,818]" italics="true" pageId="46" pageNumber="47">12 8</emphasis>
|
||
) was the best performing substitution model. We then ran RAxML v8.2.9 (
|
||
<bibRefCitation author="D. Silvestro & I. Michalak" box="[571,603,863,891]" journalOrPublisher="Org. Divers. Evol." pageId="46" pageNumber="47" pagination="335 - 337" part="12" refId="ref31914" refString="96. D. Silvestro, I. Michalak, raxmlGUI: A graphical front-end for RAxML. Org. Divers. Evol. 12, 335 - 337 (2012). doi: 10.1007 / s 13127 - 011 - 0056 - 0" title="raxmlGUI: A graphical front-end for RAxML" type="journal article" year="2012">
|
||
<emphasis box="[571,603,863,891]" italics="true" pageId="46" pageNumber="47">96</emphasis>
|
||
</bibRefCitation>
|
||
) using the extensive subtree-pruning-regrafting tree search algorithm.
|
||
</paragraph>
|
||
<paragraph blockId="46.[192,1389,201,1923]" pageId="46" pageNumber="47">
|
||
<emphasis bold="true" box="[288,617,1010,1038]" pageId="46" pageNumber="47">Genomic tree inference:</emphasis>
|
||
We applied three different genomic tree inference analyses: coalescent-based species tree inference (applied to the SNP dataset), maximum likelihood tree inference (applied to concatenated read supermatrix), and maximum parsimony tree inference (applied to the concatenated SNP dataset). We performed species tree inference using SNAPP (
|
||
<emphasis box="[388,436,1305,1333]" italics="true" pageId="46" pageNumber="47">1 29</emphasis>
|
||
) as implemented in BEAST 2.3.0, performing two iterations using default settings. Tracer 1.6 was used after each iteration to ensure that the runs had reached convergence, after which LogCombiner v2.3.0 and DensiTree (
|
||
<emphasis box="[1004,1052,1452,1480]" italics="true" pageId="46" pageNumber="47">13 0</emphasis>
|
||
) were used to process results. We carried out ML tree inference using RAxML v8.2.9 (
|
||
<bibRefCitation author="D. Silvestro & I. Michalak" box="[1021,1053,1526,1554]" journalOrPublisher="Org. Divers. Evol." pageId="46" pageNumber="47" pagination="335 - 337" part="12" refId="ref31914" refString="96. D. Silvestro, I. Michalak, raxmlGUI: A graphical front-end for RAxML. Org. Divers. Evol. 12, 335 - 337 (2012). doi: 10.1007 / s 13127 - 011 - 0056 - 0" title="raxmlGUI: A graphical front-end for RAxML" type="journal article" year="2012">
|
||
<emphasis box="[1021,1053,1526,1554]" italics="true" pageId="46" pageNumber="47">96</emphasis>
|
||
</bibRefCitation>
|
||
) on the concatenated read supermatrix using the general-time-reversible gamma-invariant (GTRGAMMA) model and performed 1,000 rapid bootstrap searches. Finally, we conducted conventional MP analysis on the concatenated SNPs of each taxon set, using the seqboot, dnapars, and consense algorithms in PHYLIP v3.695 (
|
||
<emphasis box="[596,644,1820,1849]" italics="true" pageId="46" pageNumber="47">12 7</emphasis>
|
||
) and running 10,000 bootstrap replicates to evaluate branch support.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |