304 lines
33 KiB
XML
304 lines
33 KiB
XML
<document id="E7EE86CA2D81B4623CF93C8FE6A44AAA" ID-CLB-Dataset="54552" ID-DOI="10.1093/zoolinnean/zlab084" ID-GBIF-Dataset="74fd1505-6f9d-47e3-acd2-f96be7fb2df1" ID-ISSN="0024-4082" ID-Zenodo-Dep="7471675" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.tables_requiresApprovalFor="existingObjects,plazi" IM.taxonomicNames_approvedBy="felipe" checkinTime="1671693640761" checkinUser="plazi" docAuthor="Iorgu, Ionuț Ştefan, Iorgu, Elena Iulia, Stalling, Thomas, Puskás, Gellért, Chobanov, Dragan, Szövényi, Gergely, Moscaliuc, Liviu Aurel, Motoc, Rozalia, Tăuşan, Ioan & Fusu, Lucian" docDate="2023" docId="426A87ECFFDF7035925EFD6791DEFD68" docLanguage="en" docName="zlab084.pdf" docOrigin="Zoological Journal of the Linnean Society 197 (1)" docSource="https://academic.oup.com/zoolinnean/article/197/1/211/6413619" docStyle="DocumentStyle:36B3BD6A90C22AB4F7F465C853188CC8.7:ZoolJLinnSoc.2017-2023.journal_article" docStyleId="36B3BD6A90C22AB4F7F465C853188CC8" docStyleName="ZoolJLinnSoc.2017-2023.journal_article" docStyleVersion="7" docTitle="Wolbachia Hertig 1936" docType="treatment" docVersion="8" lastPageNumber="214" masterDocId="BE53FF94FFDC7031935BFFA2901FFFAD" masterDocTitle="Ant crickets and their secrets: Myrmecophilus acerŋorum is not always parthenogenetic (Insecta: Orthoptera: Myrmecophilidae)" masterLastPageNumber="228" masterPageNumber="211" pageNumber="214" updateTime="1699413866715" updateUser="ExternalLinkService">
|
||
<mods:mods id="D1ABBEA6605D417D51CEF4370A0FECFA" xmlns:mods="http://www.loc.gov/mods/v3">
|
||
<mods:titleInfo id="2D3236F4E5B7CB04A339B4F788C5C808">
|
||
<mods:title id="716704DC9A10A970ECA9557AE6AD9BC0">Ant crickets and their secrets: Myrmecophilus acerŋorum is not always parthenogenetic (Insecta: Orthoptera: Myrmecophilidae)</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:name id="A98D0C21FFA8E166BF67A41CA4588F2B" type="personal">
|
||
<mods:role id="338EC97A61253676E6725D795C915BE6">
|
||
<mods:roleTerm id="0B26CD166D24DD747C9FB0022651A522">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="4929685578BE98134E53A75DF852F47B">Iorgu, Ionuț Ştefan</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="64719B238763CEB52A6FB7747FB11628" type="personal">
|
||
<mods:role id="302FBE79EE91308FD862E488D74D7551">
|
||
<mods:roleTerm id="89A0C2F2EC397D988379B2AAD1DBA89C">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="256F1B82CEEB60DC8DD11C6514DD962C">Iorgu, Elena Iulia</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="F33D95A75F16AD33E7854D8816ED75AA" type="personal">
|
||
<mods:role id="1C1871C110EDE171390FC45030137E21">
|
||
<mods:roleTerm id="B6E3074E26CA948369E4C86C4F163CA6">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="EBE8223C54144D234EC4DC8F92F36830">Stalling, Thomas</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="67230FA4A10C540F954AEC92FBFC8619" type="personal">
|
||
<mods:role id="A6FD017D47FF42E254B57F5EA439DA0F">
|
||
<mods:roleTerm id="EB820A3504C26D0B05FB210D731BEB8E">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="484B7236D77BC377078B8F130C986222">Puskás, Gellért</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="A1A792C48C127EED3B6AED50D02F1900" type="personal">
|
||
<mods:role id="2BBAB2BC6FD7B031C07D7055188A11B6">
|
||
<mods:roleTerm id="58A39B177F33D0704233765190A05D0F">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="00DDBA51FD758F84DBE1FD615F9D2860">Chobanov, Dragan</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="F763B703D9066913177FC33B20EFDCD9" type="personal">
|
||
<mods:role id="295A434A76A4FCA0219E1F6F1A3EA59B">
|
||
<mods:roleTerm id="DF42DBE07E6AC006E6C4D6B7E52BC097">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="B3EDDEFC0DBC66FB7082BB1BCF18B596">Szövényi, Gergely</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="5BC310454166459082F3E9C78568EDDA" type="personal">
|
||
<mods:role id="6513308D638206CD2D7FDCF240E52E35">
|
||
