160 lines
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160 lines
17 KiB
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<document ID-DOI="10.1093/jmammal/gyz196" ID-ISSN="0022-2372" ID-Zenodo-Dep="7832477" IM.bibliography_approvedBy="juliana" IM.illustrations_approvedBy="juliana" IM.tables_approvedBy="juliana" IM.taxonomicNames_approvedBy="juliana" IM.treatments_approvedBy="juliana" checkinTime="1681613584457" checkinUser="felipe" docAuthor="Jackson, Donavan J & Cook, Joseph A" docDate="2020" docId="03B5185B0B087A73FF0CF94BFE62FE62" docLanguage="en" docName="JourMammal.101.1.36-51.pdf" docOrigin="Journal of Mammalogy 101 (1)" docSource="http://dx.doi.org/10.1093/jmammal/gyz196" docStyle="DocumentStyle:8488A0FD6434D222CC79ECAD85E66EFE.1:JourMammal.2015-.journal_article" docStyleId="8488A0FD6434D222CC79ECAD85E66EFE" docStyleName="JourMammal.2015-.journal_article" docStyleVersion="1" docTitle="Microtus Schrank 1798" docType="treatment" docVersion="3" lastPageNumber="38" masterDocId="FF8C60230B0A7A70FFBCFFEEFF80FF82" masterDocTitle="A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus)" masterLastPageNumber="51" masterPageNumber="36" pageNumber="38" updateTime="1682018437050" updateUser="juliana">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus)</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Jackson, Donavan J</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Cook, Joseph A</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>Journal of Mammalogy</mods:title>
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</mods:titleInfo>
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<mods:part>
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<mods:date>2020</mods:date>
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<mods:detail type="pubDate">
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<mods:number>2019-12-28</mods:number>
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</mods:detail>
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<mods:detail type="volume">
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<mods:number>101</mods:number>
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</mods:detail>
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<mods:detail type="issue">
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<mods:number>1</mods:number>
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</mods:detail>
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<mods:extent unit="page">
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<mods:start>36</mods:start>
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<mods:end>51</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:location>
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<mods:url>http://dx.doi.org/10.1093/jmammal/gyz196</mods:url>
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</mods:location>
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<mods:classification>journal article</mods:classification>
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<mods:identifier type="DOI">10.1093/jmammal/gyz196</mods:identifier>
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<mods:identifier type="ISSN">0022-2372</mods:identifier>
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<mods:identifier type="Zenodo-Dep">7832477</mods:identifier>
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</mods:mods>
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<treatment LSID="urn:lsid:plazi:treatment:03B5185B0B087A73FF0CF94BFE62FE62" httpUri="http://treatment.plazi.org/id/03B5185B0B087A73FF0CF94BFE62FE62" lastPageId="3" lastPageNumber="38" pageId="2" pageNumber="38">
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<subSubSection box="[176,695,1701,1724]" pageId="2" pageNumber="38" type="nomenclature">
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<paragraph blockId="2.[176,695,1701,1724]" box="[176,695,1701,1724]" pageId="2" pageNumber="38">
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<heading box="[176,695,1701,1724]" centered="true" fontSize="10" level="2" pageId="2" pageNumber="38" reason="8">
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<taxonomicName ID-CoL="5SL9" ID-ENA="10053" authorityName="Schrank" authorityYear="1798" box="[176,272,1701,1724]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="genus">Microtus</taxonomicName>
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<emphasis box="[279,695,1701,1724]" italics="true" pageId="2" pageNumber="38">Phylogeny Inferred from Cytochrome b</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection lastPageId="3" lastPageNumber="39" pageId="2" pageNumber="38" type="description">
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<paragraph blockId="2.[101,771,1741,1988]" lastBlockId="2.[819,1488,1229,1988]" pageId="2" pageNumber="38">
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<emphasis box="[128,608,1741,1764]" italics="true" pageId="2" pageNumber="38">Sampling and phylogenetic reconstruction.—</emphasis>
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We inferred the phylogeny of species of
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<taxonomicName authorityName="Schrank" authorityYear="1798" box="[362,458,1773,1796]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="genus">
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<emphasis box="[362,458,1773,1796]" italics="true" pageId="2" pageNumber="38">Microtus</emphasis>
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</taxonomicName>
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, generally accepting the species designations of Musser and Carleton (2005). Cytochrome
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<emphasis box="[101,114,1837,1860]" italics="true" pageId="2" pageNumber="38">b</emphasis>
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(
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<emphasis box="[131,182,1837,1860]" italics="true" pageId="2" pageNumber="38">Cytb</emphasis>
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) sequences were downloaded for 110 individuals representing 62 species from GenBank (Supplementary Data SD1) with eight newly sequenced individuals (two represent the first sequences for
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<taxonomicName baseAuthorityName="Baird" baseAuthorityYear="1857" box="[349,468,1933,1956]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="breweri">
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<emphasis box="[349,468,1933,1956]" italics="true" pageId="2" pageNumber="38">M. breweri</emphasis>
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</taxonomicName>
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; Supplementary Data SD2) for a total of 118 individuals and 64 species of
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<taxonomicName authorityName="Schrank" authorityYear="1798" box="[613,709,1965,1988]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="genus">
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<emphasis box="[613,709,1965,1988]" italics="true" pageId="2" pageNumber="38">Microtus</emphasis>
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</taxonomicName>
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, with two outgroup species (
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<taxonomicName baseAuthorityName="Thomas" baseAuthorityYear="1906" box="[1081,1299,1229,1252]" class="Mammalia" family="Cricetidae" genus="Chionomys" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="robertsi">
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<emphasis box="[1081,1299,1229,1252]" italics="true" pageId="2" pageNumber="38">Chionomys robertsi</emphasis>
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</taxonomicName>
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and
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<taxonomicName baseAuthorityName="Martins" baseAuthorityYear="1842" box="[1363,1472,1229,1252]" class="Mammalia" family="Cricetidae" genus="Chionomys" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="nivalis">
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<emphasis box="[1363,1472,1229,1252]" italics="true" pageId="2" pageNumber="38">C. nivalis</emphasis>
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</taxonomicName>
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). Exceptions to Musser and Carleton (2005) include the formally unrecognized species
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<taxonomicName authority="(Bannikova et al. 2010)" baseAuthorityName="Bannikova" baseAuthorityYear="2010" box="[1067,1482,1293,1316]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="gromovi">
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<emphasis box="[1067,1197,1293,1316]" italics="true" pageId="2" pageNumber="38">M. gromovi</emphasis>
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(
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<bibRefCitation author="BANNIKOVA, A. A." box="[1219,1472,1293,1316]" pageId="2" pageNumber="38" pagination="595 - 613" refId="ref10850" refString="BANNIKOVA, A. A., ET AL. 2010. Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequence. Biological Journal of the Linnean Society 99: 595 - 613." type="journal article" year="2010">Bannikova et al. 2010</bibRefCitation>
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)
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</taxonomicName>
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,
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<taxonomicName authority="(KryStufek et al. 2012)" baseAuthorityName="KryStufek" baseAuthorityYear="2012" box="[819,1203,1325,1348]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="hartingi">
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<emphasis box="[819,943,1325,1348]" italics="true" pageId="2" pageNumber="38">M. hartingi</emphasis>
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(
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<bibRefCitation author="KRYSTUFEK, B. & T. ZORENKO & E. V. BUZAN" box="[960,1193,1325,1348]" pageId="2" pageNumber="38" pagination="178 - 182" refId="ref13560" refString="KRYSTUFEK, B., T. ZORENKO, AND E. V. BUZAN. 2012. New insights into the taxonomy and phylogeny of social voles inferred from mitochondrial cytochrome b sequences. Mammalian Biology 77: 178 - 182." type="journal article" year="2012">KryŠtufek et al. 2012</bibRefCitation>
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)
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</taxonomicName>
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,
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<taxonomicName authority="(Rovatsos and Giagia-Athanasopoulou 2012)" baseAuthorityName="Rovatsos and Giagia-Athanasopoulou" baseAuthorityYear="2012" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="atticus">
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<emphasis box="[1217,1326,1325,1348]" italics="true" pageId="2" pageNumber="38">M. atticus</emphasis>
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(Rovatsos and Giagia-Athanasopoulou 2012)
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</taxonomicName>
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, and two controversial species
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<taxonomicName authorityName="Ognev" authorityYear="1924" box="[819,1069,1389,1412]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="rossiaemeridionalis">
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<emphasis box="[819,1069,1389,1412]" italics="true" pageId="2" pageNumber="38">M. rossiaemeridionalis</emphasis>
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</taxonomicName>
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and
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<taxonomicName baseAuthorityName="Eversmann" baseAuthorityYear="1841" box="[1126,1261,1389,1412]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="obscurus">
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<emphasis box="[1126,1261,1389,1412]" italics="true" pageId="2" pageNumber="38">M. obscurus</emphasis>
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</taxonomicName>
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(
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<bibRefCitation author="JAAROLA, M." box="[1279,1481,1389,1412]" pageId="2" pageNumber="38" pagination="647 - 663" refId="ref13244" refString="JAAROLA, M., ET AL. 2004. Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 33: 647 - 663." type="journal article" year="2004">Jaarola et al. 2004</bibRefCitation>
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;
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<bibRefCitation author="BANNIKOVA, A. A." box="[819,998,1421,1444]" pageId="2" pageNumber="38" pagination="595 - 613" refId="ref10850" refString="BANNIKOVA, A. A., ET AL. 2010. Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequence. Biological Journal of the Linnean Society 99: 595 - 613." type="journal article" year="2010">Bannikova 2010</bibRefCitation>
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;
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<bibRefCitation author="TOUGARD, C." box="[1014,1231,1421,1444]" pageId="2" pageNumber="38" pagination="434 - 452" refId="ref15793" refString="TOUGARD, C., ET AL. 2013. Exploring phylogeography and species limits in the Altai vole (Rodentia: Cricetidae). Biological Journal of the Linnean Society 108: 434 - 452." type="journal article" year="2013">Tougard et al. 2013</bibRefCitation>
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;
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<bibRefCitation author="MARKOVA E & V. P. STARIKOV & L. E. YALKOVSKAYA & S. V. ZYKOV & A. V. MOROZKINA & P. A. SIBIRYAKOV" box="[1248,1472,1421,1444]" pageId="2" pageNumber="38" pagination="129 - 131" refId="ref14242" refString="MARKOVA E. A., V. P. STARIKOV, L. E. YALKOVSKAYA, S. V. ZYKOV, A. V. MOROZKINA, AND P. A. SIBIRYAKOV. 2014. Molecular and cytogenetic evidence for the occurrence of the East European vole Microtus rossiaemeridionalis (Arvicolinae, Rodentia) in the North of West Siberia. Doklady Biological Sciences 455: 129 - 131." type="journal article" year="2014">Markova et al. 2014</bibRefCitation>
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), which we treat as distinct species. In addition, we included a single randomly chosen individual from each of four independent mtDNA lineages identified in
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<taxonomicName baseAuthorityName="Ord" baseAuthorityYear="1815" box="[1283,1488,1517,1540]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="pennsylvanicus">
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<emphasis box="[1283,1488,1517,1540]" italics="true" pageId="2" pageNumber="38">M. pennsylvanicus</emphasis>
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</taxonomicName>
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(this study). All sequences were aligned in Geneious v. 8.1.9 (
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<bibRefCitation author="KEARSE, M." box="[828,1039,1581,1604]" pageId="2" pageNumber="38" pagination="1647 - 1649" refId="ref13345" refString="KEARSE, M., ET AL. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647 - 1649." type="journal article" year="2012">Kearse et al. 2012</bibRefCitation>
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) using the MUSCLE (
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<bibRefCitation author="EDGAR, R. C." box="[1307,1438,1581,1604]" pageId="2" pageNumber="38" pagination="1792 - 1797" refId="ref12004" refString="EDGAR, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792 - 1797." type="journal article" year="2004">Edgar 2004</bibRefCitation>
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) algorithm and phylogenetic reconstruction was carried out in BEAST v1.10.4 (
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<bibRefCitation author="SUCHARD, M. A. & P. LEMEY & G. BAELE & D. L. AYRES & A. J. DRUMMOND & A. RAMBAUT" box="[1007,1215,1645,1668]" pageId="2" pageNumber="38" refId="ref15702" refString="SUCHARD, M. A., P. LEMEY, G. BAELE, D. L. AYRES, A. J. DRUMMOND, AND A. RAMBAUT. 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution 4: vey 016." type="book" year="2018">Suchard et al. 2018</bibRefCitation>
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) using the best-fit substitution model, GTR+I+G, from jModelTest with a uncorrelated relaxed lognormal clock prior. We used a Coalescent Constant Population tree prior and ran analyses for 40 million generations, sampling every 2,000 generations and excluding a 20% burn-in. Independent runs were assessed in TRACER v1.6.0 (
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<bibRefCitation author="RAMBAUT, A. & M. A. SUCHARD & D. XIE & A. J. DRUMMOND" box="[828,1057,1837,1860]" pageId="2" pageNumber="38" refId="ref15070" refString="RAMBAUT, A., M. A. SUCHARD, D. XIE, AND A. J. DRUMMOND. 2014. TRACER 1.6. www. beast. bio. ed. ac. uk / Tracer. Accessed 23 March 2015." type="book" year="2014">Rambaut et al. 2014</bibRefCitation>
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) ensuring effective sample size (ESS) was above 200 for all parameters and that independent runs had converged.
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</paragraph>
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<paragraph blockId="2.[819,1488,1229,1988]" lastBlockId="3.[144,814,201,480]" lastPageId="3" lastPageNumber="39" pageId="2" pageNumber="38">
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<emphasis box="[845,1126,1933,1956]" italics="true" pageId="2" pageNumber="38">Genetic distance between</emphasis>
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<taxonomicName box="[1137,1323,1933,1956]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="2" pageNumber="38" phylum="Chordata" rank="species" species="undetermined">
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Microtus
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<emphasis box="[1244,1323,1933,1956]" italics="true" pageId="2" pageNumber="38">species.</emphasis>
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</taxonomicName>
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<emphasis box="[1323,1352,1933,1956]" italics="true" pageId="2" pageNumber="38">—</emphasis>
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Pairwise genetic distance (uncorrected
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<emphasis box="[1111,1124,1965,1988]" italics="true" pageId="2" pageNumber="38">p</emphasis>
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-distance and Kimura 2-parameter [K2P]) of
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<emphasis box="[260,310,201,224]" italics="true" pageId="3" pageNumber="39">Cytb</emphasis>
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sequences (excluding
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<taxonomicName baseAuthorityName="Ord" baseAuthorityYear="1815" box="[563,765,201,224]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="3" pageNumber="39" phylum="Chordata" rank="species" species="pennsylvanicus">
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<emphasis box="[563,765,201,224]" italics="true" pageId="3" pageNumber="39">M. pennsylvanicus</emphasis>
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</taxonomicName>
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and its putative sister species
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<taxonomicName baseAuthorityName="Peale" baseAuthorityYear="1848" box="[428,570,233,256]" class="Mammalia" family="Cricetidae" genus="Microtus" kingdom="Animalia" order="Rodentia" pageId="3" pageNumber="39" phylum="Chordata" rank="species" species="montanus">
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<emphasis box="[428,570,233,256]" italics="true" pageId="3" pageNumber="39">M. montanus</emphasis>
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</taxonomicName>
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) was computed using the program MEGA7 (
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<bibRefCitation author="KUMAR, S. & G. STECHER & K. TAMURA" box="[386,577,265,288]" pageId="3" pageNumber="39" pagination="1870 - 1874" refId="ref13603" refString="KUMAR, S., G. STECHER, AND K. TAMURA. 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 et al. 2016</bibRefCitation>
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). All individuals were grouped by species if more than one individual was used in analyses and sister relationships were inferred from our Bayesian phylogeny. Mean between-group distance was computed under both uncorrelated
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<emphasis box="[347,360,393,416]" italics="true" pageId="3" pageNumber="39">p</emphasis>
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-distance and the K2P model; both were computed by bootstrapping with 1,000 replicates, with pairwise deletions for missing data.
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</paragraph>
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</subSubSection>
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</treatment>
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</document> |