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<document id="D5223474C136968F60032BB27460BFDF" ID-DOI="10.1093/zoolinnean/zlae018" ID-ISSN="0024-4082" IM.bibliography_approvedBy="juliana" IM.illustrations_approvedBy="juliana" IM.materialsCitations_approvedBy="juliana" IM.metadata_approvedBy="juliana" IM.tables_approvedBy="juliana" IM.taxonomicNames_approvedBy="juliana" IM.treatments_approvedBy="juliana" checkinTime="1738154100336" checkinUser="plazi" docAuthor="Myers, Edward A., Gehara, Marcelo, Burgoon, Jamie L., McKelvy, Alexander D., Vonnahme, Lauren &amp; Burbrink, Frank T." docDate="2025" docId="03E2AC42FF90FFF7FE1DFB6ADD2FF8D9" docLanguage="en" docName="zlae018.pdf" docOrigin="Zoological Journal of the Linnean Society 203 (1)" docSource="https://doi.org/10.1093/zoolinnean/zlae018" docStyle="DocumentStyle:4F230B9370E98E256D973D6DFB57F36C.10:ZoolJLinnSoc.2023-.journal_article" docStyleId="4F230B9370E98E256D973D6DFB57F36C" docStyleName="ZoolJLinnSoc.2023-.journal_article" docStyleVersion="10" docTitle="Coluber constrictor" docType="treatment" docVersion="1" lastPageNumber="13" masterDocId="FFDBD43AFF96FFFBFF9AFFB5DE29FFFD" masterDocTitle="Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American racers (Colubridae: Coluber constrictor)" masterLastPageNumber="17" masterPageNumber="1" pageNumber="7" updateTime="1739275827928" updateUser="juliana">
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<mods:title id="97996177D070CC3B1381B3594A696EEC">Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American racers (Colubridae: Coluber constrictor)</mods:title>
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<mods:namePart id="5D5FBA1B94E7F57579BE690B15FB1195">Myers, Edward A.</mods:namePart>
<mods:affiliation id="D47FAE052A3ADA47F9316537CEC1757D">Department of Herpetology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118, USA &amp; Department of Herpetology, The American Museum of Natural History, Central Park West and 79 Street, New York, NY 10024, USA</mods:affiliation>
<mods:nameIdentifier id="966CB08B3A7B7E1FCCD0513D53A27899" type="email">eddie.a.myers@gmail.com</mods:nameIdentifier>
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<mods:namePart id="34B24D30AF5546BC228F78E023E41D20">Gehara, Marcelo</mods:namePart>
<mods:affiliation id="CDFA628B0A58BC84D0B1B0E83180A164">Sackler Institute for Comparative Genomics, American Museum of Natural History, NY 10024, USA &amp; Department of Biological Sciences, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA</mods:affiliation>
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<mods:namePart id="556BB9BDC620C617ADE68210DF6C4F61">Burgoon, Jamie L.</mods:namePart>
<mods:affiliation id="A9836312220CD26B7B8DC4C62A6454E8">Department of Herpetology, The American Museum of Natural History, Central Park West and 79 Street, New York, NY 10024, USA</mods:affiliation>
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<mods:namePart id="234555F8BD99B0241FBC85DDEB74BFB2">McKelvy, Alexander D.</mods:namePart>
<mods:affiliation id="3ABDDCAD3A57DF4F8023BCA5EF609649">Department of Biology, The Graduate School and Center, City University of New York, New York, New York 10016, USA &amp; Snake Evolution and Biogeography, Wacissa, FL 32361, USA</mods:affiliation>
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<mods:namePart id="0FBCDC3B11054372FD6B8DF6A68C83ED">Vonnahme, Lauren</mods:namePart>
<mods:affiliation id="5AB84F705622F5A909ACED3A1DB158F9">Department of Herpetology, The American Museum of Natural History, Central Park West and 79 Street, New York, NY 10024, USA</mods:affiliation>
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<mods:affiliation id="3D53DDE99810DE2B381B716E6BACC563">Department of Herpetology, The American Museum of Natural History, Central Park West and 79 Street, New York, NY 10024, USA</mods:affiliation>
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<mods:date id="40D61863038CDD34F99034AAE48D56FF">2025</mods:date>
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<treatment id="03E2AC42FF90FFF7FE1DFB6ADD2FF8D9" LSID="urn:lsid:plazi:treatment:03E2AC42FF90FFF7FE1DFB6ADD2FF8D9" httpUri="http://treatment.plazi.org/id/03E2AC42FF90FFF7FE1DFB6ADD2FF8D9" lastPageId="12" lastPageNumber="13" pageId="6" pageNumber="7">
<subSubSection id="C3514EDFFF90FFFDFE1DFB6ADC2BFB04" box="[391,514,1247,1273]" pageId="6" pageNumber="7" type="nomenclature">
<paragraph id="8BF41D54FF90FFFDFE1DFB6ADC2BFB04" blockId="6.[391,514,1247,1273]" box="[391,514,1247,1273]" pageId="6" pageNumber="7">
<heading id="D0BCAA38FF90FFFDFE1DFB6ADC2BFB04" allCaps="true" bold="true" box="[391,514,1247,1273]" centered="true" fontSize="11" level="1" pageId="6" pageNumber="7" reason="1">
<taxonomicName id="4C4B66D7FF90FFFDFE1DFB6ADC2BFB04" ID-CoL="5ZP35" box="[391,514,1247,1273]" family="Colubridae" genus="Coluber" kingdom="Animalia" order="Squamata" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF90FFFDFE1DFB6ADC2BFB04" bold="true" box="[391,514,1247,1273]" pageId="6" pageNumber="7">RESULTS</emphasis>
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</heading>
</paragraph>
</subSubSection>
<subSubSection id="C3514EDFFF90FFF3FECFFABADB7CFA1A" lastPageId="8" lastPageNumber="9" pageId="6" pageNumber="7" type="description">
<paragraph id="8BF41D54FF90FFFDFECFFABADC1CFAD4" blockId="6.[341,565,1295,1321]" box="[341,565,1295,1321]" pageId="6" pageNumber="7">
<emphasis id="B93FC146FF90FFFDFECFFABADC1CFAD4" bold="true" box="[341,565,1295,1321]" pageId="6" pageNumber="7">Sequence alignments</emphasis>
</paragraph>
<paragraph id="8BF41D54FF90FFFDFF1BFA83DC46F97B" blockId="6.[129,778,1333,1671]" pageId="6" pageNumber="7">
The final assembled dataset consisted of 3417 loci (3348 UCE loci, 61 AHE loci, and eight of the ‘legacy Sanger’ loci). The mean proportion of loci recovered within each sample was 94% (range: 65–97%). The mean length of these assembled loci after trimming was 230.2 base pairs (range: 2–1731) and the mean number of segregating sites was 3.9 (range: 0–30). All raw sequence data have been accessioned on the NCBI Sequence Read Archive (BioProject ID PRJNA1082780; Supporting Information,
<tableCitation id="C6C928EFFF90FFFDFE93F985DF4BF9B5" box="[265,354,1584,1608]" captionStart="Table 1" captionStartId="11.[113,168,143,167]" captionTargetPageId="11" captionText="Table 1. Morphological differences from PERMANOVA." pageId="6" pageNumber="7">Table S1</tableCitation>
). The mtDNA sequence assembled from these raw reads ranged in length from 124 to 7083 bp in length and were trimmed to the 1117 bp length of
<emphasis id="B93FC146FF90FFFDFDA0F9DADC40F97A" box="[570,617,1647,1671]" italics="true" pageId="6" pageNumber="7">Cytb</emphasis>
.
</paragraph>
<paragraph id="8BF41D54FF90FFFDFF08F913DC36F922" blockId="6.[146,760,1702,1759]" pageId="6" pageNumber="7">
<emphasis id="B93FC146FF90FFFDFF08F913DC36F922" bold="true" pageId="6" pageNumber="7">Population structure, phylogenetic relationships, and gene divergence times</emphasis>
</paragraph>
<paragraph id="8BF41D54FF90FFFDFF1BF959DA13FE5E" blockId="6.[129,778,1772,1984]" lastBlockId="6.[825,1475,144,1515]" pageId="6" pageNumber="7">
Results from sNMF analyses indicate that
<emphasis id="B93FC146FF90FFFDFDA4F958DC66F8F9" box="[574,591,1773,1796]" italics="true" pageId="6" pageNumber="7">K</emphasis>
= 5 is the best fit (
<figureCitation id="137001D1FF90FFFDFF11F8BEDEEFF8DE" box="[139,198,1803,1827]" captionStart="Figure 3" captionStartId="7.[113,178,1212,1236]" captionTargetBox="[116,1449,146,1177]" captionTargetId="figure-365@7.[114,1458,144,1179]" captionTargetPageId="7" captionText="Figure 3. A, population structure inferred from the genomic sequence capture data using sNMF. Different colours within the pie charts correspond to admixture coefficients between each of the five lineages; Florida, eastern, central, south Texas, and western. Light grey highlighting represents the geographic distribution of Coluber constrictor. B, results of admixture coefficients from sNMF represented as a bar plot where each bar is a sampled individual.C, PCA of the genomic data demonstrating the differentiation of these phylogeographic lineages. D, SplitsTree network showing population structure and nestedness of these populations." pageId="6" pageNumber="7">Fig. 3</figureCitation>
). These five populations correspond to a population in peninsular
<collectingRegion id="498FD3B6FF90FFFDFF69F89EDF69F8BE" box="[243,320,1835,1859]" country="United States of America" name="Florida" pageId="6" pageNumber="7">Florida</collectingRegion>
, an eastern population in the temperate deciduous forests, a central population within the
<collectingMunicipality id="6B90872EFF90FFFDFDFBF8FFDD20F89F" box="[609,777,1866,1890]" pageId="6" pageNumber="7">North American</collectingMunicipality>
grasslands, a western population isolated across the
<location id="8E944B8FFF90FFFDFD52F8DCDEDBF85C" LSID="urn:lsid:plazi:treatment:03E2AC42FF90FFF7FE1DFB6ADD2FF8D9:8E944B8FFF90FFFDFD52F8DCDEDBF85C" municipality="North American" name="Rocky Mountains" pageId="6" pageNumber="7" stateProvince="Florida">Rocky Mountains</location>
, and a population from south
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. Hereafter these populations will be referred to as the
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, eastern, central, western, and south
<collectingRegion id="498FD3B6FF90FFFDFB96FF25DA6FFF5A" box="[1036,1094,144,167]" country="United States of America" name="Texas" pageId="6" pageNumber="7">Texas</collectingRegion>
populations, respectively. The PCA plot was visualized with the
<emphasis id="B93FC146FF90FFFDFBC3FF05DA43FF3A" box="[1113,1130,176,199]" italics="true" pageId="6" pageNumber="7">K</emphasis>
= 5 population structure inferred from sNMF (
<figureCitation id="137001D1FF90FFFDFC5CFF7ADDD6FF1A" box="[966,1023,207,231]" captionStart="Figure 3" captionStartId="7.[113,178,1212,1236]" captionTargetBox="[116,1449,146,1177]" captionTargetId="figure-365@7.[114,1458,144,1179]" captionTargetPageId="7" captionText="Figure 3. A, population structure inferred from the genomic sequence capture data using sNMF. Different colours within the pie charts correspond to admixture coefficients between each of the five lineages; Florida, eastern, central, south Texas, and western. Light grey highlighting represents the geographic distribution of Coluber constrictor. B, results of admixture coefficients from sNMF represented as a bar plot where each bar is a sampled individual.C, PCA of the genomic data demonstrating the differentiation of these phylogeographic lineages. D, SplitsTree network showing population structure and nestedness of these populations." pageId="6" pageNumber="7">Fig. 3</figureCitation>
). This plot shows clear separation of all five lineages, with only some overlap in PC space between the central and western populations. The network inferred from SplitsTree largely identifies these clusters, albeit with some degree of nestedness (
<figureCitation id="137001D1FF90FFFDFC26FEF9DA23FE99" box="[956,1034,332,356]" captionStart="Figure 3" captionStartId="7.[113,178,1212,1236]" captionTargetBox="[116,1449,146,1177]" captionTargetId="figure-365@7.[114,1458,144,1179]" captionTargetPageId="7" captionText="Figure 3. A, population structure inferred from the genomic sequence capture data using sNMF. Different colours within the pie charts correspond to admixture coefficients between each of the five lineages; Florida, eastern, central, south Texas, and western. Light grey highlighting represents the geographic distribution of Coluber constrictor. B, results of admixture coefficients from sNMF represented as a bar plot where each bar is a sampled individual.C, PCA of the genomic data demonstrating the differentiation of these phylogeographic lineages. D, SplitsTree network showing population structure and nestedness of these populations." pageId="6" pageNumber="7">Fig. 3D</figureCitation>
). For example, the western population is nested within the central group, while the eastern population is divided into two clusters.
</paragraph>
<paragraph id="8BF41D54FF90FFFDFCCFFE1FDA4AFBA9" blockId="6.[825,1475,144,1515]" pageId="6" pageNumber="7">
The SNAPP-based species tree recovered a pectinate phylogeny with divergences as follows: south
<collectingRegion id="498FD3B6FF90FFFDFA90FE7FDB6FFE1C" box="[1290,1350,458,481]" country="United States of America" name="Texas" pageId="6" pageNumber="7">Texas</collectingRegion>
, peninsular
<collectingRegion id="498FD3B6FF90FFFDFCA3FE5CDDAFFDFC" box="[825,902,489,513]" country="United States of America" name="Florida" pageId="6" pageNumber="7">Florida</collectingRegion>
, eastern, and a sister-relationship between the western and central populations (
<figureCitation id="137001D1FF90FFFDFBACFDBDDA44FDDD" box="[1078,1133,520,544]" captionStart="Figure 4" captionStartId="8.[129,194,1087,1111]" captionTargetBox="[132,1470,146,1055]" captionTargetId="figure-397@8.[129,1473,144,1059]" captionTargetPageId="8" captionText="Figure 4. Gene trees and species tree based on sequence capture and by-catch mtDNA data. A, maximum likelihood concatenated tree inferred from phased sequence capture data. B, species’ tree based on SNPs from assembled genomic data inferred using SNAPP. C, divergence dated tree from BEAST based on concatenated genomic sequence data.D, maximum likelihood mtDNA phylogeny for nearly all samples for which sequence capture data was generated.E, dated mtDNA gene tree inferred in BEAST including representative species from the sistergenus Masticophis. In (A) and (D) black circles at nodes represent bootstrap support values ≥95 and in (C), (D), and (E) represent posterior probabilities ≥0.9." pageId="6" pageNumber="7">Fig. 4</figureCitation>
). All relationships within this tree were strongly supported with posterior probabilities ≥0.99. All ESS values from this analysis were&gt;200 as assessed in TRACER v.1.7.1 (
<bibRefCitation id="EFDA60A5FF90FFFDFC16FDD3DA75FD83" author="Rambaut A &amp; Drummond AJ &amp; Xie D" box="[908,1116,614,638]" pageId="6" pageNumber="7" pagination="901 - 4" refId="ref15953" refString="Rambaut A, Drummond AJ, Xie D et al. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 2018; 67: 901 - 4. htps: // doi. org / 10.1093 / sysbio / syy 032" type="journal article" year="2018">
Rambaut
<emphasis id="B93FC146FF90FFFDFC68FDD2DA0BFD83" box="[1010,1058,614,638]" italics="true" pageId="6" pageNumber="7">et al.</emphasis>
2018
</bibRefCitation>
). The concatenated phylogenomic tree from IQ-Tree, while finding each of these populations as a cluster, differs in their relationships. Here the monophyletic western population is nested within the central lineage, the eastern and
<collectingRegion id="498FD3B6FF90FFFDFC23FD56DA2DFD06" box="[953,1028,739,763]" country="United States of America" name="Florida" pageId="6" pageNumber="7">Florida</collectingRegion>
populations are sister-taxa, with the south
<collectingRegion id="498FD3B6FF90FFFDFCA3FCB6DD5AFCE7" box="[825,883,771,794]" country="United States of America" name="Texas" pageId="6" pageNumber="7">Texas</collectingRegion>
population being the earliest diverging group; again, these relationships are well supported (bootstrap ≥ 90). Within the concatenated tree there are two samples that have ‘ladder-like’ relationships between the eastern and
<collectingRegion id="498FD3B6FF90FFFDFB26FCD4DB2EFC84" box="[1212,1287,865,889]" country="United States of America" name="Florida" pageId="6" pageNumber="7">Florida</collectingRegion>
lineages, and both samples have high admixture proportions from sNMF (LSU-H2967 and FTB2688; both assigned to the eastern population). The mtDNA gene tree recovered the same phylogenetic relationships as the coalescent-based species tree, with moderate to high support (
<figureCitation id="137001D1FF90FFFDFC00FC48DDFAFBE8" box="[922,979,1021,1045]" captionStart="Figure 4" captionStartId="8.[129,194,1087,1111]" captionTargetBox="[132,1470,146,1055]" captionTargetId="figure-397@8.[129,1473,144,1059]" captionTargetPageId="8" captionText="Figure 4. Gene trees and species tree based on sequence capture and by-catch mtDNA data. A, maximum likelihood concatenated tree inferred from phased sequence capture data. B, species’ tree based on SNPs from assembled genomic data inferred using SNAPP. C, divergence dated tree from BEAST based on concatenated genomic sequence data.D, maximum likelihood mtDNA phylogeny for nearly all samples for which sequence capture data was generated.E, dated mtDNA gene tree inferred in BEAST including representative species from the sistergenus Masticophis. In (A) and (D) black circles at nodes represent bootstrap support values ≥95 and in (C), (D), and (E) represent posterior probabilities ≥0.9." pageId="6" pageNumber="7">Fig. 4</figureCitation>
). One sample (LSU H-2967) clustered with the eastern lineage samples using genomic data but mtDNA originated from the eastern lineage.
</paragraph>
<paragraph id="8BF41D54FF90FFFDFCCFFBEEDAC7FA16" blockId="6.[825,1475,144,1515]" pageId="6" pageNumber="7">
Divergence times were estimated based on both a single locus mtDNA dataset and the concatenated genomic data (
<figureCitation id="137001D1FF90FFFDFAEFFBCEDB98FB6E" box="[1397,1457,1147,1171]" captionStart="Figure 4" captionStartId="8.[129,194,1087,1111]" captionTargetBox="[132,1470,146,1055]" captionTargetId="figure-397@8.[129,1473,144,1059]" captionTargetPageId="8" captionText="Figure 4. Gene trees and species tree based on sequence capture and by-catch mtDNA data. A, maximum likelihood concatenated tree inferred from phased sequence capture data. B, species’ tree based on SNPs from assembled genomic data inferred using SNAPP. C, divergence dated tree from BEAST based on concatenated genomic sequence data.D, maximum likelihood mtDNA phylogeny for nearly all samples for which sequence capture data was generated.E, dated mtDNA gene tree inferred in BEAST including representative species from the sistergenus Masticophis. In (A) and (D) black circles at nodes represent bootstrap support values ≥95 and in (C), (D), and (E) represent posterior probabilities ≥0.9." pageId="6" pageNumber="7">Fig. 4</figureCitation>
). The mtDNA analysis suggests that
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<emphasis id="B93FC146FF90FFFDFB3DFB2FDADDFB4F" box="[1191,1268,1178,1202]" italics="true" pageId="6" pageNumber="7">Coluber</emphasis>
</taxonomicName>
and
<taxonomicName id="4C4B66D7FF90FFFDFAB0FB2FDBB6FB4F" authorityName="Baird &amp; Girard" authorityYear="1853" box="[1322,1439,1178,1202]" class="Reptilia" family="Colubridae" genus="Masticophis" higherTaxonomySource="GBIF" kingdom="Animalia" order="Squamata" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B93FC146FF90FFFDFAB0FB2FDBB6FB4F" box="[1322,1439,1178,1202]" italics="true" pageId="6" pageNumber="7">Masticophis</emphasis>
</taxonomicName>
diverged 10.8 Mya (95% HPD: 8.9–12.7 Mya). In this gene tree, the earliest divergence within
<taxonomicName id="4C4B66D7FF90FFFDFBEEFB6DDAE8FB0D" box="[1140,1217,1240,1264]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B93FC146FF90FFFDFBEEFB6DDAE8FB0D" box="[1140,1217,1240,1264]" italics="true" pageId="6" pageNumber="7">Coluber</emphasis>
</taxonomicName>
occurred 8.2 Mya (6.3– 10.2 Mya), corresponding to the south
<collectingRegion id="498FD3B6FF90FFFDFB5EFB4DDAD7FAF2" box="[1220,1278,1272,1295]" country="United States of America" name="Texas" pageId="6" pageNumber="7">Texas</collectingRegion>
lineage divergence, demonstrating that these lineages began diversifying during the Mid to Late Miocene. The concatenated genomic analysis also suggests that
<taxonomicName id="4C4B66D7FF90FFFDFC6BFAE3DA17FA93" box="[1009,1086,1366,1390]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B93FC146FF90FFFDFC6BFAE3DA17FA93" box="[1009,1086,1366,1390]" italics="true" pageId="6" pageNumber="7">Coluber</emphasis>
</taxonomicName>
began diversifying in the Mid to Late Miocene with an estimated crown age of 10.7 Mya (8.7–12.8 Mya;
<figureCitation id="137001D1FF90FFFDFCE3FA21DD9EFA50" box="[889,951,1428,1453]" captionStart="Figure 4" captionStartId="8.[129,194,1087,1111]" captionTargetBox="[132,1470,146,1055]" captionTargetId="figure-397@8.[129,1473,144,1059]" captionTargetPageId="8" captionText="Figure 4. Gene trees and species tree based on sequence capture and by-catch mtDNA data. A, maximum likelihood concatenated tree inferred from phased sequence capture data. B, species’ tree based on SNPs from assembled genomic data inferred using SNAPP. C, divergence dated tree from BEAST based on concatenated genomic sequence data.D, maximum likelihood mtDNA phylogeny for nearly all samples for which sequence capture data was generated.E, dated mtDNA gene tree inferred in BEAST including representative species from the sistergenus Masticophis. In (A) and (D) black circles at nodes represent bootstrap support values ≥95 and in (C), (D), and (E) represent posterior probabilities ≥0.9." pageId="6" pageNumber="7">Fig. 4</figureCitation>
). The youngest divergence times between these phylogeographic lineages occurred 6.2 Mya (3.3–8.9 Mya) between the western and central populations.
</paragraph>
<paragraph id="8BF41D54FF90FFFDFCCEF9BEDB81F9D8" blockId="6.[852,1448,1547,1573]" box="[852,1448,1547,1573]" pageId="6" pageNumber="7">
<emphasis id="B93FC146FF90FFFDFCCEF9BEDB81F9D8" bold="true" box="[852,1448,1547,1573]" pageId="6" pageNumber="7">Demographic model selection and parameter estimation</emphasis>
</paragraph>
<paragraph id="8BF41D54FF90FFFDFCA3F987DA69F8D8" blockId="6.[825,1475,1585,1986]" pageId="6" pageNumber="7">The trained neural network classified the six models with relatively low accuracy (0.82) due to confusion among the ancient divergence models. This unidentifiability among the ancient divergence models is more evident in the classification using the mtDNA alone where the accuracy was 0.44. When comparing one of the five ancient divergence models with the recent divergence model (Is), the accuracy was 1.0 for the genomic data and 0.88 for the mtDNA data.</paragraph>
<paragraph id="8BF41D54FF90FFFCFCCFF899DF85F923" blockId="6.[825,1475,1585,1986]" lastBlockId="7.[113,762,1420,1758]" lastPageId="7" lastPageNumber="8" pageId="6" pageNumber="7">
The genomic data strongly supports the model with recent divergence without migration (Is), with a probability of ~1.0. Parameter estimates from this model suggest that lineage divergence of all populations occurred ~33 kya (25–43 kya 95% confidence interval) with no gene flow. These estimates also suggest small effective population sizes for the western and central populations and larger population sizes for the eastern and
<collectingRegion id="498FD3B6FF91FFFCFFEBFA7EDE95FA1E" box="[113,188,1483,1507]" country="United States of America" name="Florida" pageId="7" pageNumber="8">Florida</collectingRegion>
populations, with a much stronger population size increase in the latter two. The timing of population size change also shows a more recent demographic change for the western population. These parameter estimates are available in the Supporting Information (Table S4;
<figureCitation id="137001D1FF91FFFCFEF3F9FDDF99F99D" box="[361,432,1608,1632]" captionStart="Figure 2" captionStartId="4.[129,194,1129,1153]" captionTargetBox="[131,1470,146,1097]" captionTargetId="figure-479@4.[129,1473,144,1100]" captionTargetPageId="4" captionText="Figure 2. The six demographic models tested in PipeMaster using supervised machine learning. The four isolation-with-migration (IMD) models differ in topology or whether migration was restricted to geographically adjacent lineages only. IS represents a recent isolation without migration model." pageId="7" pageNumber="8">Fig. S2</figureCitation>
). By contrast, the mtDNA data support one of the ancient IMD models, with the model where the western population is sister to the central population and the eastern population is sister to the
<collectingRegion id="498FD3B6FF91FFFCFE5FF913DC39F943" box="[453,528,1702,1726]" country="United States of America" name="Florida" pageId="7" pageNumber="8">Florida</collectingRegion>
population, having the highest probability (
<emphasis id="B93FC146FF91FFFCFED8F973DF79F920" box="[322,336,1734,1757]" italics="true" pageId="7" pageNumber="8">P</emphasis>
= 0.43).
</paragraph>
<caption id="DF344DDCFF91FFFCFFEBFB09DD91FAB9" pageId="7" pageNumber="8" startId="7.[113,178,1212,1236]" targetBox="[116,1449,146,1177]" targetPageId="7" targetType="figure">
<paragraph id="8BF41D54FF91FFFCFFEBFB09DD91FAB9" blockId="7.[113,1438,1212,1348]" pageId="7" pageNumber="8">
<emphasis id="B93FC146FF91FFFCFFEBFB09DEE0FB29" bold="true" box="[113,201,1212,1236]" pageId="7" pageNumber="8">Figure 3.</emphasis>
A, population structure inferred from the genomic sequence capture data using sNMF. Different colours within the pie charts correspond to admixture coefficients between each of the five lineages; Florida, eastern, central, south Texas, and western. Light grey highlighting represents the geographic distribution of
<taxonomicName id="4C4B66D7FF91FFFCFDF7FB41DD3EFAF1" box="[621,791,1268,1292]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF91FFFCFDF7FB41DD3EFAF1" box="[621,791,1268,1292]" italics="true" pageId="7" pageNumber="8">Coluber constrictor</emphasis>
</taxonomicName>
. B, results of admixture coefficients from sNMF represented as a bar plot where each bar is a sampled individual. C, PCA of the genomic data demonstrating the differentiation of these phylogeographic lineages. D, SplitsTree network showing population structure and nestedness of these populations.
</paragraph>
</caption>
<paragraph id="8BF41D54FF91FFFCFF79F948DCA0F8EA" blockId="7.[227,649,1789,1815]" box="[227,649,1789,1815]" pageId="7" pageNumber="8">
<emphasis id="B93FC146FF91FFFCFF79F948DCA0F8EA" bold="true" box="[227,649,1789,1815]" pageId="7" pageNumber="8">Ecological niche models and divergence</emphasis>
</paragraph>
<paragraph id="8BF41D54FF91FFFCFFEBF891DD97F962" blockId="7.[113,762,1828,1977]" lastBlockId="7.[810,1461,1420,1977]" pageId="7" pageNumber="8">
After thinning locality records, we retained
<specimenCount id="9D4DD6DDFF91FFFCFDADF891DC93F8C1" box="[567,698,1828,1852]" count="28" pageId="7" pageNumber="8" type="generic">28 specimen</specimenCount>
localities for the south
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population, 116 for the
<collectingRegion id="498FD3B6FF91FFFCFDF1F8F6DC9FF8A6" box="[619,694,1859,1883]" country="United States of America" name="Florida" pageId="7" pageNumber="8">Florida</collectingRegion>
population, 138 for the western, 431 for the central, and 463 for the eastern (localities and associated natural history specimen numbers are accessioned on Dryad).
<collectingCounty id="629565D8FF91FFFCFE6CF814DC3DF844" box="[502,532,1953,1977]" pageId="7" pageNumber="8">All</collectingCounty>
comparisons of niche equivalency were significant but suggest varying levels of divergence in ecological niche between lineages.
<collectingMunicipality id="6B90872EFF91FFFCFA96FA19DB1AFA3E" box="[1292,1331,1452,1475]" pageId="7" pageNumber="8">The</collectingMunicipality>
greatest differences were between the
<collectingRegion id="498FD3B6FF91FFFCFBDEFA7EDAA6FA1E" box="[1092,1167,1483,1507]" country="United States of America" name="Florida" pageId="7" pageNumber="8">Florida</collectingRegion>
and the eastern lineages (
<emphasis id="B93FC146FF91FFFCFA3AFA79DB9AFA1E" box="[1440,1459,1484,1507]" italics="true" pageId="7" pageNumber="8">D</emphasis>
statistic = 0.02,
<emphasis id="B93FC146FF91FFFCFC49FA5EDDC9F9FF" box="[979,992,1515,1538]" italics="true" pageId="7" pageNumber="8">P</emphasis>
-value = 0.01) and between the central and south
<collectingRegion id="498FD3B6FF91FFFCFCF5F9BFDD80F9DC" box="[879,937,1546,1569]" country="United States of America" name="Texas" pageId="7" pageNumber="8">Texas</collectingRegion>
lineage (
<emphasis id="B93FC146FF91FFFCFB8BF9BFDA0DF9DC" box="[1041,1060,1546,1569]" italics="true" pageId="7" pageNumber="8">D</emphasis>
statistic = 0.03,
<emphasis id="B93FC146FF91FFFCFB42F9BFDACCF9DC" box="[1240,1253,1546,1569]" italics="true" pageId="7" pageNumber="8">P</emphasis>
-value = 0.01).
<location id="8E944B8FFF91FFFCFA13F9BFDB9CF9DF" LSID="urn:lsid:plazi:treatment:03E2AC42FF90FFF7FE1DFB6ADD2FF8D9:8E944B8FFF91FFFCFA13F9BFDB9CF9DF" box="[1417,1461,1546,1570]" county="All" municipality="Te" name="Tis" pageId="7" pageNumber="8" stateProvince="Texas">This</location>
test suggests that both the eastern and central lineages (
<emphasis id="B93FC146FF91FFFCFAF4F99FDBA8F9BC" box="[1390,1409,1578,1601]" italics="true" pageId="7" pageNumber="8">D</emphasis>
statistic = 0.14,
<emphasis id="B93FC146FF91FFFCFC34F9FCDD92F99D" box="[942,955,1609,1632]" italics="true" pageId="7" pageNumber="8">P</emphasis>
-value = 0.01), and the central and western lineages (
<emphasis id="B93FC146FF91FFFCFCE9F9DDDDAFF982" box="[883,902,1640,1663]" italics="true" pageId="7" pageNumber="8">D</emphasis>
statistic = 0.27,
<emphasis id="B93FC146FF91FFFCFBA9F9DDDA69F982" box="[1075,1088,1640,1663]" italics="true" pageId="7" pageNumber="8">P</emphasis>
-value = 0.01), occupy more similar environments.
</paragraph>
<paragraph id="8BF41D54FF91FFF3FCDFF913DC89FA97" blockId="7.[810,1461,1420,1977]" lastBlockId="8.[129,777,1299,1386]" lastPageId="8" lastPageNumber="9" pageId="7" pageNumber="8">
Each lineage had a unique, best-fit combination of feature class and regularization multipliers (Supporting Information, Table S5) that were used to construct ENMs in MaxEnt. All ENMs performed well with high area under the receiver operating characteristic curve values (AUC = 0.89 for south
<collectingRegion id="498FD3B6FF91FFFCFAA7F891DB53F8C6" box="[1341,1402,1828,1851]" country="United States of America" name="Texas" pageId="7" pageNumber="8">Texas</collectingRegion>
; 0.99 for
<collectingRegion id="498FD3B6FF91FFFCFCCAF8F6DDB2F8A6" box="[848,923,1859,1883]" country="United States of America" name="Florida" pageId="7" pageNumber="8">Florida</collectingRegion>
population; 0.96 for eastern; 0.93 for central; 0.96 for western). All ENMs predict the geographic distribution of the focal lineage with little overlap in predicted geographic distribution between geographically adjacent populations (
<figureCitation id="137001D1FF91FFFCFAF3F814DB8BF844" box="[1385,1442,1953,1977]" captionStart="Figure 5" captionStartId="9.[114,179,1008,1032]" captionTargetBox="[117,1456,145,978]" captionTargetId="figure-517@9.[114,1458,144,980]" captionTargetPageId="9" captionText="Figure 5. Ecological niche models constructed for each of the five phylogeographic lineages based on current climate and paleo-climate models from ~21 kya. All panels are labelled with their corresponding lineage and if they correspond to late Pleistocene projections. Regions shaded in green are those that were inferred to have higher environmental suitability for each lineage based on locality data used in the ENMs." pageId="7" pageNumber="8">Fig. 5</figureCitation>
). ENMs projected on to the Mid-Pleistocene suggests that all five lineages would have had reduced geographic distributions into refugia that were allopatric from one another (
<figureCitation id="137001D1FF9EFFF3FDCDFAE7DCA6FA97" box="[599,655,1362,1386]" captionStart="Figure 5" captionStartId="9.[114,179,1008,1032]" captionTargetBox="[117,1456,145,978]" captionTargetId="figure-517@9.[114,1458,144,980]" captionTargetPageId="9" captionText="Figure 5. Ecological niche models constructed for each of the five phylogeographic lineages based on current climate and paleo-climate models from ~21 kya. All panels are labelled with their corresponding lineage and if they correspond to late Pleistocene projections. Regions shaded in green are those that were inferred to have higher environmental suitability for each lineage based on locality data used in the ENMs." pageId="8" pageNumber="9">Fig. 5</figureCitation>
).
</paragraph>
<caption id="DF344DDCFF9EFFF3FF1BFB8ADF04FB19" pageId="8" pageNumber="9" startId="8.[129,194,1087,1111]" targetBox="[132,1470,146,1055]" targetPageId="8" targetType="figure">
<paragraph id="8BF41D54FF9EFFF3FF1BFB8ADF04FB19" blockId="8.[129,1470,1087,1252]" pageId="8" pageNumber="9">
<emphasis id="B93FC146FF9EFFF3FF1BFB8ADEF1FBAA" bold="true" box="[129,216,1087,1111]" pageId="8" pageNumber="9">Figure 4.</emphasis>
Gene trees and species tree based on sequence capture and by-catch mtDNA data. A, maximum likelihood concatenated tree inferred from phased sequence capture data. B, species’ tree based on SNPs from assembled genomic data inferred using SNAPP. C, divergence dated tree from BEAST based on concatenated genomic sequence data. D, maximum likelihood mtDNA phylogeny for nearly all samples for which sequence capture data was generated. E, dated mtDNA gene tree inferred in BEAST including representative species from the sistergenus
<taxonomicName id="4C4B66D7FF9EFFF3FF26FB05DF01FB35" authorityName="Baird &amp; Girard" authorityYear="1853" box="[188,296,1200,1224]" class="Reptilia" family="Colubridae" genus="Masticophis" higherTaxonomySource="GBIF" kingdom="Animalia" order="Squamata" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B93FC146FF9EFFF3FF26FB05DF01FB35" box="[188,296,1200,1224]" italics="true" pageId="8" pageNumber="9">Masticophis</emphasis>
</taxonomicName>
. In (A) and (D) black circles at nodes represent bootstrap support values ≥95 and in (C), (D), and (E) represent posterior probabilities ≥0.9.
</paragraph>
</caption>
<paragraph id="8BF41D54FF9EFFF3FEA3FA3CDC78FA5E" blockId="8.[313,593,1417,1443]" box="[313,593,1417,1443]" pageId="8" pageNumber="9">
<emphasis id="B93FC146FF9EFFF3FEA3FA3CDC78FA5E" bold="true" box="[313,593,1417,1443]" pageId="8" pageNumber="9">Morphological divergence</emphasis>
</paragraph>
<paragraph id="8BF41D54FF9EFFF3FF1BFA05DB7CFA1A" blockId="8.[129,780,1456,1981]" lastBlockId="8.[825,1474,1299,1511]" pageId="8" pageNumber="9">
Sexual dimorphism was found in tail length, head width and length, eye diameter, and rostral length (
<emphasis id="B93FC146FF9EFFF3FDC1FA65DC40FA1A" box="[603,617,1488,1511]" italics="true" pageId="8" pageNumber="9">P</emphasis>
-values &lt;0.05). Principal component analyses are significant (
<emphasis id="B93FC146FF9EFFF3FDEEFA45DCABF9FA" box="[628,642,1520,1543]" italics="true" pageId="8" pageNumber="9">P</emphasis>
-value = 0 in both cases); however, there is no clear pattern of separation between lineages (
<figureCitation id="137001D1FF9EFFF3FEBEF998DF75F9B8" box="[292,348,1581,1605]" captionStart="Figure 6" captionStartId="10.[129,194,1908,1932]" captionTargetBox="[257,1343,152,1875]" captionTargetId="figure-7@10.[254,1346,149,1877]" captionTargetPageId="10" captionText="Figure 6. Morphological differentiation between phylogeographic lineages in Coluber constrictor. A, B, PCA of morphological variables; A, males; B, females. C, D, are boxplots of each linear measurement showing the differentiation of each of these traits between the five lineages:C, represents males; D, females. In panels (C) and (D), pairwise comparisons significant at an adjusted P &lt;.05 with a Tukey’s honest significant difference test are indicated by letters, where shared letters indicate that pair-wise comparisons are significantly different." pageId="8" pageNumber="9">Fig. 6</figureCitation>
). PC1 accounts for 39.1% of variation and PC2 for 19.7% variation in males, with the highest loadings contributed to head width, length, and eye diameter in PC1 and SVL in PC2. Within females, PC1 accounts for 41.0% of the total variation and PC2 for 16.7%, with the highest loadings contributed to head width, head length, rostral length, prefrontal width, and internasal width on PC1. Using PERMANOVA tests, males of the eastern and
<collectingRegion id="498FD3B6FF9EFFF3FEBDF8BCDF5BF8DC" box="[295,370,1801,1825]" country="United States of America" name="Florida" pageId="8" pageNumber="9">Florida</collectingRegion>
lineages are significantly different from the other three lineages but not distinct from one another in morphology; similarly, the central, western, and south
<collectingRegion id="498FD3B6FF9EFFF3FD32F8FDDCCBF8A2" box="[680,738,1864,1887]" country="United States of America" name="Texas" pageId="8" pageNumber="9">Texas</collectingRegion>
lineages are indistinguishable (
<tableCitation id="C6C928EFFF9EFFF3FE04F8D2DFC1F882" box="[414,488,1895,1919]" captionStart="Table 1" captionStartId="11.[113,168,143,167]" captionTargetPageId="11" captionText="Table 1. Morphological differences from PERMANOVA." pageId="8" pageNumber="9">Table 1</tableCitation>
). PERMANOVA tests demonstrate that with morphological data from females, the eastern lineage is distinct from the western and south
<collectingRegion id="498FD3B6FF9EFFF3FDEAF813DC83F840" box="[624,682,1958,1981]" country="United States of America" name="Texas" pageId="8" pageNumber="9">Texas</collectingRegion>
lineages, and the
<collectingRegion id="498FD3B6FF9EFFF3FC0BFAA6DDF5FAD6" box="[913,988,1299,1323]" country="United States of America" name="Florida" pageId="8" pageNumber="9">Florida</collectingRegion>
lineage is distinct from the south
<collectingRegion id="498FD3B6FF9EFFF3FADCFAA1DBA9FAD6" box="[1350,1408,1300,1323]" country="United States of America" name="Texas" pageId="8" pageNumber="9">Texas</collectingRegion>
clade, whereas all other comparisons were not significant (
<tableCitation id="C6C928EFFF9EFFF3FAF9FA86DB98FAB6" box="[1379,1457,1331,1355]" captionStart="Table 1" captionStartId="11.[113,168,143,167]" captionTargetPageId="11" captionText="Table 1. Morphological differences from PERMANOVA." pageId="8" pageNumber="9">Table 1</tableCitation>
). Discriminant function analysis with cross-validation demonstrates that these lineages can be differentiated from one another with an accuracy of 56.2% in males and 47.5% in females. In all attempts to classify specimens, there are misclassifications between all lineages using both morphological datasets.
</paragraph>
</subSubSection>
<subSubSection id="C3514EDFFF9EFFF7FBBEF9ABDD2FF8D9" lastPageId="12" lastPageNumber="13" pageId="8" pageNumber="9" type="discussion">
<paragraph id="8BF41D54FF9EFFF3FBBEF9ABDAF1F9C5" blockId="8.[1060,1240,1566,1592]" box="[1060,1240,1566,1592]" pageId="8" pageNumber="9">
<heading id="D0BCAA38FF9EFFF3FBBEF9ABDAF1F9C5" allCaps="true" bold="true" box="[1060,1240,1566,1592]" centered="true" fontSize="11" level="1" pageId="8" pageNumber="9" reason="1">
<emphasis id="B93FC146FF9EFFF3FBBEF9ABDAF1F9C5" bold="true" box="[1060,1240,1566,1592]" pageId="8" pageNumber="9">DISCUSSION</emphasis>
</heading>
</paragraph>
<paragraph id="8BF41D54FF9EFFF2FCA3F9FFDCE6FA5F" blockId="8.[825,1475,1610,1979]" lastBlockId="9.[113,762,1136,1443]" lastPageId="9" lastPageNumber="10" pageId="8" pageNumber="9">
Previous studies have suggested morphological variation and extensive population genetic structure across the distribution of the North American racers (e.g.
<bibRefCitation id="EFDA60A5FF9EFFF3FB0BF93CDB66F95C" author="Ortenburger AI" box="[1169,1359,1673,1697]" pageId="8" pageNumber="9" refId="ref15349" refString="Ortenburger AI. Te Whip Snakes and Racers: Genera Masticophis and Coluber. Ann Arbor, MI: Memoirs of the University of Michigan Museums, 1928." type="book" year="1928">Ortenburger 1928</bibRefCitation>
, Anderson 1996,
<bibRefCitation id="EFDA60A5FF9EFFF3FCE0F91DDA60F93D" author="Burbrink FT &amp; Fontanella F &amp; Pyron R" box="[890,1097,1704,1728]" pageId="8" pageNumber="9" pagination="274 - 88" refId="ref12057" refString="Burbrink FT, Fontanella F, Pyron R et al. Phylogeography across a continent: the evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor). Molecular Phylogenetics and Evolution 2008; 47: 274 - 88." type="journal article" year="2008">
Burbrink
<emphasis id="B93FC146FF9EFFF3FC44F91CDA26F93D" box="[990,1039,1704,1728]" italics="true" pageId="8" pageNumber="9">et al.</emphasis>
2008
</bibRefCitation>
). Here we corroborate much of this lineage divergence using a combination of genomic sequence capture data, mtDNA, morphology, and ecological niche models. We demonstrate that this structure corresponds to several well-known biogeographic barriers across North America. The genome-scale data and mtDNA show similar geographic lineages and largely agree in the phylogenetic relationships among these lineages. However, demographic models based on the genomic data strongly disagree with the best-fit model to the mtDNA in divergence times and topology. Furthermore, comparing divergence times estimated from mtDNA and concatenated genomic data to the divergence times estimated from demographic models suggests that these discrepancies are the result of differences between gene- vs. coalescent-divergence time estimates. Additionally, we find that several of these lineages are distinguishable morphologically, largely across the
<collectingRegion id="498FD3B6FF9FFFF2FD12FA99DCD3FAB9" box="[648,762,1324,1348]" country="United States of America" name="Mississippi" pageId="9" pageNumber="10">Mississippi</collectingRegion>
River, and several adjacent population pairs have diverged in environmental niche. Lastly, hindcast ENMs suggest that all lineages were distributed allopatrically in the Mid-Pleistocene.
</paragraph>
<caption id="DF344DDCFF9FFFF2FFE8FC45DB6CFBBD" pageId="9" pageNumber="10" startId="9.[114,179,1008,1032]" targetBox="[117,1456,145,978]" targetPageId="9" targetType="figure">
<paragraph id="8BF41D54FF9FFFF2FFE8FC45DB6CFBBD" blockId="9.[113,1457,1008,1089]" pageId="9" pageNumber="10">
<emphasis id="B93FC146FF9FFFF2FFE8FC45DEE0FBF4" bold="true" box="[114,201,1008,1033]" pageId="9" pageNumber="10">Figure 5.</emphasis>
Ecological niche models constructed for each of the five phylogeographic lineages based on current climate and paleo-climate models from ~21 kya. All panels are labelled with their corresponding lineage and if they correspond to late Pleistocene projections. Regions shaded in green are those that were inferred to have higher environmental suitability for each lineage based on locality data used in the ENMs.
</paragraph>
</caption>
<paragraph id="8BF41D54FF9FFFF2FE8CFA77DC7FFA21" blockId="9.[278,598,1474,1500]" box="[278,598,1474,1500]" pageId="9" pageNumber="10">
<emphasis id="B93FC146FF9FFFF2FE8CFA77DC7FFA21" bold="true" box="[278,598,1474,1500]" pageId="9" pageNumber="10">Demographic model selection</emphasis>
</paragraph>
<paragraph id="8BF41D54FF9FFFF2FFEBFA5DDF83F82A" blockId="9.[113,764,1512,2007]" pageId="9" pageNumber="10">
Model selection approaches were ambiguous to the evolutionary and demographic history of the North American racers. First, the best-fit model, that of recent divergence and no gene flow, could not determine the phylogenetic relationships among these lineages and instead suggested that a polytomy best represented the divergence history. Second, the timing of divergence and amount of gene flow is unclear; the model of recent divergence (~33 kya) obtained the highest support (
<emphasis id="B93FC146FF9FFFF2FD8BF971DC36F926" box="[529,543,1732,1755]" italics="true" pageId="9" pageNumber="10">P</emphasis>
= 1.0), contradicting results based on mtDNA and concatenation, where divergence was estimated to be several orders of magnitude older. This conundrum is unsatisfying given that the goal of phylogeography is to infer historical relationships and estimate population genetic parameters (
<bibRefCitation id="EFDA60A5FF9FFFF2FF6FF8D5DFFAF885" author="Hickerson MJ &amp; Carstens BC &amp; Cavender-Bares J" box="[245,467,1888,1912]" pageId="9" pageNumber="10" pagination="291 - 301" refId="ref13926" refString="Hickerson MJ, Carstens BC, Cavender-Bares J et al. Phylogeography's past, present, and future: 10 years afer Avise, 2000. Molecular Phylogenetics and Evolution 2010; 54: 291 - 301. htps: // doi. org / 10.1016 / j. ympev. 2009.09.016" type="journal article" year="2010">
Hickerson
<emphasis id="B93FC146FF9FFFF2FEFDF8D4DFB1F885" box="[359,408,1888,1912]" italics="true" pageId="9" pageNumber="10">et al.</emphasis>
2010
</bibRefCitation>
), where the combination of model-based approaches with high throughput sequencing technologies have promised to do this with high accuracy and precision (
<bibRefCitation id="EFDA60A5FF9FFFF2FF37F80BDFB3F82B" author="McCormack JE &amp; Maley JM &amp; Hird SM" box="[173,410,1982,2006]" pageId="9" pageNumber="10" pagination="397 - 406" refId="ref14621" refString="McCormack JE, Maley JM, Hird SM et al. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution 2012; 62: 397 - 406. htps: // doi. org / 10.1016 / j. ympev. 2011.10.012" type="journal article" year="2012">
McCormack
<emphasis id="B93FC146FF9FFFF2FEA9F80ADF48F82B" box="[307,353,1982,2006]" italics="true" pageId="9" pageNumber="10">et al.</emphasis>
2012
</bibRefCitation>
).
</paragraph>
<paragraph id="8BF41D54FF9FFFF2FCDFFBC5DB7CF885" blockId="9.[810,1460,1136,2007]" pageId="9" pageNumber="10">
Much of this uncertainty could stem from several historical processes. For example, the rapid diversification of these lineages may have resulted in difficulty discerning relationships and, therefore, a soft polytomy may be the best representation of historical relationships of these lineages. However, this may be unlikely given the inferred relationships based on multispecies coalescent, concatenated, and mtDNA tree-based analyses (
<figureCitation id="137001D1FF9FFFF2FA17FA99DD1EFA99" captionStart="Figure 3" captionStartId="7.[113,178,1212,1236]" captionTargetBox="[116,1449,146,1177]" captionTargetId="figure-365@7.[114,1458,144,1179]" captionTargetPageId="7" captionText="Figure 3. A, population structure inferred from the genomic sequence capture data using sNMF. Different colours within the pie charts correspond to admixture coefficients between each of the five lineages; Florida, eastern, central, south Texas, and western. Light grey highlighting represents the geographic distribution of Coluber constrictor. B, results of admixture coefficients from sNMF represented as a bar plot where each bar is a sampled individual.C, PCA of the genomic data demonstrating the differentiation of these phylogeographic lineages. D, SplitsTree network showing population structure and nestedness of these populations." pageId="9" pageNumber="10">Fig. 3</figureCitation>
). It is well known that rapid and successive lineage divergence can result in high gene tree heterogeneity and this has been shown to be widespread in many taxa (
<bibRefCitation id="EFDA60A5FF9FFFF2FBE4FA3FDB6AFA5F" author="Linkem CW &amp; Minin VN &amp; Leache AD" box="[1150,1347,1418,1442]" pageId="9" pageNumber="10" pagination="465 - 77" refId="ref14469" refString="Linkem CW, Minin VN, Leache AD. Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae). Systematic Biology 2016; 65: 465 - 77. htps: // doi. org / 10.1093 / sysbio / syw 001" type="journal article" year="2016">
Linkem
<emphasis id="B93FC146FF9FFFF2FB4CFA3EDB2EFA5F" box="[1238,1287,1418,1442]" italics="true" pageId="9" pageNumber="10">et al.</emphasis>
2016
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9FFFF2FACAFA3FDDF4FA3F" author="Pardo-De la Hoz CJ &amp; Magain N &amp; Piatkowski B" pageId="9" pageNumber="10" pagination="694 - 712" refId="ref15467" refString="Pardo-De la Hoz CJ, Magain N, Piatkowski B et al. Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of Nostocalean Cyanobacteria. Systematic Biology 2023; 72: 694 - 712. htps: // doi. org / 10.1093 / sysbio / syad 008" type="journal article" year="2023">
Pardo-De la Hoz
<emphasis id="B93FC146FF9FFFF2FCEEFA1FDD8DFA3F" box="[884,932,1450,1474]" italics="true" pageId="9" pageNumber="10">et al.</emphasis>
2023
</bibRefCitation>
). The topological differences between our inferred species’ tree and the concatenated tree suggest that there is extensive heterogeneity among gene trees within
<taxonomicName id="4C4B66D7FF9FFFF2FAB7FA5CDB84F9FD" box="[1325,1453,1513,1536]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="9" pageNumber="10" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF9FFFF2FAB7FA5CDB84F9FD" box="[1325,1453,1513,1536]" italics="true" pageId="9" pageNumber="10">C. constrictor</emphasis>
</taxonomicName>
. These differences between gene-tree and coalescent-based analyses are also observed in comparing estimates of divergence times. For example, the timing of diversification largely agreed between the single locus mtDNA analysis and the concatenated genomic analysis. Both of these gene-based approaches suggest that
<taxonomicName id="4C4B66D7FF9FFFF2FCC2F911DD8CF941" box="[856,933,1700,1724]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B93FC146FF9FFFF2FCC2F911DD8CF941" box="[856,933,1700,1724]" italics="true" pageId="9" pageNumber="10">Coluber</emphasis>
</taxonomicName>
began diversifying during the Late Miocene, which contrasts the coalescent-based estimate suggesting the Late Pleistocene. Whether summary statistic-based methods, like the neural network approach that we implemented here, are influenced by extreme heterogeneity among gene trees is unknown. Future simulation studies are needed to examine this issue (but see:
<bibRefCitation id="EFDA60A5FF9FFFF2FCCDF8D4DA16F885" author="Fan HH &amp; Kubatko LS" box="[855,1087,1888,1912]" pageId="9" pageNumber="10" pagination="354 - 63" refId="ref13084" refString="Fan HH, Kubatko LS. Estimating species trees using approximate Bayesian computation. Molecular Phylogenetics and Evolution 2011; 59: 354 - 63. htps: // doi. org / 10.1016 / j. ympev. 2011.02.019" type="journal article" year="2011">Fan and Kubatko 2011</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9FFFF2FBD3F8D5DB6CF885" author="Alanzi AR &amp; Degnan JH" box="[1097,1349,1888,1913]" pageId="9" pageNumber="10" pagination="13 - 24" refId="ref11471" refString="Alanzi AR, Degnan JH. Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation. Molecular Phylogenetics and Evolution 2017; 116: 13 - 24. htps: // doi. org / 10.1016 / j. ympev. 2017.07.017" type="journal article" year="2017">Alanzi and Degnan 2017</bibRefCitation>
).
</paragraph>
<paragraph id="8BF41D54FF9FFFF0FCDFF8CADCE5FA62" blockId="9.[810,1460,1136,2007]" lastBlockId="11.[113,763,1039,1972]" lastPageId="11" lastPageNumber="12" pageId="9" pageNumber="10">
This extreme discordance seen between the mtDNA and sequence capture data in reconstructing the demographic history of this taxon could also be the result of sex-biased dispersal (
<bibRefCitation id="EFDA60A5FF9DFFF0FFE6FBA5DFA6FBD5" author="Toews DPL &amp; Brelsford A" box="[124,399,1039,1064]" pageId="11" pageNumber="12" pagination="3907 - 30" refId="ref16641" refString="Toews DPL, Brelsford A. Te biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology 2012; 21: 3907 - 30. htps: // doi. org / 10.1111 / j. 1365 - 294 X. 2012.05664. x" type="journal article" year="2012">Toews and Brelsford 2012</bibRefCitation>
). In this case it is possible that females are highly philopatric, with high dispersal in males. This could result in a situation where ancient mtDNA lineages are maintained with much shallower divergence throughout the nuclear genome. Mark–recapture (
<bibRefCitation id="EFDA60A5FF9DFFF0FE20FB38DE8CFB39" author="Glaudas X &amp; Rodriguez-Robles JA" pageId="11" pageNumber="12" pagination="681 - 95" refId="ref13387" refString="Glaudas X, Rodriguez-Robles JA. Vagabond males and sedentary females: spatial ecology and mating system of the speckled ratlesnake (Crotalus mitchellii). Biological Journal of the Linnean Society 2011; 103: 681 - 95." type="journal article" year="2011">Glaudas and Rodriguez-Robles 2011</bibRefCitation>
), as well as population genetic and phylogeographic analyses (
<bibRefCitation id="EFDA60A5FF9DFFF0FF2EFB7EDF46FB19" author="Dubey S &amp; Brown GP &amp; Madsen T" box="[180,367,1227,1252]" pageId="11" pageNumber="12" pagination="3506 - 14" refId="ref12660" refString="Dubey S, Brown GP, Madsen T et al. Male-biased dispersal in a tropical Australian snake (Stegonotus cucullatus, Colubridae). Molecular Ecology 2008; 17: 3506 - 14. htps: // doi. org / 10.1111 / j. 1365 - 294 x. 2008.03859. x" type="journal article" year="2008">
Dubey
<emphasis id="B93FC146FF9DFFF0FE98FB79DF1DFB1E" box="[258,308,1227,1251]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2008
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FEE7FB79DC6EFB19" author="Perneta AP &amp; Allen JA &amp; Beebee TJC" box="[381,583,1227,1252]" pageId="11" pageNumber="12" pagination="231 - 8" refId="ref15582" refString="Perneta AP, Allen JA, Beebee TJC et al. Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England. Heredity 2011; 107: 231 - 8. htps: // doi. org / 10.1038 / hdy. 2011.7" type="journal article" year="2011">
Pernetta
<emphasis id="B93FC146FF9DFFF0FE40FB79DC25FB1E" box="[474,524,1227,1251]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2011
</bibRefCitation>
), have suggested that male-biased dispersal is common within snakes. While this could explain the observed pattern here, it is expected that we would find a signal of gene flow in the nuclear genome, which is not the case in our demographic modelling. Additionally, when estimating divergence times based on the concatenated genomic data, we do not find the expected shallow divergence times.
</paragraph>
<caption id="DF344DDCFF9CFFF1FF1BF8C1DAC2F81D" pageId="10" pageNumber="11" startId="10.[129,194,1908,1932]" targetBox="[257,1343,152,1875]" targetPageId="10" targetType="figure">
<paragraph id="8BF41D54FF9CFFF1FF1BF8C1DAC2F81D" blockId="10.[129,1468,1908,2016]" pageId="10" pageNumber="11">
<emphasis id="B93FC146FF9CFFF1FF1BF8C1DEF1F871" bold="true" box="[129,216,1908,1932]" pageId="10" pageNumber="11">Figure 6.</emphasis>
Morphological differentiation between phylogeographic lineages in
<taxonomicName id="4C4B66D7FF9CFFF1FCC1F8C1DA2CF871" box="[859,1029,1908,1932]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF9CFFF1FCC1F8C1DA2CF871" box="[859,1029,1908,1932]" italics="true" pageId="10" pageNumber="11">Coluber constrictor</emphasis>
</taxonomicName>
. A, B, PCA of morphological variables; A, males; B, females. C, D, are boxplots of each linear measurement showing the differentiation of each of these traits between the five lineages: C, represents males; D, females. In panels (C) and (D), pairwise comparisons significant at an adjusted
<emphasis id="B93FC146FF9CFFF1FBB5F818DA15F839" box="[1071,1084,1965,1988]" italics="true" pageId="10" pageNumber="11">P</emphasis>
&lt;.05 with a Tukey’s honest significant difference test are indicated by letters, where shared letters indicate that pair-wise comparisons are significantly different.
</paragraph>
</caption>
<caption id="DF344DDCFF9DFFF0FFEBFF3ADCB9FF5A" box="[113,656,142,167]" pageId="11" pageNumber="12" startId="11.[113,168,143,167]" targetBox="[113,762,188,972]" targetIsTable="true" targetPageId="11" targetType="table">
<paragraph id="8BF41D54FF9DFFF0FFEBFF3ADCB9FF5A" blockId="11.[113,656,142,167]" box="[113,656,142,167]" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FFEBFF3ADEE9FF5B" bold="true" box="[113,192,142,167]" pageId="11" pageNumber="12">Table 1.</emphasis>
Morphological differences from PERMANOVA.
</paragraph>
</caption>
<paragraph id="8BF41D54FF9DFFF0FEECFF08DCF9FC31" pageId="11" pageNumber="12">
<table id="F94BEFF4FF9D0004FFEBFF09DCD3FC31" box="[113,762,188,972]" gridcols="4" gridrows="23" pageId="11" pageNumber="12">
<tr id="357B1F16FF9D0004FFEBFF09DCD3FF24" box="[113,762,188,217]" gridrow="0" pageId="11" pageNumber="12" rowspan-0="1">
<th id="76AA766AFF9D0004FEECFF09DFF1FF24" box="[374,472,188,217]" gridcol="1" gridrow="0" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FEECFF08DFF1FF28" bold="true" box="[374,472,189,213]" pageId="11" pageNumber="12">F-statistic</emphasis>
</th>
<th id="76AA766AFF9D0004FDB0FF09DC76FF24" box="[554,607,188,217]" gridcol="2" gridrow="0" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FDB0FF08DC13FF28" bold="true" box="[554,570,189,213]" pageId="11" pageNumber="12">R</emphasis>
<emphasis id="B93FC146FF9DFFF0FDA0FF09DC68FF37" bold="true" box="[570,577,188,202]" pageId="11" pageNumber="12">2</emphasis>
</th>
<th id="76AA766AFF9D0004FD2AFF09DCD3FF24" box="[688,762,188,217]" gridcol="3" gridrow="0" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FD2AFF75DCD3FF28" bold="true" box="[688,762,189,217]" italics="true" pageId="11" pageNumber="12">P -value</emphasis>
</th>
</tr>
<tr id="357B1F16FF9D0004FFEBFF58DCD3FEF8" box="[113,762,237,261]" gridrow="1" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFF58DCD3FEF8" box="[113,762,237,261]" colspan="4" colspanRight="3" gridcol="0" gridrow="1" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FFEBFF58DE8AFEF8" bold="true" box="[113,163,237,261]" pageId="11" pageNumber="12">Male</emphasis>
</th>
</tr>
<tr id="357B1F16FF9D0004FFEBFEBADCD3FEDA" box="[113,762,271,295]" gridrow="2" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFEBADF0FFEDA" box="[113,294,271,295]" gridcol="0" gridrow="2" pageId="11" pageNumber="12">East—Florida</th>
<td id="76AA766AFF9D0004FEECFEBADFF1FEDA" box="[374,472,271,295]" gridcol="1" gridrow="2" pageId="11" pageNumber="12">0.62</td>
<td id="76AA766AFF9D0004FDB0FEBADC76FEDA" box="[554,607,271,295]" gridcol="2" gridrow="2" pageId="11" pageNumber="12">0.009</td>
<td id="76AA766AFF9D0004FD2AFEBADCD3FEDA" box="[688,762,271,295]" gridcol="3" gridrow="2" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFE84DCD3FEB4" box="[113,762,305,329]" gridrow="3" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFE84DF0FFEB4" box="[113,294,305,329]" gridcol="0" gridrow="3" pageId="11" pageNumber="12">East—Central</th>
<td id="76AA766AFF9D0004FEECFE84DFF1FEB4" box="[374,472,305,329]" gridcol="1" gridrow="3" pageId="11" pageNumber="12">4.12</td>
<td id="76AA766AFF9D0004FDB0FE84DC76FEB4" box="[554,607,305,329]" gridcol="2" gridrow="3" pageId="11" pageNumber="12">0.14</td>
<td id="76AA766AFF9D0004FD2AFE84DCD3FEB4" box="[688,762,305,329]" gridcol="3" gridrow="3" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFEE7DCD3FE96" box="[113,762,338,363]" gridrow="4" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFEE7DF0FFE96" box="[113,294,338,363]" gridcol="0" gridrow="4" pageId="11" pageNumber="12">East—Western</th>
<td id="76AA766AFF9D0004FEECFEE7DFF1FE96" box="[374,472,338,363]" gridcol="1" gridrow="4" pageId="11" pageNumber="12">6.93</td>
<td id="76AA766AFF9D0004FDB0FEE7DC76FE96" box="[554,607,338,363]" gridcol="2" gridrow="4" pageId="11" pageNumber="12">0.22</td>
<td id="76AA766AFF9D0004FD2AFEE7DCD3FE96" box="[688,762,338,363]" gridcol="3" gridrow="4" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFEC1DCD3FE70" box="[113,762,372,397]" gridrow="5" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFEC1DF0FFE70" box="[113,294,372,397]" gridcol="0" gridrow="5" pageId="11" pageNumber="12">East—S. Texas</th>
<td id="76AA766AFF9D0004FEECFEC1DFF1FE70" box="[374,472,372,397]" gridcol="1" gridrow="5" pageId="11" pageNumber="12">5.37</td>
<td id="76AA766AFF9D0004FDB0FEC1DC76FE70" box="[554,607,372,397]" gridcol="2" gridrow="5" pageId="11" pageNumber="12">0.20</td>
<td id="76AA766AFF9D0004FD2AFEC1DCD3FE70" box="[688,762,372,397]" gridcol="3" gridrow="5" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFE23DCD3FE53" box="[113,762,406,430]" gridrow="6" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFE23DF0FFE53" box="[113,294,406,430]" gridcol="0" gridrow="6" pageId="11" pageNumber="12">Florida—Central</th>
<td id="76AA766AFF9D0004FEECFE23DFF1FE53" box="[374,472,406,430]" gridcol="1" gridrow="6" pageId="11" pageNumber="12">3.19</td>
<td id="76AA766AFF9D0004FDB0FE23DC76FE53" box="[554,607,406,430]" gridcol="2" gridrow="6" pageId="11" pageNumber="12">0.06</td>
<td id="76AA766AFF9D0004FD2AFE23DCD3FE53" box="[688,762,406,430]" gridcol="3" gridrow="6" pageId="11" pageNumber="12">0.05</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFE0DDCD3FE2D" box="[113,762,440,464]" gridrow="7" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFE0DDF0FFE2D" box="[113,294,440,464]" gridcol="0" gridrow="7" pageId="11" pageNumber="12">Florida—Western</th>
<td id="76AA766AFF9D0004FEECFE0DDFF1FE2D" box="[374,472,440,464]" gridcol="1" gridrow="7" pageId="11" pageNumber="12">5.56</td>
<td id="76AA766AFF9D0004FDB0FE0DDC76FE2D" box="[554,607,440,464]" gridcol="2" gridrow="7" pageId="11" pageNumber="12">0.1</td>
<td id="76AA766AFF9D0004FD2AFE0DDCD3FE2D" box="[688,762,440,464]" gridcol="3" gridrow="7" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFE6FDCD3FE0F" box="[113,762,474,498]" gridrow="8" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFE6FDF0FFE0F" box="[113,294,474,498]" gridcol="0" gridrow="8" pageId="11" pageNumber="12">Florida—S. Texas</th>
<td id="76AA766AFF9D0004FEECFE6FDFF1FE0F" box="[374,472,474,498]" gridcol="1" gridrow="8" pageId="11" pageNumber="12">4.16</td>
<td id="76AA766AFF9D0004FDB0FE6FDC76FE0F" box="[554,607,474,498]" gridcol="2" gridrow="8" pageId="11" pageNumber="12">0.08</td>
<td id="76AA766AFF9D0004FD2AFE6FDCD3FE0F" box="[688,762,474,498]" gridcol="3" gridrow="8" pageId="11" pageNumber="12">0.05</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFE49DCD3FDE9" box="[113,762,508,532]" gridrow="9" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFE49DF0FFDE9" box="[113,294,508,532]" gridcol="0" gridrow="9" pageId="11" pageNumber="12">Central—Western</th>
<td id="76AA766AFF9D0004FEECFE49DFF1FDE9" box="[374,472,508,532]" gridcol="1" gridrow="9" pageId="11" pageNumber="12">0.67</td>
<td id="76AA766AFF9D0004FDB0FE49DC76FDE9" box="[554,607,508,532]" gridcol="2" gridrow="9" pageId="11" pageNumber="12">0.06</td>
<td id="76AA766AFF9D0004FD2AFE49DCD3FDE9" box="[688,762,508,532]" gridcol="3" gridrow="9" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFDA8DCD3FDCB" box="[113,762,541,566]" gridrow="10" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFDA8DF0FFDCB" box="[113,294,541,566]" gridcol="0" gridrow="10" pageId="11" pageNumber="12">Central—S. Texas</th>
<td id="76AA766AFF9D0004FEECFDA8DFF1FDCB" box="[374,472,541,566]" gridcol="1" gridrow="10" pageId="11" pageNumber="12">1.42</td>
<td id="76AA766AFF9D0004FDB0FDA8DC76FDCB" box="[554,607,541,566]" gridcol="2" gridrow="10" pageId="11" pageNumber="12">0.15</td>
<td id="76AA766AFF9D0004FD2AFDA8DCD3FDCB" box="[688,762,541,566]" gridcol="3" gridrow="10" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFDF5DCD3FDA5" box="[113,762,576,600]" gridrow="11" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFDF5DF0FFDA5" box="[113,294,576,600]" gridcol="0" gridrow="11" pageId="11" pageNumber="12">Western—S. Texas</th>
<td id="76AA766AFF9D0004FEECFDF5DFF1FDA5" box="[374,472,576,600]" gridcol="1" gridrow="11" pageId="11" pageNumber="12">0.78</td>
<td id="76AA766AFF9D0004FDB0FDF5DC76FDA5" box="[554,607,576,600]" gridcol="2" gridrow="11" pageId="11" pageNumber="12">0.08</td>
<td id="76AA766AFF9D0004FD2AFDF5DCD3FDA5" box="[688,762,576,600]" gridcol="3" gridrow="11" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFDD4DCD3FD84" box="[113,762,609,633]" gridrow="12" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFDD4DCD3FD84" box="[113,762,609,633]" colspan="4" colspanRight="3" gridcol="0" gridrow="12" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FFE8FDD4DE95FD84" bold="true" box="[114,188,609,633]" pageId="11" pageNumber="12">Female</emphasis>
</th>
</tr>
<tr id="357B1F16FF9D0004FFEBFD36DCD3FD66" box="[113,762,643,667]" gridrow="13" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFD36DF0FFD66" box="[113,294,643,667]" gridcol="0" gridrow="13" pageId="11" pageNumber="12">East—Florida</th>
<td id="76AA766AFF9D0004FEECFD36DFF1FD66" box="[374,472,643,667]" gridcol="1" gridrow="13" pageId="11" pageNumber="12">1.04</td>
<td id="76AA766AFF9D0004FDB0FD36DC76FD66" box="[554,607,643,667]" gridcol="2" gridrow="13" pageId="11" pageNumber="12">0.06</td>
<td id="76AA766AFF9D0004FD2AFD36DCD3FD66" box="[688,762,643,667]" gridcol="3" gridrow="13" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFD10DCD3FD40" box="[113,762,677,701]" gridrow="14" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFD10DF0FFD40" box="[113,294,677,701]" gridcol="0" gridrow="14" pageId="11" pageNumber="12">East—Central</th>
<td id="76AA766AFF9D0004FEECFD10DFF1FD40" box="[374,472,677,701]" gridcol="1" gridrow="14" pageId="11" pageNumber="12">1.31</td>
<td id="76AA766AFF9D0004FDB0FD10DC76FD40" box="[554,607,677,701]" gridcol="2" gridrow="14" pageId="11" pageNumber="12">0.10</td>
<td id="76AA766AFF9D0004FD2AFD10DCD3FD40" box="[688,762,677,701]" gridcol="3" gridrow="14" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFD72DCD3FD22" box="[113,762,711,735]" gridrow="15" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFD72DF0FFD22" box="[113,294,711,735]" gridcol="0" gridrow="15" pageId="11" pageNumber="12">East—Western</th>
<td id="76AA766AFF9D0004FEECFD72DFF1FD22" box="[374,472,711,735]" gridcol="1" gridrow="15" pageId="11" pageNumber="12">4.56</td>
<td id="76AA766AFF9D0004FDB0FD72DC76FD22" box="[554,607,711,735]" gridcol="2" gridrow="15" pageId="11" pageNumber="12">0.28</td>
<td id="76AA766AFF9D0004FD2AFD72DCD3FD22" box="[688,762,711,735]" gridcol="3" gridrow="15" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFD5CDCD3FCFC" box="[113,762,745,769]" gridrow="16" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFD5CDF0FFCFC" box="[113,294,745,769]" gridcol="0" gridrow="16" pageId="11" pageNumber="12">East—s. Texas</th>
<td id="76AA766AFF9D0004FEECFD5CDFF1FCFC" box="[374,472,745,769]" gridcol="1" gridrow="16" pageId="11" pageNumber="12">5.17</td>
<td id="76AA766AFF9D0004FDB0FD5CDC76FCFC" box="[554,607,745,769]" gridcol="2" gridrow="16" pageId="11" pageNumber="12">0.27</td>
<td id="76AA766AFF9D0004FD2AFD5CDCD3FCFC" box="[688,762,745,769]" gridcol="3" gridrow="16" pageId="11" pageNumber="12">0.01</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFCBFDCD3FCDE" box="[113,762,778,803]" gridrow="17" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFCBFDF0FFCDE" box="[113,294,778,803]" gridcol="0" gridrow="17" pageId="11" pageNumber="12">Florida—Central</th>
<td id="76AA766AFF9D0004FEECFCBFDFF1FCDE" box="[374,472,778,803]" gridcol="1" gridrow="17" pageId="11" pageNumber="12">0.62</td>
<td id="76AA766AFF9D0004FDB0FCBFDC76FCDE" box="[554,607,778,803]" gridcol="2" gridrow="17" pageId="11" pageNumber="12">0.06</td>
<td id="76AA766AFF9D0004FD2AFCBFDCD3FCDE" box="[688,762,778,803]" gridcol="3" gridrow="17" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFC99DCD3FCB9" box="[113,762,812,836]" gridrow="18" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFC99DF0FFCB9" box="[113,294,812,836]" gridcol="0" gridrow="18" pageId="11" pageNumber="12">Florida—Western</th>
<td id="76AA766AFF9D0004FEECFC99DFF1FCB9" box="[374,472,812,836]" gridcol="1" gridrow="18" pageId="11" pageNumber="12">1.88</td>
<td id="76AA766AFF9D0004FDB0FC99DC76FCB9" box="[554,607,812,836]" gridcol="2" gridrow="18" pageId="11" pageNumber="12">0.16</td>
<td id="76AA766AFF9D0004FD2AFC99DCD3FCB9" box="[688,762,812,836]" gridcol="3" gridrow="18" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFCFBDCD3FC9B" box="[113,762,846,870]" gridrow="19" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFCFBDF0FFC9B" box="[113,294,846,870]" gridcol="0" gridrow="19" pageId="11" pageNumber="12">Florida—S. Texas</th>
<td id="76AA766AFF9D0004FEECFCFBDFF1FC9B" box="[374,472,846,870]" gridcol="1" gridrow="19" pageId="11" pageNumber="12">3.20</td>
<td id="76AA766AFF9D0004FDB0FCFBDC76FC9B" box="[554,607,846,870]" gridcol="2" gridrow="19" pageId="11" pageNumber="12">0.21</td>
<td id="76AA766AFF9D0004FD2AFCFBDCD3FC9B" box="[688,762,846,870]" gridcol="3" gridrow="19" pageId="11" pageNumber="12">0.05</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFCC5DCD3FC75" box="[113,762,880,904]" gridrow="20" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFCC5DF0FFC75" box="[113,294,880,904]" gridcol="0" gridrow="20" pageId="11" pageNumber="12">Central—Western</th>
<td id="76AA766AFF9D0004FEECFCC5DFF1FC75" box="[374,472,880,904]" gridcol="1" gridrow="20" pageId="11" pageNumber="12">1.10</td>
<td id="76AA766AFF9D0004FDB0FCC5DC76FC75" box="[554,607,880,904]" gridcol="2" gridrow="20" pageId="11" pageNumber="12">0.16</td>
<td id="76AA766AFF9D0004FD2AFCC5DCD3FC75" box="[688,762,880,904]" gridcol="3" gridrow="20" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFC27DCD3FC57" box="[113,762,914,938]" gridrow="21" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFC27DF0FFC57" box="[113,294,914,938]" gridcol="0" gridrow="21" pageId="11" pageNumber="12">Central—S. Texas</th>
<td id="76AA766AFF9D0004FEECFC27DFF1FC57" box="[374,472,914,938]" gridcol="1" gridrow="21" pageId="11" pageNumber="12">1.65</td>
<td id="76AA766AFF9D0004FDB0FC27DC76FC57" box="[554,607,914,938]" gridcol="2" gridrow="21" pageId="11" pageNumber="12">0.22</td>
<td id="76AA766AFF9D0004FD2AFC27DCD3FC57" box="[688,762,914,938]" gridcol="3" gridrow="21" pageId="11" pageNumber="12">NS</td>
</tr>
<tr id="357B1F16FF9D0004FFEBFC01DCD3FC31" box="[113,762,948,972]" gridrow="22" pageId="11" pageNumber="12">
<th id="76AA766AFF9D0004FFEBFC01DF0FFC31" box="[113,294,948,972]" gridcol="0" gridrow="22" pageId="11" pageNumber="12">Western—S. Texas</th>
<td id="76AA766AFF9D0004FEECFC01DFF1FC31" box="[374,472,948,972]" gridcol="1" gridrow="22" pageId="11" pageNumber="12">0.14</td>
<td id="76AA766AFF9D0004FDB0FC01DC76FC31" box="[554,607,948,972]" gridcol="2" gridrow="22" pageId="11" pageNumber="12">0.15</td>
<td id="76AA766AFF9D0004FD2AFC01DCD3FC31" box="[688,762,948,972]" gridcol="3" gridrow="22" pageId="11" pageNumber="12">NS</td>
</tr>
</table>
</paragraph>
<paragraph id="8BF41D54FF9DFFF0FF17FA12DBB8FF3A" blockId="11.[113,763,1039,1972]" lastBlockId="11.[810,1460,144,1766]" pageId="11" pageNumber="12">
It is also possible that the history of this group is too complex for the most commonly used isolation-migration models, where repeated bouts of isolation and contact are the cause of model selection uncertainty. Complex demographic histories of rapid divergence coupled with gene flow during glacial and interglacial periods is common in many temperate zone taxa (
<bibRefCitation id="EFDA60A5FF9DFFF0FD3CF9F6DEC8F986" author="DeRaad DA &amp; McCormack JE &amp; Chen N" pageId="11" pageNumber="12" pagination="1453 - 70" refId="ref12608" refString="DeRaad DA, McCormack JE, Chen N et al. Combining species delimitation, species trees, and tests for gene flow clarifies complex speciation in scrub-jays. Systematic Biology 2022; 71: 1453 - 70. htps: // doi. org / 10.1093 / sysbio / syac 034" type="journal article" year="2022">
DeRaad
<emphasis id="B93FC146FF9DFFF0FFEBF9D6DE8DF986" box="[113,164,1635,1659]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2022
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FF6AF9D6DC1EF986" author="Harrington S &amp; Burbrink FT" box="[240,567,1635,1659]" pageId="11" pageNumber="12" pagination="341 - 51" refId="ref13722" refString="Harrington S, Burbrink FT. Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex. Journal of Biogeography 2023; 50: 341 - 51. htps: // doi. org / 10.1111 / jbi. 14536" type="journal article" year="2023">Harrington and Burbrink 2023</bibRefCitation>
). Similar histories of divergence have been suggested to be widespread and have been called the ‘mixing-isolation-mixing’ model of divergence (
<bibRefCitation id="EFDA60A5FF9DFFF0FFE6F974DF3CF924" author="He Z &amp; Li X &amp; Yang M" box="[124,277,1729,1753]" pageId="11" pageNumber="12" pagination="275 - 88" refId="ref13813" refString="He Z, Li X, Yang M et al. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. National Science Review 2019; 6: 275 - 88. htps: // doi. org / 10.1093 / nsr / nwy 078" type="journal article" year="2019">
He
<emphasis id="B93FC146FF9DFFF0FF3FF974DEF1F924" box="[165,216,1729,1753]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2019
</bibRefCitation>
). If this is the true underlying history of the group, then the expectation might be that model selection approaches would default to a history of ancient divergence with high gene-flow. However, previous studies have demonstrated that discriminating between isolation-only and secondary-contact models is difficult. For example, data simulated under a secondary-contact model could only be confidently assigned back to this true model when the period of isolation was sufficiently long. When shorter periods of isolation were simulated, ABC approaches were inconclusive (
<bibRefCitation id="EFDA60A5FF9DFFF0FB47FF05DBA9FF3A" author="Roux C &amp; Fraisse C &amp; Romiguier J" box="[1245,1408,175,199]" pageId="11" pageNumber="12" refId="ref16136" refString="Roux C, Fraisse C, Romiguier J et al. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology 2016; 14: e 2000234. htps: // doi. org / 10.1371 / journal. pbio. 2000234" type="journal volume" year="2016">
Roux
<emphasis id="B93FC146FF9DFFF0FA83FF05DB61FF3A" box="[1305,1352,175,199]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2016
</bibRefCitation>
).
</paragraph>
<paragraph id="8BF41D54FF9DFFF0FCDCFF7ADD93FC2A" blockId="11.[810,1460,144,1766]" pageId="11" pageNumber="12">
How then can we choose among competing models of historical demography? Our demographic analyses suggest that the phylogeographic relationships are best represented as a polytomy with very recent divergence and no migration. However, this disagrees with the best-fit model based on mtDNA, estimated gene-divergence times, and with previous phylogeographic estimates (
<bibRefCitation id="EFDA60A5FF9DFFF0FCECFE3FDA17FE5F" author="Burbrink FT &amp; Fontanella F &amp; Pyron R" box="[886,1086,394,418]" pageId="11" pageNumber="12" pagination="274 - 88" refId="ref12057" refString="Burbrink FT, Fontanella F, Pyron R et al. Phylogeography across a continent: the evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor). Molecular Phylogenetics and Evolution 2008; 47: 274 - 88." type="journal article" year="2008">
Burbrink
<emphasis id="B93FC146FF9DFFF0FC4DFE3EDA2FFE5F" box="[983,1030,394,418]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2008
</bibRefCitation>
). Here, we have a strong signal of divergence in the mtDNA phylogeographic analyses that matches both the population structure and SNAPP-based species’ tree topology reconstructed from the genomic data, all dating the origin of diversification to the Miocene. We note, however, that both the mtDNA and concatenated genomic divergence times are gene-divergence, not lineage-divergence times (
<bibRefCitation id="EFDA60A5FF9DFFF0FAAAFDF3DD8BFD83" author="Edwards SV &amp; Beerli P" pageId="11" pageNumber="12" pagination="1839 - 54" refId="ref12778" refString="Edwards SV, Beerli P. Perspective: gene divergence, population divergence, andthevarianceincoalescencetimeinphylogeographicstudies. Evolution; International Journal of Organic Evolution 2000; 54: 1839 - 54. htps: // doi. org / 10.1111 / j. 0014 - 3820.2000. tb 01231. x" type="journal article" year="2000">Edwards and Beerli 2000</bibRefCitation>
) and we do not take them to be reflective of species divergence times. A caveat of overly relying on gene-tree based (e.g. mtDNA alone) inferences is that increased levels of genetic diversity may be explained by the persistence of large N
<subScript id="17CF1F11FF9DFFF0FCA7FD41DD6DFCFF" attach="left" box="[829,836,756,770]" fontSize="6" pageId="11" pageNumber="12">e</subScript>
at mutation-drift equilibrium (
<bibRefCitation id="EFDA60A5FF9DFFF0FB1DFD56DB67FD06" author="Charlesworth B" box="[1159,1358,739,763]" pageId="11" pageNumber="12" pagination="195 - 205" refId="ref12276" refString="Charlesworth B. Effective population size and paterns of molecular evolution and variation. Nature Reviews Genetics 2009; 10: 195 - 205. htps: // doi. org / 10.1038 / nrg 2526" type="journal article" year="2009">Charlesworth 2009</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FAC0FD51DDD1FCE6" author="Morgan-Richards M &amp; Bulgarella M &amp; Sivyer L" pageId="11" pageNumber="12" refId="ref14901" refString="Morgan-Richards M, Bulgarella M, Sivyer L et al. Explaining large mitochondrial sequence differences within a population sample. Royal Society Open Science 2017; 4: 170730. htps: // doi. org / 10.1098 / rsos. 170730" type="journal volume" year="2017">
Morgan-Richards
<emphasis id="B93FC146FF9DFFF0FC16FCB6DD94FCE6" box="[908,957,771,795]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2017
</bibRefCitation>
). A pattern of high genetic polymorphism within sampling sites has been demonstrated to be the result of elevated levels of N
<subScript id="17CF1F11FF9DFFF0FBB9FCE7DA03FC9D" attach="left" box="[1059,1066,850,864]" fontSize="6" pageId="11" pageNumber="12">e</subScript>
maintained through time (
<bibRefCitation id="EFDA60A5FF9DFFF0FAC0FCF7DDDDFC84" author="Morgan-Richards M &amp; Bulgarella M &amp; Sivyer L" pageId="11" pageNumber="12" refId="ref14901" refString="Morgan-Richards M, Bulgarella M, Sivyer L et al. Explaining large mitochondrial sequence differences within a population sample. Royal Society Open Science 2017; 4: 170730. htps: // doi. org / 10.1098 / rsos. 170730" type="journal volume" year="2017">
Morgan-Richards
<emphasis id="B93FC146FF9DFFF0FC11FCD4DD92FC84" box="[907,955,865,889]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2017
</bibRefCitation>
). However, this seems less likely here given that the deep mtDNA lineages of racers are geographically structured and match population genetic structure observed with the genomic data.
</paragraph>
<paragraph id="8BF41D54FF9DFFF0FCDFFC6BDDA1F91B" blockId="11.[810,1460,144,1766]" pageId="11" pageNumber="12">
In cases where demographic model selection and divergencetime estimates between datasets strongly disagree, there are two additional methods that may prove useful in future analyses. First, whole genome resequencing data could provide more accurate and precise model selection and demographic parameter estimates over commonly used sequence capture loci like UCEs. It is now possible to generate low-coverage, whole-genome resequencing data (~2× coverage) for similar costs compared to reduced representation sequencing methods, and by spreading sequencing effort across more samples, albeit at a lower per base pair coverage, while increasing the accuracy of many population genetic inferences (
<bibRefCitation id="EFDA60A5FF9DFFF0FBBBFA82DA91FAB2" author="Lou RN &amp; Jacobs A &amp; Wilder AP" box="[1057,1208,1334,1359]" pageId="11" pageNumber="12" pagination="5966 - 93" refId="ref14524" refString="Lou RN, Jacobs A, Wilder AP et al. A beginner's guide to low-coverage whole genome sequencing for population genomics. Molecular Ecology 2021; 30: 5966 - 93. htps: // doi. org / 10.1111 / mec. 16077" type="journal article" year="2021">
Lou
<emphasis id="B93FC146FF9DFFF0FBCAFA82DA56FAB3" box="[1104,1151,1334,1358]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2021
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FB59FA83DB8BFAB2" author="Reid BN &amp; Pinsky ML" box="[1219,1442,1334,1359]" pageId="11" pageNumber="12" pagination="1849 - 63" refId="ref15996" refString="Reid BN, Pinsky ML. Simulation-based evaluation of methods, data types, and temporal sampling schemes for detecting recent population declines. Integrative and Comparative Biology 2022; 62: 1849 - 63. htps: // doi. org / 10.1093 / icb / icac 144" type="journal article" year="2022">Reid and Pinsky 2022</bibRefCitation>
). Second, ancient DNA sampled from Pleistocene subfossils will improve our understanding of the demographic histories and evolutionary relationships of many taxa (
<bibRefCitation id="EFDA60A5FF9DFFF0FB5FFA20DBACFA50" author="Orlando L &amp; Metcalf JL &amp; Alberdi MT" box="[1221,1413,1429,1453]" pageId="11" pageNumber="12" pagination="21754 - 9" refId="ref15294" refString="Orlando L, Metcalf JL, Alberdi MT et al. Revising the recent evolutionary history of equids using ancient DNA. Proceedings of the National Academy of Sciences of the United States of America 2009; 106: 21754 - 9. htps: // doi. org / 10.1073 / pnas. 0903672106" type="journal article" year="2009">
Orlando
<emphasis id="B93FC146FF9DFFF0FABAFA20DB67FA50" box="[1312,1358,1429,1453]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2009
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FA15FA20DDD9FA31" author="van der Valk T &amp; Pecnerova P &amp; Diez-del-Molino D" pageId="11" pageNumber="12" pagination="265 - 9" refId="ref16743" refString="van der Valk T, Pecnerova P, Diez-del-Molino D et al. Million-year-old DNA sheds light on the genomic history of mammoths. Nature 2021; 591: 265 - 9. htps: // doi. org / 10.1038 / s 41586 - 021 - 03224 - 9" type="journal article" year="2021">
van der Valk
<emphasis id="B93FC146FF9DFFF0FC1CFA00DD9FFA31" box="[902,950,1460,1484]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2021
</bibRefCitation>
). These approaches have also recently been used to better understand both taxonomy and biogeographic history in squamate reptiles and, in some cases, DNA has been obtained with minimally destructive sampling methods (
<bibRefCitation id="EFDA60A5FF9DFFF0FAF3F9A7DDFFF9B4" author="Torres-Roig E &amp; Mitchell KJ &amp; Alcover JA" pageId="11" pageNumber="12" pagination="144 - 68" refId="ref16686" refString="Torres-Roig E, Mitchell KJ, Alcover JA et al. Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration. Zoological Journal of the Linnean Society 2021; 192: 144 - 68. htps: // doi. org / 10.1093 / zoolinnean / zlaa 094" type="journal article" year="2021">
Torres-Roig
<emphasis id="B93FC146FF9DFFF0FCFFF987DDB0F9B4" box="[869,921,1585,1609]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2021
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FC7CF984DAFAF9B4" author="Scarsbrook L &amp; Verry AJF &amp; Walton K" box="[998,1235,1585,1609]" pageId="11" pageNumber="12" pagination="2964 - 2984" refId="ref16272" refString="Scarsbrook L, Verry AJF, Walton K et al. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus. Molecular Ecology 2022; 32: 2964 - 2984." type="journal article" year="2022">
Scarsbrook
<emphasis id="B93FC146FF9DFFF0FBF8F987DABFF9B4" box="[1122,1174,1585,1609]" italics="true" pageId="11" pageNumber="12">et al.</emphasis>
2022
</bibRefCitation>
). Throughout North America, Pleistocene snake subfossils are remarkably common (
<bibRefCitation id="EFDA60A5FF9DFFF0FCAFF9C5DDF6F975" author="Bratstrom BH" box="[821,991,1648,1672]" pageId="11" pageNumber="12" pagination="188 - 202" refId="ref11763" refString="Bratstrom BH. A succession of pliocene and pleistocene snake faunas from the high plains of the United States. Copeia 1967; 1967: 188 - 202. htps: // doi. org / 10.2307 / 1442194" type="journal article" year="1967">Brattstrom 1967</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9DFFF0FC77F9C5DA57F975" author="Holman JA" box="[1005,1150,1648,1672]" pageId="11" pageNumber="12" refId="ref14024" refString="Holman JA. Fossil Snakes of North America: Origin, Evolution, Distribution, Paleoecology (Life of the Past). Bloomington, IN: Indiana University Press, 2000." type="book" year="2000">Holman 2000</bibRefCitation>
) and future efforts to extract and sequence DNA from these fossils may further improve our understanding of species’ diversification and demographic histories.
</paragraph>
<paragraph id="8BF41D54FF9DFFF0FC2DF943DB0FF8ED" blockId="11.[951,1318,1782,1809]" box="[951,1318,1782,1809]" pageId="11" pageNumber="12">
<emphasis id="B93FC146FF9DFFF0FC2DF943DB0FF8ED" bold="true" box="[951,1318,1782,1809]" pageId="11" pageNumber="12">
<taxonomicName id="4C4B66D7FF9DFFF0FC2DF943DA5CF8ED" box="[951,1141,1782,1809]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="11" pageNumber="12" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF9DFFF0FC2DF943DA5CF8ED" bold="true" box="[951,1141,1782,1809]" italics="true" pageId="11" pageNumber="12">Coluber constrictor</emphasis>
</taxonomicName>
phylogeography
</emphasis>
</paragraph>
<paragraph id="8BF41D54FF9DFFF7FCB0F8A8DF0BFEFB" blockId="11.[810,1459,1821,1970]" lastBlockId="12.[129,779,144,1828]" lastPageId="12" lastPageNumber="13" pageId="11" pageNumber="12">
The observed population genetic structure within
<taxonomicName id="4C4B66D7FF9DFFF0FAAFF8A8DD47F8A9" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="11" pageNumber="12" phylum="Chordata" rank="species" species="constrictor">
<emphasis id="B93FC146FF9DFFF0FAAFF8A8DD47F8A9" italics="true" pageId="11" pageNumber="12">Coluber constrictor</emphasis>
</taxonomicName>
corroborate previously identified phylogeographic breaks within this taxon to known barriers across North America, and, in some cases, subspecific taxonomy. This structure that we find is associated with the Florida peninsula, across the transition between the forested region of eastern North America and the central grasslands, across the Rocky Mountains, and a south Texas group that may extend as far south as southern
<collectingCountry id="F35C5DC4FF9AFFF7FD27FF7ADD23FF1A" box="[701,778,207,231]" name="Mexico" pageId="12" pageNumber="13">Mexico</collectingCountry>
and
<collectingCountry id="F35C5DC4FF9AFFF7FF36FF5BDF37FEFB" box="[172,286,238,262]" name="Guatemala" pageId="12" pageNumber="13">Guatemala</collectingCountry>
.
</paragraph>
<paragraph id="8BF41D54FF9AFFF7FF06FEB8DCF7FC2B" blockId="12.[129,779,144,1828]" pageId="12" pageNumber="13">
Divergence between the
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peninsula and continental North America, as well as across the transition between the forested region of eastern North America and the central grasslands, is commonly found in many taxa (
<bibRefCitation id="EFDA60A5FF9AFFF7FE49FEDEDC5DFE7E" author="Soltis DE &amp; Morris AB &amp; McLachlan JS" box="[467,628,363,387]" pageId="12" pageNumber="13" pagination="4261 - 93" refId="ref16450" refString="Soltis DE, Morris AB, McLachlan JS et al. Comparative phylogeography of unglaciatedeasternNorthAmerica. MolecularEcology 2006; 15: 4261 - 93. htps: // doi. org / 10.1111 / j. 1365 - 294 X. 2006.03061. x" type="journal article" year="2006">
Soltis
<emphasis id="B93FC146FF9AFFF7FD8AFED9DC14FE7E" box="[528,573,363,387]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2006
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FDE7FEDEDE9CFE5E" author="Burbrink FT &amp; Bernstein JM &amp; Kuhn A" pageId="12" pageNumber="13" pagination="839 - 58" refId="ref12104" refString="Burbrink FT, Bernstein JM, Kuhn A et al. Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex). Systematic Biology 2022; 71: 839 - 58. htps: // doi. org / 10.1093 / sysbio / syab 093" type="journal article" year="2022">
Burbrink
<emphasis id="B93FC146FF9AFFF7FD47FED9DD23FE7E" box="[733,778,363,387]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2022
</bibRefCitation>
). Although both regions have been shown to be important for promoting population genetic divergence across entire communities of organisms, the timing and causes of divergence are not well known. For example, across the Florida-continental discontinuity several non-mutually exclusive hypotheses have been proposed, including Pliocene sea-level rises resulting in
<collectingRegion id="498FD3B6FF9AFFF7FF1BFDF3DEE5FDA3" box="[129,204,582,606]" country="United States of America" name="Florida" pageId="12" pageNumber="13">Florida</collectingRegion>
being mostly submerged, consisting of only a series of islands in the centre of the peninsula (
<bibRefCitation id="EFDA60A5FF9AFFF7FD8EFDD3DCA5FD83" author="Webb SD" box="[532,652,614,638]" pageId="12" pageNumber="13" pagination="70 - 102" refId="ref16995" refString="Webb SD. Historical biogeography. Ecosystems of Florida. Orlando, FL: University of Central Florida Press, 1990, 70 - 102." type="book chapter" year="1990">Webb 1990</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FD03FDD3DE9CFD60" author="Clark AM &amp; Bowen BW &amp; Branch LC" pageId="12" pageNumber="13" pagination="1093 - 104" refId="ref12312" refString="Clark AM, Bowen BW, Branch LC. Effects of natural habitat fragmentation on an endemic scrub lizard (Sceloporus woodi): an historical perspective based on a mitochondrial DNA gene genealogy. Molecular Ecology 1999; 8: 1093 - 104. htps: // doi. org / 10.1046 / j. 1365 - 294 x. 1999.00653. x" type="journal article" year="1999">
Clark
<emphasis id="B93FC146FF9AFFF7FD43FDD2DD23FD83" box="[729,778,614,638]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
1999
</bibRefCitation>
), Pleistocene refugia (
<bibRefCitation id="EFDA60A5FF9AFFF7FE3CFD30DC4EFD60" author="Waltari E &amp; Hijmans RJ &amp; Peterson AT" box="[422,615,645,669]" pageId="12" pageNumber="13" refId="ref16909" refString="Waltari E, Hijmans RJ, Peterson AT et al. Locating Pleistocene Refugia: comparing phylogeographic and ecological niche model predictions. PLoS One 2007; 2: e 563. htps: // doi. org / 10.1371 / journal. pone. 0000563" type="journal volume" year="2007">
Waltari
<emphasis id="B93FC146FF9AFFF7FE63FD33DC02FD60" box="[505,555,645,669]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2007
</bibRefCitation>
), which is also supported in our hindcast ENMs, or, as we have demonstrated here, the potential for divergent ecological selection on environmental niche. Similarly, population genetic structure across the middle Nearctic has contributed to both the ecotonal transition from deciduous, broadleaf forests into grasslands, as well as vicariance across the
<collectingRegion id="498FD3B6FF9AFFF7FEECFCF4DFC1FCA4" box="[374,488,833,857]" country="United States of America" name="Mississippi" pageId="12" pageNumber="13">Mississippi</collectingRegion>
River (
<bibRefCitation id="EFDA60A5FF9AFFF7FDADFCF4DD2DFCA4" author="Burbrink FT &amp; Lawson R &amp; Slowinski JB" box="[567,772,833,857]" pageId="12" pageNumber="13" pagination="2107 - 18" refId="ref11985" refString="Burbrink FT, Lawson R, Slowinski JB. Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution; International Journal of Organic Evolution 2000; 54: 2107 - 18. htps: // doi. org / 10.1554 / 0014 - 3820 (2000) 054 [2107: MDPOTP] 2.0. CO; 2" type="journal article" year="2000">
Burbrink
<emphasis id="B93FC146FF9AFFF7FD00FCF7DCE3FCA4" box="[666,714,833,857]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2000
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FF1BFCD5DFA8FC84" author="Leache AD &amp; Reeder TW" box="[129,385,864,889]" pageId="12" pageNumber="13" pagination="44 - 68" refId="ref14380" refString="Leache AD, Reeder TW. Molecular systematics of the Eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology 2002; 51: 44 - 68. htps: // doi. org / 10.1080 / 106351502753475871" type="journal article" year="2002">Leaché and Reeder 2002</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FE17FCD4DCBFFC84" author="Pyron R &amp; Burbrink FT" box="[397,662,864,889]" pageId="12" pageNumber="13" pagination="2005 - 15" refId="ref15853" refString="Pyron R, Burbrink FT. Hard and sof allopatry: physically and ecologically mediated modes of geographic speciation. Journal of Biogeography 2010; 37: 2005 - 15. htps: // doi. org / 10.1111 / j. 1365 - 2699.2010.02336. x" type="journal article" year="2010">Pyron and Burbrink 2010</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FD39FCD5DF3FFC65" author="Satler JD &amp; Carstens BC" pageId="12" pageNumber="13" pagination="3533 - 45" refId="ref16233" refString="Satler JD, Carstens BC. Do ecological communities disperse across biogeographic barriers as a unit? Molecular Ecology 2017; 26: 3533 - 45. htps: // doi. org / 10.1111 / mec. 14137" type="journal article" year="2017">Satler and Carstens 2017</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FEB9FC35DFFEFC65" author="Myers EA &amp; McKelvy AD &amp; Burbrink FT" box="[291,471,896,920]" pageId="12" pageNumber="13" pagination="797 - 811" refId="ref15137" refString="Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis gutatus complex). Molecular Ecology 2020; 29: 797 - 811. htps: // doi. org / 10.1111 / mec. 15358" type="journal article" year="2020">
Myers
<emphasis id="B93FC146FF9AFFF7FEF1FC34DFB5FC65" box="[363,412,896,920]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2020
</bibRefCitation>
). Future comparative studies should focus on the interaction of vicariance and adaptation in shaping shared patterns of biodiversity at these two regions.
</paragraph>
<paragraph id="8BF41D54FF9AFFF7FF06FC6BDC54F9F7" blockId="12.[129,779,144,1828]" pageId="12" pageNumber="13">
Two lineages identified here also correspond to previously named taxonomic units,
<emphasis id="B93FC146FF9AFFF7FE12FC48DC3BFBE8" box="[392,530,1021,1045]" italics="true" pageId="12" pageNumber="13">
C. c.
<taxonomicName id="4C4B66D7FF9AFFF7FE25FC4BDC3BFBE8" authorityName="Baird &amp; Girard" authorityYear="1852" box="[447,530,1022,1045]" class="Squamata" family="Colubridae" genus="Coluber" kingdom="Animalia" pageId="12" pageNumber="13" phylum="Chordata" rank="species" species="mormon">mormon</taxonomicName>
</emphasis>
and
<emphasis id="B93FC146FF9AFFF7FDD1FC48DCEEFBE8" box="[587,711,1021,1045]" italics="true" pageId="12" pageNumber="13">C. c. oaxaca</emphasis>
. Both of these taxa were originally described as species (
<bibRefCitation id="EFDA60A5FF9AFFF7FD38FBA9DED7FBA9" author="Baird SF &amp; Girard C" pageId="12" pageNumber="13" pagination="68 - 70" refId="ref11589" refString="Baird SF, Girard C. Characteristics of some new reptiles in the Museum of the Smithsonian Institution. Proceedings of the Academy of Natural Sciences of Philadelphia 1852; 6: 68 - 70." type="journal article" year="1852">Baird and Girard 1852</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FE90FB89DF4CFBA9" author="Jan G" box="[266,357,1084,1108]" pageId="12" pageNumber="13" refId="ref14096" refString="Jan G. Elenco Sistematico degli Ofidi Descriti e Disegnati per L'iconografia Generale. Milano: Tip. di A. Lombardi, 1863." type="book" year="1863">
<date id="FFF53B94FF9AFFF7FE90FB89DF4CFBA9" box="[266,357,1084,1108]" pageId="12" pageNumber="13" value="1863-01">Jan 1863</date>
</bibRefCitation>
) and there has been disagreement in the literature regarding the specific status of these taxa (
<bibRefCitation id="EFDA60A5FF9AFFF7FD04FBEEDE9CFB6F" author="Fitch HS &amp; Brown WS &amp; Parker WS" pageId="12" pageNumber="13" pagination="196 - 203" refId="ref13169" refString="Fitch HS, Brown WS, Parker WS. Coluber mormon, a species distinct from C. constrictor. Transactions of the Kansas Academy of Science 1981; 84: 196 - 203. htps: // doi. org / 10.2307 / 3628274" type="journal article" year="1981">
Fitch
<emphasis id="B93FC146FF9AFFF7FD40FBE9DD23FB8E" box="[730,778,1115,1139]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
1981
</bibRefCitation>
,
<bibRefCitation id="EFDA60A5FF9AFFF7FF5BFBCFDF61FB6F" author="Greene HW" box="[193,328,1146,1170]" pageId="12" pageNumber="13" pagination="210 - 1" refId="ref13448" refString="Greene HW. Taxonomic status of the western racer, Coluber constrictor mormon. Journal of Herpetology 1984; 18: 210 - 1. htps: // doi. org / 10.2307 / 1563756" type="journal article" year="1984">Greene 1984</bibRefCitation>
). The geographic distribution of the North American racers is allopatric across the Rocky Mountains and, therefore, it is not surprising to find population genetic structure across this region (but see:
<bibRefCitation id="EFDA60A5FF9AFFF7FE50FB6DDCB7FB0D" author="Corn PS &amp; Bury RB" box="[458,670,1240,1265]" pageId="12" pageNumber="13" pagination="258 - 64" refId="ref12376" refString="Corn PS, Bury RB. Morphological variation and zoogeography of racers (Coluber constrictor) in the Central Rocky Mountains. Herpetologica 1986; 42: 258 - 64." type="journal article" year="1986">Corn and Bury 1986</bibRefCitation>
). The two samples from southern Texas that form a distinct population fall within the geographic range of
<emphasis id="B93FC146FF9AFFF7FE57FAA2DFF7FAD3" box="[461,478,1303,1326]" italics="true" pageId="12" pageNumber="13">C</emphasis>
.
<emphasis id="B93FC146FF9AFFF7FE76FAADDC60FAD2" box="[492,585,1304,1327]" italics="true" pageId="12" pageNumber="13">c. oaxaca</emphasis>
; however, the full distribution of this subspecies is discontinuous from southern Texas along the east coast of
<collectingCountry id="F35C5DC4FF9AFFF7FE2BFAE3DFD7FA93" box="[433,510,1366,1390]" name="Mexico" pageId="12" pageNumber="13">Mexico</collectingCountry>
to
<collectingCountry id="F35C5DC4FF9AFFF7FDB8FAE3DCB8FA93" box="[546,657,1366,1390]" name="Guatemala" pageId="12" pageNumber="13">Guatemala</collectingCountry>
and
<collectingCountry id="F35C5DC4FF9AFFF7FD5CFAE3DD2FFA93" box="[710,774,1366,1390]" name="Belize" pageId="12" pageNumber="13">Belize</collectingCountry>
. Whether the entirety of this distribution belongs to this lineage is unknown. Furthermore, with our sampling of only two individuals, we were unable to include this lineage in our demographic analyses, so whether there is gene flow between this lineage and adjacent populations is also unknown.
</paragraph>
<paragraph id="8BF41D54FF9AFFF7FF06F9A7DD2FF8D9" blockId="12.[129,779,144,1828]" pageId="12" pageNumber="13">
Model selection with genomic data supported population size expansion in all lineages. These demographic size changes probably reflect population expansion associated with the end of the last glacial maxima in the Late Pleistocene, a common finding in phylogeographic studies of taxa in eastern North America (
<bibRefCitation id="EFDA60A5FF9AFFF7FF11F91BDF22F93B" author="Hewit G" box="[139,267,1710,1734]" pageId="12" pageNumber="13" pagination="907 - 13" refId="ref13865" refString="Hewit G. Te genetic legacy of the quaternary ice ages. Nature 2000; 405: 907 - 13. htps: // doi. org / 10.1038 / 35016000" type="journal article" year="2000">Hewitt 2000</bibRefCitation>
), and is in agreement with previous single-locus phylogeographic analyses of this taxon (
<bibRefCitation id="EFDA60A5FF9AFFF7FE63F978DC9BF91B" author="Burbrink FT &amp; Fontanella F &amp; Pyron R" box="[505,690,1741,1766]" pageId="12" pageNumber="13" pagination="274 - 88" refId="ref12057" refString="Burbrink FT, Fontanella F, Pyron R et al. Phylogeography across a continent: the evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor). Molecular Phylogenetics and Evolution 2008; 47: 274 - 88." type="journal article" year="2008">
Burbrink
<emphasis id="B93FC146FF9AFFF7FDCEF97BDC56F918" box="[596,639,1741,1765]" italics="true" pageId="12" pageNumber="13">et al.</emphasis>
2008
</bibRefCitation>
). The inferred population expansions also agree with the ENMs projected to the LGM where all lineages have large reductions in suitable habitat.
</paragraph>
</subSubSection>
</treatment>
</document>