<mods:roleTerm id="B06FC91628FE4BE2BC045534873E2493">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="7E5BAB8A52C52B8237CA530BC5D3914A">Moscaliuc, Liviu Aurel</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="95CFF0F3B6E6146871E4F6957D4193BA" type="personal">
|
||
<mods:role id="3550735D2E4E491F62DB20AE715E48FC">
|
||
<mods:roleTerm id="3697D6ED23E3068285CD1DE7558F3AB9">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="0B18388E8A0B699AB7597921B9BD1367">Motoc, Rozalia</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="FDE78195CC0154BD0B0150B6904CAC7F" type="personal">
|
||
<mods:role id="75AA30E0E87BE72AFBE12E7381C6D26E">
|
||
<mods:roleTerm id="C7BE2364437E957657E06FDD67370950">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="8BAB8737E568948746B6C16EB05F34C1">Tăuşan, Ioan</mods:namePart>
|
||
</mods:name>
|
||
<mods:name id="4485AD6ACD8913F9D8710CDC2F354445" type="personal">
|
||
<mods:role id="A3F1E060B6DDB82099567F8EBE6CED1A">
|
||
<mods:roleTerm id="A0C7BD612DB5DF0DC342FBC07CE5097D">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="19ABD1A31D637F41C6EE5C18E44A6CA7">Fusu, Lucian</mods:namePart>
|
||
</mods:name>
|
||
<mods:typeOfResource id="C20564040D3CD9F811B46E9BD53ADA0B">text</mods:typeOfResource>
|
||
<mods:relatedItem id="A62A662A1C81CE3626B9713FCFC355AE" type="host">
|
||
<mods:titleInfo id="A9B480C86D0154FB5CA42799F311328B">
|
||
<mods:title id="014C104114839257D339565B0B8E1B65">Zoological Journal of the Linnean Society</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:part id="CF5FAFE0DD54F2347E828EA0EAD8D17A">
|
||
<mods:date id="B993A364167EFB107762B83A815283FB">2023</mods:date>
|
||
<mods:detail id="82E807977480DC071BC0B788B52B7235" type="pubDate">
|
||
<mods:number id="74D834268BA13EDBEA9AE07FBF2701D5">2023-01-01</mods:number>
|
||
</mods:detail>
|
||
<mods:detail id="A7F02202BD1991EA72B0A5EAE98091B2" type="volume">
|
||
<mods:number id="0AA5FAEA88C3D12B1CA7191AE9A71903">197</mods:number>
|
||
</mods:detail>
|
||
<mods:detail id="5B662FFE150BD0B213BE5B7CB1CF11F0" type="issue">
|
||
<mods:number id="2935966B673A2E4F128018D1837345E4">1</mods:number>
|
||
</mods:detail>
|
||
<mods:extent id="5436128D36745B4A63127E074046D112" unit="page">
|
||
<mods:start id="76144B247BF0A247F4FDE5DF734B1A03">211</mods:start>
|
||
<mods:end id="101BB77AE33FA8E30496A1EE4FF88937">228</mods:end>
|
||
</mods:extent>
|
||
</mods:part>
|
||
</mods:relatedItem>
|
||
<mods:location id="5B671C8105C2AF8C726EDBA2F1A08420">
|
||
<mods:url id="1D98365EEC81BD9C935C864B79978E01">https://academic.oup.com/zoolinnean/article/197/1/211/6413619</mods:url>
|
||
</mods:location>
|
||
<mods:classification id="F2D3DCE7AC20FAD0F418C06646B1787A">journal article</mods:classification>
|
||
<mods:identifier id="14156AF00E9AB2914570CF9D652F3CD2" type="CLB-Dataset">54552</mods:identifier>
|
||
<mods:identifier id="BF10919126F3E0AC6893183B82236E3F" type="DOI">10.1093/zoolinnean/zlab084</mods:identifier>
|
||
<mods:identifier id="0B2109A95B1FB26E5D030E0D21E634BB" type="GBIF-Dataset">74fd1505-6f9d-47e3-acd2-f96be7fb2df1</mods:identifier>
|
||
<mods:identifier id="2517C745E8C21A49A40F21E5952A6737" type="ISSN">0024-4082</mods:identifier>
|
||
<mods:identifier id="A1D16BC529836F6A88061C442CBFAB22" type="Zenodo-Dep">7471675</mods:identifier>
|
||
</mods:mods>
|
||
<treatment id="426A87ECFFDF7035925EFD6791DEFD68" ID-DOI="http://doi.org/10.5281/zenodo.7473188" ID-GBIF-Taxon="207926941" ID-Zenodo-Dep="7473188" LSID="urn:lsid:plazi:treatment:426A87ECFFDF7035925EFD6791DEFD68" httpUri="http://treatment.plazi.org/id/426A87ECFFDF7035925EFD6791DEFD68" lastPageId="4" lastPageNumber="214" pageId="3" pageNumber="214">
|
||
<subSubSection id="82D96571FFDF7032925EFD6792B6FD71" box="[261,681,709,734]" pageId="3" pageNumber="214" type="nomenclature">
|
||
<paragraph id="CA7C36FAFFDF7032925EFD6792B6FD71" blockId="3.[261,681,709,734]" box="[261,681,709,734]" pageId="3" pageNumber="214">
|
||
<heading id="91348196FFDF7032925EFD6792B6FD71" box="[261,681,709,734]" centered="true" fontSize="9" level="2" pageId="3" pageNumber="214" reason="2">
|
||
TESTING FOR
|
||
<taxonomicName id="0DC34D79FFDF703292FAFD679237FD71" ID-CoL="885S" authorityName="Hertig" authorityYear="1936" box="[417,552,709,732]" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="genus">
|
||
<emphasis id="F8B7EAE8FFDF703292FAFD679237FD71" box="[417,552,709,732]" italics="true" pageId="3" pageNumber="214">WOLBACHIA</emphasis>
|
||
</taxonomicName>
|
||
INFECTION
|
||
</heading>
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection id="82D96571FFDF703593F8FD4C91DEFD68" lastPageId="4" lastPageNumber="215" pageId="3" pageNumber="214" type="description">
|
||
<paragraph id="CA7C36FAFFDF703293F8FD4C9209F9F0" blockId="3.[163,780,749,1630]" pageId="3" pageNumber="214">
|
||
We also tested our
|
||
<taxonomicName id="0DC34D79FFDF703292F6FD4C927DFCAE" baseAuthorityName="Panzer" baseAuthorityYear="1799" box="[429,610,750,771]" class="Insecta" family="Myrmecophilidae" genus="Myrmecophilus" kingdom="Animalia" order="Orthoptera" pageId="3" pageNumber="214" phylum="Arthropoda" rank="species" species="acervorum">
|
||
<emphasis id="F8B7EAE8FFDF703292F6FD4C927DFCAE" box="[429,610,750,771]" italics="true" pageId="3" pageNumber="214">M. acerƲorum</emphasis>
|
||
</taxonomicName>
|
||
samples for
|
||
<taxonomicName id="0DC34D79FFDF703293F8FCAE9138FC8C" authorityName="Hertig" authorityYear="1936" box="[163,295,780,801]" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="genus">
|
||
<emphasis id="F8B7EAE8FFDF703293F8FCAE9138FC8C" box="[163,295,780,801]" italics="true" pageId="3" pageNumber="214">Wolbachia</emphasis>
|
||
</taxonomicName>
|
||
infections in an attempt to explain the cause of parthenogenetic populations. For this, we extracted genomic DNA from the whole individual and we screened them for
|
||
<taxonomicName id="0DC34D79FFDF703291D2FCCA9315FCD0" authorityName="Hertig" authorityYear="1936" box="[649,778,872,893]" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="genus">
|
||
<emphasis id="F8B7EAE8FFDF703291D2FCCA9315FCD0" box="[649,778,872,893]" italics="true" pageId="3" pageNumber="214">Wolbachia</emphasis>
|
||
</taxonomicName>
|
||
using the W-Spec diagnostic primers: W-spec f (5′– CATACCTATTCGAAGGGATAG–3′) / W-spec r (5′– AGCTTCGAG TGAAACCAATTC–3′) (
|
||
<bibRefCitation id="AE524B0BFFDF7032912EFC6690C3FC55" author="Jeong G & Lee K & Choi J & Hwang S & Park B & Kim W & Choi Y & Park I & Kim J" pageId="3" pageNumber="214" pagination="28 - 32" refId="ref13208" refString="Jeong G, Lee K, Choi J, Hwang S, Park B, Kim W, Choi Y, Park I, Kim J. 2009. Incidence of Wolbachia and Cardinium endosymbionts in the Osmia community in Korea. The Journal of Microbiology 47: 28 - 32." type="journal article" year="2009">
|
||
Jeong
|
||
<emphasis id="F8B7EAE8FFDF7032919EFC66931BFC74" box="[709,772,964,985]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2009
|
||
</bibRefCitation>
|
||
) following the protocol implemented by
|
||
<bibRefCitation id="AE524B0BFFDF7032919DFC41913EFBBB" author="Jeong G & Ahn J & Jang Y & Choe JC & Choi H" pageId="3" pageNumber="214" pagination="563 - 566" refId="ref13260" refString="Jeong G, Ahn J, Jang Y, Choe JC, Choi H. 2012. Wolbachia infection in the Loxoblemmus complex (Orthoptera: Gryllidae) in Korea. Journal of Asia-Pacific Entomology 15: 563 - 566." type="journal article" year="2012">
|
||
Jeong
|
||
<emphasis id="F8B7EAE8FFDF703293F8FBA090C8FBBB" box="[163,215,1025,1047]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
(2012)
|
||
</bibRefCitation>
|
||
.After the initial screening we genotyped the strains on three gene regions:
|
||
<emphasis id="F8B7EAE8FFDF703292B1FB829209FB98" box="[490,534,1056,1077]" italics="true" pageId="3" pageNumber="214">ftsZ</emphasis>
|
||
,
|
||
<taxonomicName id="0DC34D79FFDF7032917BFB829253FB98" box="[544,588,1056,1077]" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="species" species="aesp">
|
||
<emphasis id="F8B7EAE8FFDF7032917BFB829253FB98" box="[544,588,1056,1077]" italics="true" pageId="3" pageNumber="214">aesp</emphasis>
|
||
</taxonomicName>
|
||
and 16S. In order to amplify the
|
||
<taxonomicName id="0DC34D79FFDF7032921FFB9C91A5FBFE" authorityName="Hertig" authorityYear="1936" box="[324,442,1086,1107]" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="genus">
|
||
<emphasis id="F8B7EAE8FFDF7032921FFB9C91A5FBFE" box="[324,442,1086,1107]" italics="true" pageId="3" pageNumber="214">Wolbachia</emphasis>
|
||
</taxonomicName>
|
||
16S rRNA gene we performed a nested PCR using an initial universal 16S rDNA primer set: 27f (5′–AGAGTTTGATCMTGGCTCAG–3′) / 1513r (5′–ACGGYTACCTTGTTACGACTT–3′) (
|
||
<bibRefCitation id="AE524B0BFFDF703293F0FB1B91B9FB63" author="Weisburg WG & Barns SM & Pelletier DA & Lane DJ" box="[171,422,1209,1231]" pageId="3" pageNumber="214" pagination="697 - 703" refId="ref15328" refString="Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16 S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 172: 697 - 703." type="journal article" year="1991">
|
||
Weisburg
|
||
<emphasis id="F8B7EAE8FFDF70329278FB189140FB63" box="[291,351,1209,1231]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 1991
|
||
</bibRefCitation>
|
||
) and a second primer set: 76f (5′–TTGTAGCCTGCTATGGTATAAYT–3′) / 1012r (5′–GAATAGGTATRATTTYCATGT–3′) (
|
||
<bibRefCitation id="AE524B0BFFDF7032912EFB5490C5FA87" author="O'Neill SL & Giordano R & Colbert AME & Karr TL & Robertson HM" pageId="3" pageNumber="214" pagination="2699 - 2702" refId="ref14210" refString="O'Neill SL, Giordano R, Colbert AME, Karr TL, Robertson HM. 1992. 16 S ribosomal- RNA phylogenetic analysis of the bacterial endosymbionts associated with cytoplasmic incompatability in insects. Proceedings of the National Academy of Sciences 89: 2699 - 2702." type="journal article" year="1992">
|
||
O’Neill
|
||
<emphasis id="F8B7EAE8FFDF70329197FB55931AFAA6" box="[716,773,1270,1292]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 1992
|
||
</bibRefCitation>
|
||
). The reaction protocol and PCR conditions were adapted from
|
||
<bibRefCitation id="AE524B0BFFDF70329265FA969218FAE4" author="Jeong G & Ahn J & Jang Y & Choe JC & Choi H" box="[318,519,1332,1353]" pageId="3" pageNumber="214" pagination="563 - 566" refId="ref13260" refString="Jeong G, Ahn J, Jang Y, Choe JC, Choi H. 2012. Wolbachia infection in the Loxoblemmus complex (Orthoptera: Gryllidae) in Korea. Journal of Asia-Pacific Entomology 15: 563 - 566." type="journal article" year="2012">
|
||
Jeong
|
||
<emphasis id="F8B7EAE8FFDF703292DEFA9691A4FAE4" box="[389,443,1332,1353]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
(2012)
|
||
</bibRefCitation>
|
||
. The partial
|
||
<taxonomicName id="0DC34D79FFDF703291CEFA9690D0FAC5" class="Alphaproteobacteria" family="Anaplasmataceae" genus="Wolbachia" kingdom="Bacteria" order="Rickettsiales" pageId="3" pageNumber="214" phylum="Proteobacteria" rank="species" species="aesp">
|
||
<emphasis id="F8B7EAE8FFDF703291CEFA9690D0FAC5" italics="true" pageId="3" pageNumber="214">Wolbachia aesp</emphasis>
|
||
</taxonomicName>
|
||
gene for outer surface protein was obtained using the 81F (5′–TGGTCCAATAAGTGATGAAGAAAC–3′) / 691R (5′–AAAAATTAAACGCTACTCCA–3′) primer set (
|
||
<bibRefCitation id="AE524B0BFFDF7032938CFA0C9182FA6E" author="Zhou W & Rousset F & O'neill SL" box="[215,413,1454,1476]" pageId="3" pageNumber="214" pagination="509 - 515" refId="ref15482" refString="Zhou W, Rousset F, O'neill SL. 1998. Phylogeny and PCRbased classification of Wolbachia strains using aesp gene sequences. Proceedings of the Royal Society of London. Series B: Biological Sciences 265: 509 - 515." type="journal article" year="1998">
|
||
Zhou
|
||
<emphasis id="F8B7EAE8FFDF70329240FA0D9149FA6E" box="[283,342,1454,1476]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 1998
|
||
</bibRefCitation>
|
||
) following the PCR conditions from
|
||
<bibRefCitation id="AE524B0BFFDF703293BFFA6F922AFA4F" author="Vaishampayan PA & Dhotre DP & Gupta RP & Lalwani P & Ghate H & Patole MS & Shouche YS" box="[228,565,1485,1507]" pageId="3" pageNumber="214" pagination="1346 - 1351" refId="ref15162" refString="Vaishampayan PA, Dhotre DP, Gupta RP, Lalwani P, Ghate H, Patole MS, Shouche YS. 2007. Molecular evidence and phylogenetic affiliations of Wolbachia in cockroaches. Molecular Phylogenetics and EVolution 44: 1346 - 1351." type="journal article" year="2007">
|
||
Vaishampayan
|
||
<emphasis id="F8B7EAE8FFDF703292FAFA6C91C0FA4F" box="[417,479,1485,1507]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
(2007)
|
||
</bibRefCitation>
|
||
. Finally, the
|
||
<emphasis id="F8B7EAE8FFDF70329187FA6F9314FA4F" box="[732,779,1485,1506]" italics="true" pageId="3" pageNumber="214">ftsZ</emphasis>
|
||
gene was amplified using the primers ftsZ_F1 (5′–ATYATGGARCATATAAARGATAG– 3′) / ftsZ_R1 (5′–TCRAGYAATGGATTRGATAT–3′) and the PCR protocol from
|
||
<bibRefCitation id="AE524B0BFFDF7032921BF9EA9211F9F3" author="Baldo L & Hotopp JCD & Jolley KA & Bordenstein SR & Biber SA & Choudhury RR & Hayashi C & Maiden MCJ & Tettelin H & Werren JH" box="[320,526,1608,1630]" pageId="3" pageNumber="214" pagination="7098 - 7110" refId="ref11806" refString="Baldo L, Hotopp JCD, Jolley KA, Bordenstein SR, Biber SA, Choudhury RR, Hayashi C, Maiden MCJ, Tettelin H, Werren JH. 2006. Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Applied and EnVironmental Microbiology 72: 7098 - 7110." type="journal article" year="2006">
|
||
Baldo
|
||
<emphasis id="F8B7EAE8FFDF703292D2F9EA91DEF9F0" box="[393,449,1608,1629]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
(2006)
|
||
</bibRefCitation>
|
||
.
|
||
</paragraph>
|
||
<paragraph id="CA7C36FAFFDF70329218F9389275F91F" blockId="3.[323,618,1690,1715]" box="[323,618,1690,1715]" pageId="3" pageNumber="214">PHYLOGENETIC ANALYSES</paragraph>
|
||
<paragraph id="CA7C36FAFFDF703293F8F9619542FD68" blockId="3.[163,778,1730,1875]" lastBlockId="3.[827,1444,197,1170]" pageId="3" pageNumber="214">
|
||
Sequences were aligned using MEGA 7 (
|
||
<bibRefCitation id="AE524B0BFFDF703291EFF9619135F95A" author="Kumar S & Stecher G & Tamura K" pageId="3" pageNumber="214" pagination="1870 - 1874" refId="ref13583" refString="Kumar S, Stecher G, Tamura K. 2016. MEGA 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and EVolution 33: 1870 - 1874." type="journal article" year="2016">
|
||
Kumar
|
||
<emphasis id="F8B7EAE8FFDF703293F8F94090FFF95B" box="[163,224,1761,1783]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2016
|
||
</bibRefCitation>
|
||
). We also compared our
|
||
<emphasis id="F8B7EAE8FFDF7032910CF9409297F95A" box="[599,648,1762,1783]" italics="true" pageId="3" pageNumber="214">COI</emphasis>
|
||
sequences with those found in GenBank and BOLD databases (Supporting Information,
|
||
<tableCitation id="87410341FFDF70329158F8BD9267F899" box="[515,632,1822,1844]" captionStart="Table 1" captionStartId="8.[145,209,1169,1190]" captionTargetPageId="8" captionText="Table 1. mtDNA diversity estimates for Myrmecophilus species for different datasets used. Variables provided: number of sequences (N), total number of nucleotides, number of variable and parsimony informative sites (P), number of observed haplotypes (Nh), haplotype diversity (hd), nucleotide diversity (Π) and nucleotide substitution model" httpUri="http://table.plazi.org/id/9EBC6672FFD4703993CAFB3394B6FB4C" pageId="3" pageNumber="214" tableUuid="9EBC6672FFD4703993CAFB3394B6FB4C">Table S1</tableCitation>
|
||
). Pairwise genetic distances were estimated using the Kimura 2-parameter (K2P) nucleotide substitution model implemented in MEGA 7. Haplotype identities and diversity (
|
||
<emphasis id="F8B7EAE8FFDF703290E8FEA093DDFEBA" box="[947,962,258,279]" italics="true" pageId="3" pageNumber="214">h</emphasis>
|
||
), as well as nucleotide diversity (Π) were determined using DnaSP v.5.1 (
|
||
<bibRefCitation id="AE524B0BFFDF70329790FE83936BFEF8" author="Librado P & Rozas J" pageId="3" pageNumber="214" pagination="1451 - 1452" refId="ref13769" refString="Librado P, Rozas J. 2009. DnaSP v 5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451 - 1452." type="journal article" year="2009">Librado & Rozas, 2009</bibRefCitation>
|
||
). Haplotype networks were constructed using PopART v.1.7 (
|
||
<bibRefCitation id="AE524B0BFFDF703290BCFEFC94FCFED9" author="Leigh JW & Bryant D" box="[999,1251,350,372]" pageId="3" pageNumber="214" pagination="1110 - 1116" refId="ref13741" refString="Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods in Ecology and EVolution 6: 1110 - 1116." type="journal article" year="2015">Leigh & Bryant, 2015</bibRefCitation>
|
||
) with a medianjoining algorithm (
|
||
<bibRefCitation id="AE524B0BFFDF70329745FEDF9514FE3F" author="Bandelt H & Forster P & Rohl A" box="[1054,1291,381,403]" pageId="3" pageNumber="214" pagination="37 - 48" refId="ref11858" refString="Bandelt H, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and EVolution 16: 37 - 48." type="journal article" year="1999">
|
||
Bandelt
|
||
<emphasis id="F8B7EAE8FFDF703297DDFEDC94DDFE3F" box="[1158,1218,381,403]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 1999
|
||
</bibRefCitation>
|
||
), in order to illustrate phylogenetic and geographic patterns. The best-fit model for nucleotide substitution, for each of the two mtDNA markers (16S and
|
||
<emphasis id="F8B7EAE8FFDF7032963BFE7B958DFE43" box="[1376,1426,473,494]" italics="true" pageId="3" pageNumber="214">COI</emphasis>
|
||
), was estimated using jModelTest v.2.1.5 (
|
||
<bibRefCitation id="AE524B0BFFDF70329662FE5A9411FD81" author="Guindon S & Gascuel O" pageId="3" pageNumber="214" pagination="696 - 704" refId="ref12750" refString="Guindon S, Gascuel O. 2003. A simple, fast and accurate method to estimate large phylogenies by maximumlikelihood. Systematic Biology 52: 696 - 704." type="journal article" year="2003">Guindon & Gascuel, 2003</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="AE524B0BFFDF7032977AFDB4953EFD81" author="Darriba D & Taboada GL & Doallo R & Posada D" box="[1057,1313,534,556]" pageId="3" pageNumber="214" pagination="772" refId="ref12343" refString="Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772." type="journal article" year="2012">
|
||
Darriba
|
||
<emphasis id="F8B7EAE8FFDF703297CBFDB594CDFD86" box="[1168,1234,534,556]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2012
|
||
</bibRefCitation>
|
||
) with the Akaike information criterion (AIC). Also, the best partitioning scheme for the concatenated set was determined using PartitionFinder2 (
|
||
<bibRefCitation id="AE524B0BFFDF703297ACFDD09369FD0A" author="Lanfear R & Frandsen PB & Wright AM & Sendfeld T & Calcott B" pageId="3" pageNumber="214" pagination="772 - 773" refId="ref13617" refString="Lanfear R, Frandsen PB, Wright AM, Sendfeld T, Calcott B. 2016. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and EVolution 34: 772 - 773." type="journal article" year="2016">
|
||
Lanfear
|
||
<emphasis id="F8B7EAE8FFDF7032963BFDD19583FD2A" box="[1376,1436,626,648]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2016
|
||
</bibRefCitation>
|
||
), both softwares were implemented on the CIPRES Science Gateway (
|
||
<bibRefCitation id="AE524B0BFFDF70329727FD129552FD68" author="Miller MA & Pfeiffer W & Schwartz T" box="[1148,1357,688,710]" pageId="3" pageNumber="214" pagination="1 - 8" refId="ref14059" refString="Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. Proceedings of the Gateaeay Computing EnVironments Workshop (GCE). New Orleans: GCE, 1 - 8." type="book chapter" year="2010">
|
||
Miller
|
||
<emphasis id="F8B7EAE8FFDF70329797FD129518FD68" box="[1228,1287,688,709]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2010
|
||
</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph id="CA7C36FAFFDF70329008FD6C9594FB3C" blockId="3.[827,1444,197,1170]" pageId="3" pageNumber="214">
|
||
Phylogenetic trees were generated using the maximum likelihood (ML) and Bayesian inference (BI) methods. We used RAxML v.8 (
|
||
<bibRefCitation id="AE524B0BFFDF70329651FCAE936AFCED" author="Stamatakis A" pageId="3" pageNumber="214" pagination="2688 - 2690" refId="ref14979" refString="Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688 - 2690." type="journal article" year="2006">Stamatakis, 2006</bibRefCitation>
|
||
) implemented online on the CIPRES Science Gateway for ML analyses, using 1000 bootstrap resampling and other parameters as default. Mr Bayes v.3.2 (
|
||
<bibRefCitation id="AE524B0BFFDF70329080FC24957EFC36" author="Ronquist F & Huelsenbeck JP" box="[987,1377,902,924]" pageId="3" pageNumber="214" pagination="1572 - 1574" refId="ref14423" refString="Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572 - 1574." type="journal article" year="2003">Ronquist & Huelsenbeck, 2003</bibRefCitation>
|
||
) was used for BI analyses. Two separate runs, with four Monte Carlo Markov chains were used with 10 ×
|
||
<superScript id="3DB69BB2FFDF7032902FFC409386FC43" attach="left" box="[884,921,994,1015]" fontSize="5" pageId="3" pageNumber="214">106</superScript>
|
||
generations with trees sampled every 1000 generations, the first 25% of samples being discarded as burn-in. BI posterior branch probabilities were calculated by the majority-rule consensus of the sampled trees and obtained tree diagrams were visualized using FigTree v.1.4.2 (
|
||
<bibRefCitation id="AE524B0BFFDF7032979DFBDE9564FB3C" author="Rambaut A" box="[1222,1403,1148,1170]" pageId="3" pageNumber="214" refId="ref14390" refString="Rambaut A. 2014. FigTree. Available at: http: // tree. bio. ed. ac. uk / software / figtree /. Accessed 10 December 2020." type="url" year="2014">Rambaut, 2014</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph id="CA7C36FAFFDF70329038FB6C9565FB4B" blockId="3.[867,1402,1230,1255]" box="[867,1402,1230,1255]" pageId="3" pageNumber="214">SEQUENCE- BASED SPECIES DELINEATION TESTS</paragraph>
|
||
<paragraph id="CA7C36FAFFDF70329060FB55944FF993" blockId="3.[827,1444,1270,1875]" pageId="3" pageNumber="214">
|
||
In order to identify independent evolutionary units or operational taxonomic units (OTUs) in our datasets, we applied four DNA sequence-based species delineation approaches on our
|
||
<emphasis id="F8B7EAE8FFDF70329769FAF1947BFAC5" box="[1074,1124,1363,1384]" italics="true" pageId="3" pageNumber="214">COI</emphasis>
|
||
sequences as well as on concatenated sequences of
|
||
<emphasis id="F8B7EAE8FFDF70329731FAD39486FA2B" box="[1130,1177,1393,1414]" italics="true" pageId="3" pageNumber="214">COI</emphasis>
|
||
and 16S. The
|
||
<emphasis id="F8B7EAE8FFDF70329663FAD39578FA2B" box="[1336,1383,1393,1414]" italics="true" pageId="3" pageNumber="214">COI</emphasis>
|
||
gene was used for delimiting species in many taxonomic groups, providing evidence for independently evolving lineages and recognizing genetic patterns within groups, to support morphological evidence or other traditional taxonomic studies (
|
||
<bibRefCitation id="AE524B0BFFDF703297FEF9A89582F98D" author="Hamilton CA & Hendrixson BE & Brewer MS & Bond JE" box="[1189,1437,1546,1568]" pageId="3" pageNumber="214" pagination="79 - 93" refId="ref12780" refString="Hamilton CA, Hendrixson BE, Brewer MS, Bond JE. 2014. An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: a case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae). Molecular Phylogenetics and EVolution 71: 79 - 93." type="journal article" year="2014">
|
||
Hamilton
|
||
<emphasis id="F8B7EAE8FFDF70329647F9A99549F9B2" box="[1308,1366,1546,1568]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2014
|
||
</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="AE524B0BFFDF70329060F98B945FF992" author="Costa-Silva GJ & Rodriguez MS & Roxo FF & Foresti F & Oliveira C" box="[827,1088,1577,1599]" pageId="3" pageNumber="214" pagination="0135075" refId="ref12301" refString="Costa-Silva GJ, Rodriguez MS, Roxo FF, Foresti F, Oliveira C. 2015. Using different methods to access the difficult task of delimiting species in a complex Neotropical hyperdiverse group. PLoS One 10: e 0135075." type="journal article" year="2015">
|
||
Costa-Silva
|
||
<emphasis id="F8B7EAE8FFDF7032909EF98893E2F993" box="[965,1021,1577,1599]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2015
|
||
</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph id="CA7C36FAFFDF70359008F9EA91DEFD68" blockId="3.[827,1444,1270,1875]" lastBlockId="4.[145,761,197,710]" lastPageId="4" lastPageNumber="215" pageId="3" pageNumber="214">
|
||
The first test is the statistical parsimony network analysis implemented in TCS v. 1.21 (
|
||
<bibRefCitation id="AE524B0BFFDF7032901FF9279422F937" author="Clement M & Posada DCKA & Crandall KA" box="[836,1085,1669,1691]" pageId="3" pageNumber="214" pagination="1657 - 1659" refId="ref12241" refString="Clement M, Posada DCKA, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657 - 1659." type="journal article" year="2000">
|
||
Clement
|
||
<emphasis id="F8B7EAE8FFDF703290EEF92493EDF937" box="[949,1010,1669,1691]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
, 2000
|
||
</bibRefCitation>
|
||
). The program computes the maximum number of mutations that constitutes a parsimonious connection between two haplotypes with a 95% probability and then reconstructs a network following the algorithms of
|
||
<bibRefCitation id="AE524B0BFFDF70329647F8A293D1F899" author="Templeton AR & Crandall KA & Sing CF" pageId="3" pageNumber="214" pagination="619 - 633" refId="ref15121" refString="Templeton AR, Crandall KA, Sing CF. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619 - 633." type="journal article" year="1992">
|
||
Templeton
|
||
<emphasis id="F8B7EAE8FFDF70329060F8BD9367F89E" box="[827,888,1822,1844]" italics="true" pageId="3" pageNumber="214">et al.</emphasis>
|
||
(1992)
|
||
</bibRefCitation>
|
||
. Each network is considered an OTU. The second test is the automatic barcode gap discovery (ABGD), implemented on the ABGD web platform (
|
||
<bibRefCitation id="AE524B0BFFD870359248FF46922DFF54" author="Puillandre N & Lambert A & Brouillet S & Achaz G" box="[275,562,228,250]" pageId="4" pageNumber="215" pagination="1864 - 1877" refId="ref14329" refString="Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21: 1864 - 1877." type="journal article" year="2012">
|
||
Puillandre
|
||
<emphasis id="F8B7EAE8FFD8703592FFFF4791FAFF54" box="[420,485,228,250]" italics="true" pageId="4" pageNumber="215">et al.</emphasis>
|
||
, 2012
|
||
</bibRefCitation>
|
||
). The principle of the test is that it uses the so-called ‘barcodegap’ in the distribution of the pairwise differences from the
|
||
<emphasis id="F8B7EAE8FFD87035925EFEE29129FEF8" box="[261,310,320,341]" italics="true" pageId="4" pageNumber="215">COI</emphasis>
|
||
sequences to assign organisms into hypothetical species. The third test is the general mixed yule-coalescent model (GMYC) applied on another web-based server (https://species.h-its. org/gmyc/). The GMYC method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees (
|
||
<bibRefCitation id="AE524B0BFFD870359273FDB492B0FD81" author="Fujisawa T & Barraclough TG" box="[296,687,534,556]" pageId="4" pageNumber="215" pagination="707 - 724" refId="ref12653" refString="Fujisawa T, Barraclough TG. 2013. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 62: 707 - 724." type="journal article" year="2013">Fujisawa & Barraclough, 2013</bibRefCitation>
|
||
). The fourth test is the Poisson Tree Process (PTP model). It is a model for delimiting species on a rooted phylogenetic tree, implemented also on an online platform (https://species.h-its.org/ptp/; Zhang, 2013;
|
||
<bibRefCitation id="AE524B0BFFD870359382FD1291AFFD68" author="Zhang J & Kapli P & Pavlidis P & Stamatakis A" box="[217,432,688,710]" pageId="4" pageNumber="215" pagination="2869 - 2876" refId="ref15450" refString="Zhang J, Kapli P, Pavlidis P, Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869 - 2876." type="journal article" year="2013">
|
||
Zhang
|
||
<emphasis id="F8B7EAE8FFD870359277FD129177FD68" box="[300,360,688,709]" italics="true" pageId="4" pageNumber="215">et al.</emphasis>
|
||
, 2013
|
||
</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |