300 lines
42 KiB
XML
300 lines
42 KiB
XML
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<mods:title id="BC31EE7BC31DC50B12C8DC8912F3BBCC">Systematics of Damselfishes</mods:title>
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<treatment id="A0558C73FFB8FFD1931C163091FEFC4E" ID-DOI="http://doi.org/10.5281/zenodo.7850179" ID-GBIF-Taxon="209579126" ID-Zenodo-Dep="7850179" LSID="urn:lsid:plazi:treatment:A0558C73FFB8FFD1931C163091FEFC4E" httpUri="http://treatment.plazi.org/id/A0558C73FFB8FFD1931C163091FEFC4E" lastPageId="25" lastPageNumber="282" pageId="24" pageNumber="282">
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<subSubSection id="60E66EEEFFB8FFD0931C163093D7F86C" box="[103,240,1562,1585]" pageId="24" pageNumber="282" type="nomenclature">
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<paragraph id="28433D65FFB8FFD0931C163093D7F86C" blockId="24.[103,773,1562,2024]" box="[103,240,1562,1585]" pageId="24" pageNumber="282">
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<emphasis id="1A88E177FFB8FFD0931C163093D7F86C" bold="true" box="[103,240,1562,1585]" italics="true" pageId="24" pageNumber="282">
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<taxonomicName id="EFFC46E6FFB8FFD0931C163093CBF86C" ID-CoL="5CM8" ID-ENA="646044" authority="Günther, 1862" authorityName="Günther" authorityYear="1862" box="[103,236,1562,1585]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">Lepidozygus</taxonomicName>
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.
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</emphasis>
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<subSubSection id="60E66EEEFFB8FFD1938B163091FEFC4E" lastPageId="25" lastPageNumber="283" pageId="24" pageNumber="282" type="description">
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<paragraph id="28433D65FFB8FFD1938B163091FEFC4E" blockId="24.[103,773,1562,2024]" lastBlockId="25.[142,812,178,532]" lastPageId="25" lastPageNumber="283" pageId="24" pageNumber="282">
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<emphasis id="1A88E177FFB8FFD0938B16309220F86C" bold="true" box="[240,263,1562,1585]" italics="true" pageId="24" pageNumber="282">—</emphasis>
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This is a monotypic genus found throughout the tropical Indo-West Pacific (Allen, 1975a, 1991;
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<bibRefCitation id="4C6D4094FFB8FFD091C216129386F831" author="Emery, A. R." pageId="24" pageNumber="282" pagination="1326 - 1338" refId="ref65832" refString="Emery, A. R. 1983. Geographic variation in the Indo-Pacific damselfish genus Lepidozygus (Pisces: Pomacentridae). Canadian Journal of Zoology 61: 1326 - 1338." type="journal article" year="1983">Emery, 1983</bibRefCitation>
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). The classification of the Fuselier Damsel (
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<taxonomicName id="EFFC46E6FFB8FFD091F2167F93CFF8D5" baseAuthorityName="Bleeker" baseAuthorityYear="1856" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="tapeinosoma">
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<emphasis id="1A88E177FFB8FFD091F2167F93CFF8D5" italics="true" pageId="24" pageNumber="282">Lepidozygus tapeinosoma</emphasis>
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</taxonomicName>
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) warrants further attention because our results contradict earlier works that assigned
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<taxonomicName id="EFFC46E6FFB8FFD0917416A591ACF8F8" authorityName="Günther" authorityYear="1862" box="[527,651,1679,1701]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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<emphasis id="1A88E177FFB8FFD0917416A591ACF8F8" box="[527,651,1679,1701]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
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</taxonomicName>
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to its own monotypic subfamily (Allen, 1975a, 1991; Cooper et al., 2009; Cooper and Santini, 2016). This taxon has drawn particular interest since it was accorded subfamilial status by Allen (1975a). Cooper et al. (2009) were the first to include
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<taxonomicName id="EFFC46E6FFB8FFD0931C170893C4F965" authorityName="Günther" authorityYear="1862" box="[103,227,1826,1848]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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<emphasis id="1A88E177FFB8FFD0931C170893C4F965" box="[103,227,1826,1848]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
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</taxonomicName>
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in a molecular phylogeny, and they placed it as the sister group of all pomacentrids except
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<taxonomicName id="EFFC46E6FFB8FFD0913D171593B9F92E" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="300" phylum="Chordata" rank="subFamily" subFamily="Microspathodontinae">Microspathodontinae</taxonomicName>
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(their
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<taxonomicName id="EFFC46E6FFB8FFD0938917769257F92E" box="[242,368,1884,1907]" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="301" phylum="Chordata" rank="subFamily" subFamily="Stegastinae">Stegastinae</taxonomicName>
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||
). Cooper and Santini (2016) maintained the subfamilial rank for the
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<taxonomicName id="EFFC46E6FFB8FFD0928B175091A8F9CD" box="[496,655,1914,1936]" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="299" phylum="Chordata" rank="subFamily" subFamily="Lepidozyginae">Lepidozyginae</taxonomicName>
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but noted its uncertain status, citing the long branch connecting it to other pomacentrids. Other studies have recovered relationships for
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<taxonomicName id="EFFC46E6FFB8FFD093A117FB9271F9BA" authorityName="Günther" authorityYear="1862" box="[218,342,2001,2023]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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<emphasis id="1A88E177FFB8FFD093A117FB9271F9BA" box="[218,342,2001,2023]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
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</taxonomicName>
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that are at least congruent with its treatment as a separate subfamily (e.g., Cowman and Bellwood, 2011;
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<bibRefCitation id="4C6D4094FFB8FFD0908910FA97E8FEB8" author="Litsios, G. & C. A. Sims & R. O. Wuest & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[1010,1231,208,230]" pageId="24" pageNumber="282" pagination="212" refId="ref72166" refString="Litsios, G., C. A. Sims, R. O. Wuest, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 a. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12: 212." type="journal article" year="2012">Litsios et al., 2012a</bibRefCitation>
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||
;
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<bibRefCitation id="4C6D4094FFB8FFD097A610FA96EAFEB8" author="Frederich, B. & L. Sorenson & F. Santini & G. J. Slater & M. E. Alfaro" box="[1245,1485,208,230]" pageId="24" pageNumber="282" pagination="94 - 113" refId="ref66743" refString="Frederich, B., L. Sorenson, F. Santini, G. J. Slater, and M. E. Alfaro. 2013. Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae). The American Naturalist 181: 94 - 113." type="journal article" year="2013">Frédérich et al., 2013</bibRefCitation>
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;
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<bibRefCitation id="4C6D4094FFB8FFD0904F10C49738FF5E" author="Rabosky, D. L. & F. Santini & J. Eastman & S. A. Smith & B. Sidlauskas & J. Chang & M. E. Alfaro" box="[820,1055,238,260]" pageId="24" pageNumber="282" pagination="1958" refId="ref76375" refString="Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4: 1958." type="journal article" year="2013">Rabosky et al., 2013</bibRefCitation>
|
||
;
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<bibRefCitation id="4C6D4094FFB8FFD0975410C4962CFF5E" author="Lobato, F. L. & D. R. Barneche & A. C. Siqueira & A. M. R. Liedke & A. Lindner & M. R. Pie & D. R. Bellwood & S. R. Floeter" box="[1071,1291,238,260]" pageId="24" pageNumber="282" pagination="102094" refId="ref72399" refString="Lobato, F. L., D. R. Barneche, A. C. Siqueira, A. M. R. Liedke, A. Lindner, M. R. Pie, D. R. Bellwood, and S. R. Floeter. 2014. Diet and diversification in the evolution of coral reef fishes. PLoS ONE 9: e 102094." type="journal article" year="2014">Lobato et al., 2014</bibRefCitation>
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||
; DiBattista et al., 2016;
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<bibRefCitation id="4C6D4094FFB8FFD0900311219717FF7D" author="Stieb, S. M. & F. Cortesi & L. Sueess & K. L. Carleton & W. Salzburger & N. J. Marshall" box="[888,1072,267,289]" pageId="24" pageNumber="282" pagination="1323 - 1342" refId="ref80388" refString="Stieb, S. M., F. Cortesi, L. Sueess, K. L. Carleton, W. Salzburger, and N. J. Marshall. 2017. Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes. Molecular Ecology 26: 1323 - 1342." type="journal article" year="2017">Stieb et al., 2017</bibRefCitation>
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||
;
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<bibRefCitation id="4C6D4094FFB8FFD0974011219604FF7D" author="Gaboriau, T. & F. Leprieur & D. Mouillot & N. Hubert" box="[1083,1315,267,289]" pageId="24" pageNumber="282" pagination="1295 - 1306" refId="ref67249" refString="Gaboriau, T., F. Leprieur, D. Mouillot, and N. Hubert. 2018. Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific. Ecography 41: 1295 - 1306." type="journal article" year="2018">Gaboriau et al., 2018</bibRefCitation>
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||
; Delrieu-Trottin et al., 2019). However, they all relied on the sequences of
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<taxonomicName id="EFFC46E6FFB8FFD0904F116C9097FF01" authorityName="Günther" authorityYear="1862" box="[820,944,326,348]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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<emphasis id="1A88E177FFB8FFD0904F116C9097FF01" box="[820,944,326,348]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
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</taxonomicName>
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produced by Cooper et al. (2009). In contrast, other studies have recovered a relationship similar to the one that we found:
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<taxonomicName id="EFFC46E6FFB8FFD0909911AA9779FFCB" authorityName="Günther" authorityYear="1862" box="[994,1118,384,406]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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||
<emphasis id="1A88E177FFB8FFD0909911AA9779FFCB" box="[994,1118,384,406]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
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||
closely allied with
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<emphasis id="1A88E177FFB8FFD0964C11AB9055FFE9" italics="true" pageId="24" pageNumber="282">
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||
<taxonomicName id="EFFC46E6FFB8FFD0964C11AB96F5FFCB" authorityName="Barlow" authorityYear="1972" box="[1335,1490,385,406]" class="Actinopterygii" family="Pomacentridae" genus="Stegastes" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="sensu">
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Stegastes
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||
<taxonomicNameLabel id="01BB5C0CFFB8FFD096E111AB96F5FFCB" box="[1434,1490,385,406]" pageId="24" pageNumber="282" sensu="stricto">sensu</taxonomicNameLabel>
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</taxonomicName>
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||
stricto
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||
</emphasis>
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||
(
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<bibRefCitation id="4C6D4094FFB8FFD090FD11B49757FFE9" author="Litsios, G. & L. Pellissier & F. Forest & C. Lexer & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[902,1136,414,436]" pageId="24" pageNumber="282" pagination="3662 - 3669" refId="ref72070" refString="Litsios, G., L. Pellissier, F. Forest, C. Lexer, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 b. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proceedings of the Royal Society B: Biological Sciences 279: 3662 - 3669." type="journal article" year="2012">Litsios et al., 2012b</bibRefCitation>
|
||
: figs. A1–3; Betancur-R. et al., 2013a: Dryad file ‘‘RAxMLThree_Plus_24_part.tre’’, 2015: fig. S1, 2017: ‘‘12862_2017_958_MOESM6_ESM.pdf’’;
|
||
<bibRefCitation id="4C6D4094FFB8FFD0961411F39049FC51" author="Mirande, J. M." pageId="24" pageNumber="282" pagination="333 - 350" refId="ref73614" refString="Mirande, J. M. 2016. Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses. Cladistics 33: 333 - 350." type="journal article" year="2016">Mirande, 2016</bibRefCitation>
|
||
: fig. S11;
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<bibRefCitation id="4C6D4094FFB8FFD090A311DC97FFFC51" author="Sanciangco, M. D. & K. E. Carpenter & R. Betancur-R." box="[984,1240,502,524]" pageId="24" pageNumber="282" pagination="565 - 576" refId="ref78759" refString="Sanciangco, M. D., K. E. Carpenter, and R. Betancur-R. 2016. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). Molecular Phylogenetics and Evolution 94: 565 - 576." type="journal article" year="2016">Sanciangco et al., 2016</bibRefCitation>
|
||
: fig. S1;
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<bibRefCitation id="4C6D4094FFB8FFD0964F11DC9049FC74" author="Rabosky, D. L. & J. Chang & P. O. Title & P. F. Cowman & L. Sallan & M. Friedman & K. Kaschner & C. Garilao & T. J. Near & M. Coll & M. E. Alfaro" pageId="24" pageNumber="282" pagination="392 - 395" refId="ref76299" refString="Rabosky, D. L., J. Chang, P. O. Title, P. F. Cowman, L. Sallan, M. Friedman, K. Kaschner, C. Garilao, T. J. Near, M. Coll, and M. E. Alfaro. 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559: 392 - 395." type="journal article" year="2018">Rabosky et al., 2018</bibRefCitation>
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||
: Dryad file ‘‘actinopt_12k_raxml.tre’’). What these latter studies share in common is that they either generated their own independent RAG1 sequence for
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<taxonomicName id="EFFC46E6FFB8FFD097A812649668FC39" authorityName="Günther" authorityYear="1862" box="[1235,1359,590,612]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
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<emphasis id="1A88E177FFB8FFD097A812649668FC39" box="[1235,1359,590,612]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<bibRefCitation id="4C6D4094FFB8FFD09627126490BDFCDC" author="Rabosky, D. L. & J. Chang & P. O. Title & P. F. Cowman & L. Sallan & M. Friedman & K. Kaschner & C. Garilao & T. J. Near & M. Coll & M. E. Alfaro" pageId="24" pageNumber="282" pagination="392 - 395" refId="ref76299" refString="Rabosky, D. L., J. Chang, P. O. Title, P. F. Cowman, L. Sallan, M. Friedman, K. Kaschner, C. Garilao, T. J. Near, M. Coll, and M. E. Alfaro. 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559: 392 - 395." type="journal article" year="2018">Rabosky et al., 2018</bibRefCitation>
|
||
: table S2, Dryad file ‘‘accession_numbers.csv’’) or they did not analyze its RAG1 data (
|
||
<bibRefCitation id="4C6D4094FFB8FFD097C712A396B4FCC2" author="Litsios, G. & L. Pellissier & F. Forest & C. Lexer & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[1212,1427,649,671]" pageId="24" pageNumber="282" pagination="3662 - 3669" refId="ref72070" refString="Litsios, G., L. Pellissier, F. Forest, C. Lexer, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 b. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proceedings of the Royal Society B: Biological Sciences 279: 3662 - 3669." type="journal article" year="2012">Litsios et al., 2012b</bibRefCitation>
|
||
: table A1; Betancur-R. et al., 2013a: table S1;
|
||
<bibRefCitation id="4C6D4094FFB8FFD0965B128D96E8FCE0" author="Mirande, J. M." box="[1312,1487,679,701]" pageId="24" pageNumber="282" pagination="333 - 350" refId="ref73614" refString="Mirande, J. M. 2016. Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses. Cladistics 33: 333 - 350." type="journal article" year="2016">Mirande, 2016</bibRefCitation>
|
||
: appendix S1;
|
||
<bibRefCitation id="4C6D4094FFB8FFD090B012EE97EBFC87" author="Sanciangco, M. D. & K. E. Carpenter & R. Betancur-R." box="[971,1228,708,730]" pageId="24" pageNumber="282" pagination="565 - 576" refId="ref78759" refString="Sanciangco, M. D., K. E. Carpenter, and R. Betancur-R. 2016. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). Molecular Phylogenetics and Evolution 94: 565 - 576." type="journal article" year="2016">Sanciangco et al., 2016</bibRefCitation>
|
||
: table S1). For example,
|
||
<bibRefCitation id="4C6D4094FFB8FFD0904F12CB9734FCAA" author="Litsios, G. & C. A. Sims & R. O. Wuest & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[820,1043,737,759]" pageId="24" pageNumber="282" pagination="212" refId="ref72166" refString="Litsios, G., C. A. Sims, R. O. Wuest, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 a. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12: 212." type="journal article" year="2012">Litsios et al. (2012a</bibRefCitation>
|
||
: additional file 2) used all of Cooper et al.’s (2009) data for
|
||
<taxonomicName id="EFFC46E6FFB8FFD0976712D597BFFD48" authorityName="Günther" authorityYear="1862" box="[1052,1176,767,789]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0976712D597BFFD48" box="[1052,1176,767,789]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
and found a similar result. However,
|
||
<bibRefCitation id="4C6D4094FFB8FFD090DD133697AEFD6F" author="Litsios, G. & L. Pellissier & F. Forest & C. Lexer & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[934,1161,796,818]" pageId="24" pageNumber="282" pagination="3662 - 3669" refId="ref72070" refString="Litsios, G., L. Pellissier, F. Forest, C. Lexer, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 b. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proceedings of the Royal Society B: Biological Sciences 279: 3662 - 3669." type="journal article" year="2012">Litsios et al. (2012b</bibRefCitation>
|
||
: table A1) used many of the same sequences but excluded that specific RAG1 sequence. A reason for the deletion was not given, but, with that removal, the phylogenetic position of
|
||
<taxonomicName id="EFFC46E6FFB8FFD097E9135E9629FDD7" authorityName="Günther" authorityYear="1862" box="[1170,1294,884,906]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD097E9135E9629FDD7" box="[1170,1294,884,906]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
deviated greatly between the two topologies (
|
||
<bibRefCitation id="4C6D4094FFB8FFD097F413B8965CFDFA" author="Litsios, G. & C. A. Sims & R. O. Wuest & P. B. Pearman & N. E. Zimmermann & N. Salamin" box="[1167,1403,914,936]" pageId="24" pageNumber="282" pagination="212" refId="ref72166" refString="Litsios, G., C. A. Sims, R. O. Wuest, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012 a. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12: 212." type="journal article" year="2012">Litsios et al., 2012a</bibRefCitation>
|
||
: fig. 2; 2012b: figs. A1–3). Similarly,
|
||
<bibRefCitation id="4C6D4094FFB8FFD097FD13859654FD99" author="Rabosky, D. L. & F. Santini & J. Eastman & S. A. Smith & B. Sidlauskas & J. Chang & M. E. Alfaro" box="[1158,1395,943,965]" pageId="24" pageNumber="282" pagination="1958" refId="ref76375" refString="Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4: 1958." type="journal article" year="2013">Rabosky et al. (2013</bibRefCitation>
|
||
: supplementary data 1, Dryad file ‘‘Rabosky_et_al_timetree.tre’’) used three sequences from Cooper et al. (2009), including RAG1, and recovered
|
||
<taxonomicName id="EFFC46E6FFB8FFD0974D142D9795FA40" authorityName="Günther" authorityYear="1862" box="[1078,1202,1031,1053]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0974D142D9795FA40" box="[1078,1202,1031,1053]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
sister to
|
||
<taxonomicName id="EFFC46E6FFB8FFD09652142D968DFA40" baseAuthorityName="sensu Allen" baseAuthorityYear="1975" box="[1321,1450,1031,1053]" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="300" phylum="Chordata" rank="subFamily" subFamily="Chrominae">Chrominae</taxonomicName>
|
||
. In contrast,
|
||
<bibRefCitation id="4C6D4094FFB8FFD090E7140F97A5FA61" author="Rabosky, D. L. & J. Chang & P. O. Title & P. F. Cowman & L. Sallan & M. Friedman & K. Kaschner & C. Garilao & T. J. Near & M. Coll & M. E. Alfaro" box="[924,1154,1061,1084]" pageId="24" pageNumber="282" pagination="392 - 395" refId="ref76299" refString="Rabosky, D. L., J. Chang, P. O. Title, P. F. Cowman, L. Sallan, M. Friedman, K. Kaschner, C. Garilao, T. J. Near, M. Coll, and M. E. Alfaro. 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559: 392 - 395." type="journal article" year="2018">Rabosky et al. (2018)</bibRefCitation>
|
||
replaced that RAG1 with new data. No explanation was given for the change, but they inferred a sister-group relationship between
|
||
<taxonomicName id="EFFC46E6FFB8FFD0965F14759687FA28" authorityName="Günther" authorityYear="1862" box="[1316,1440,1119,1141]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0965F14759687FA28" box="[1316,1440,1119,1141]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<emphasis id="1A88E177FFB8FFD0904F14579736FACE" box="[820,1041,1149,1171]" italics="true" pageId="24" pageNumber="282">
|
||
<taxonomicName id="EFFC46E6FFB8FFD0904F145790EAFACE" authorityName="Barlow" authorityYear="1972" box="[820,973,1149,1171]" class="Actinopterygii" family="Pomacentridae" genus="Stegastes" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="sensu">
|
||
Stegastes
|
||
<taxonomicNameLabel id="01BB5C0CFFB8FFD090EE145490EAFACE" box="[917,973,1150,1171]" pageId="24" pageNumber="282" sensu="stricto">sensu</taxonomicNameLabel>
|
||
</taxonomicName>
|
||
stricto
|
||
</emphasis>
|
||
.
|
||
<bibRefCitation id="4C6D4094FFB8FFD097641457961CFAC9" author="Hofmann, C. M. & N. J. Marshall & K. Abdilleh & Z. Patel & U. E. Siebeck & K. L. Carleton" box="[1055,1339,1149,1172]" pageId="24" pageNumber="282" pagination="79 - 91" refId="ref69319" refString="Hofmann, C. M., N. J. Marshall, K. Abdilleh, Z. Patel, U. E. Siebeck, and K. L. Carleton. 2012. Opsin evolution in damselfish: convergence, reversal, and parallel evolution across tuning sites. Journal of Molecular Evolution 75: 79 - 91." type="journal article" year="2012">Hofmann et al. (2012: 82)</bibRefCitation>
|
||
used 12S and RAG1 from Cooper et al. (2009), resolving
|
||
<taxonomicName id="EFFC46E6FFB8FFD0967614B096AEFAED" authorityName="Günther" authorityYear="1862" box="[1293,1417,1178,1200]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0967614B096AEFAED" box="[1293,1417,1178,1200]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
inside
|
||
<emphasis id="1A88E177FFB8FFD0904F14929732FA93" box="[820,1045,1208,1230]" italics="true" pageId="24" pageNumber="282">
|
||
<taxonomicName id="EFFC46E6FFB8FFD0904F149290EAFA93" authorityName="Moyer and Ida" authorityYear="1976" box="[820,973,1208,1230]" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="sensu">
|
||
Chromis
|
||
<taxonomicNameLabel id="01BB5C0CFFB8FFD090EE149390EAFA93" box="[917,973,1209,1230]" pageId="24" pageNumber="282" sensu="stricto">sensu</taxonomicNameLabel>
|
||
</taxonomicName>
|
||
stricto
|
||
</emphasis>
|
||
, which, in hindsight, gave a clue as to the underlying problem. Despite the apparent disagreement and uncertainty in the literature concerning this taxon, we are confident that our results accurately depict the subfamilial affiliation of
|
||
<taxonomicName id="EFFC46E6FFB8FFD0909015079740FB1E" authorityName="Günther" authorityYear="1862" box="[1003,1127,1325,1347]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0909015079740FB1E" box="[1003,1127,1325,1347]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
because, following an examination of the available data, we suspect that its placement in Cooper et al. (2009: fig. 1) is the result of an error in a single sequence, possibly from data transposition or PCR contamination. In a GenBank BLAST search, their RAG1 sequence for
|
||
<taxonomicName id="EFFC46E6FFB8FFD0904F15EA971CFB8B" baseAuthorityName="Bleeker" baseAuthorityYear="1856" box="[820,1083,1472,1494]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="tapeinosoma">
|
||
<emphasis id="1A88E177FFB8FFD0904F15EA971CFB8B" box="[820,1083,1472,1494]" italics="true" pageId="24" pageNumber="282">Lepidozygus tapeinosoma</emphasis>
|
||
</taxonomicName>
|
||
(GenBank
|
||
<accessionNumber id="37AFA086FFB8FFD097C515EA9601FB8A" box="[1214,1318,1472,1495]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/FJ616676" pageId="24" pageNumber="282">FJ616676</accessionNumber>
|
||
) is identical to their RAG1 sequence for
|
||
<taxonomicName id="EFFC46E6FFB8FFD0973D15F497C2FBA9" authorityName="Fowler & Bean" authorityYear="1928" box="[1094,1253,1502,1524]" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="weberi">
|
||
<emphasis id="1A88E177FFB8FFD0973D15F497C2FBA9" box="[1094,1253,1502,1524]" italics="true" pageId="24" pageNumber="282">Chromis weberi</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<accessionNumber id="37AFA086FFB8FFD0978815F49678FBA8" box="[1267,1375,1502,1525]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/FJ616653" pageId="24" pageNumber="282">FJ616653</accessionNumber>
|
||
). The next closest match (99.8% similarity) is another RAG1 sequence from
|
||
<taxonomicName id="EFFC46E6FFB8FFD0900B163390E8F873" authorityName="Fowler & Bean" authorityYear="1928" box="[880,975,1560,1582]" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="weberi">
|
||
<emphasis id="1A88E177FFB8FFD0900B163390E8F873" box="[880,975,1560,1582]" italics="true" pageId="24" pageNumber="282">C. weberi</emphasis>
|
||
</taxonomicName>
|
||
(
|
||
<accessionNumber id="37AFA086FFB8FFD090A616339775F872" box="[989,1106,1561,1583]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/AY208642" pageId="24" pageNumber="282">AY208642</accessionNumber>
|
||
;
|
||
<bibRefCitation id="4C6D4094FFB8FFD097271633967DF872" author="Quenouille, B. & E. Bermingham & S. Planes" box="[1116,1370,1560,1583]" pageId="24" pageNumber="282" pagination="66 - 88" refId="ref76154" refString="Quenouille, B., E. Bermingham, and S. Planes. 2004. Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution 31: 66 - 88." type="journal article" year="2004">Quenouille et al., 2004</bibRefCitation>
|
||
); the other top ten BLAST results (.97.8%) were all RAG1 sequences from species of
|
||
<emphasis id="1A88E177FFB8FFD090A51679979FF834" box="[990,1208,1619,1641]" italics="true" pageId="24" pageNumber="282">
|
||
<taxonomicName id="EFFC46E6FFB8FFD090A516799753F834" authorityName="Moyer and Ida" authorityYear="1976" box="[990,1140,1619,1641]" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="sensu">
|
||
Chromis
|
||
<taxonomicNameLabel id="01BB5C0CFFB8FFD09747167E9753F834" box="[1084,1140,1620,1641]" pageId="24" pageNumber="282" sensu="stricto">sensu</taxonomicNameLabel>
|
||
</taxonomicName>
|
||
stricto
|
||
</emphasis>
|
||
. That RAG1 sequence is a 99.6% match with the RAG1 sequence from our
|
||
<taxonomicName id="EFFC46E6FFB8FFD09600165B9050F8F9" authorityName="Fowler & Bean" authorityYear="1928" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="weberi">
|
||
<emphasis id="1A88E177FFB8FFD09600165B9050F8F9" italics="true" pageId="24" pageNumber="282">Chromis weberi</emphasis>
|
||
</taxonomicName>
|
||
but has only 91–92% similarity with the RAG1 sequences from our samples of
|
||
<taxonomicName id="EFFC46E6FFB8FFD097C116819611F89C" authorityName="Günther" authorityYear="1862" box="[1210,1334,1707,1729]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD097C116819611F89C" box="[1210,1334,1707,1729]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
and that of
|
||
<bibRefCitation id="4C6D4094FFB8FFD0904F16E39702F883" author="Rabosky, D. L. & J. Chang & P. O. Title & P. F. Cowman & L. Sallan & M. Friedman & K. Kaschner & C. Garilao & T. J. Near & M. Coll & M. E. Alfaro" box="[820,1061,1737,1759]" pageId="24" pageNumber="282" pagination="392 - 395" refId="ref76299" refString="Rabosky, D. L., J. Chang, P. O. Title, P. F. Cowman, L. Sallan, M. Friedman, K. Kaschner, C. Garilao, T. J. Near, M. Coll, and M. E. Alfaro. 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559: 392 - 395." type="journal article" year="2018">Rabosky et al. (2018</bibRefCitation>
|
||
: Dryad file ‘‘alignment.phylip’’). Our RAG1 and Rabosky et al.’s (2018) share 99.1% similarity. Comparing 12S and 16S sequences, the only other genes where our dataset overlaps with Cooper et al. (2009), we found high degrees of similarity between their
|
||
<taxonomicName id="EFFC46E6FFB8FFD0962D171496F5F909" authorityName="Günther" authorityYear="1862" box="[1366,1490,1854,1876]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD0962D171496F5F909" box="[1366,1490,1854,1876]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
data and ours (12S: 97.2%; 16S: 96.8%). Conversely, their 12S and 16S for
|
||
<taxonomicName id="EFFC46E6FFB8FFD090CC17539714F9D2" authorityName="Günther" authorityYear="1862" box="[951,1075,1913,1935]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB8FFD090CC17539714F9D2" box="[951,1075,1913,1935]" italics="true" pageId="24" pageNumber="282">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
showed limited similarity with our
|
||
<taxonomicName id="EFFC46E6FFB8FFD096C117509052F9F0" authorityName="Fowler & Bean" authorityYear="1928" class="Actinopterygii" family="Pomacentridae" genus="Chromis" kingdom="Animalia" order="Perciformes" pageId="24" pageNumber="282" phylum="Chordata" rank="species" species="weberi">
|
||
<emphasis id="1A88E177FFB8FFD096C117509052F9F0" italics="true" pageId="24" pageNumber="282">C. weberi</emphasis>
|
||
</taxonomicName>
|
||
(12S: 83.8%; 16S: 85.2%). This suggests that misidentification of their voucher specimen is unlikely. When we analyzed their non-RAG1 loci in single-gene tree searches,
|
||
<taxonomicName id="EFFC46E6FFB9FFD193F51098922DFE95" authorityName="Günther" authorityYear="1862" box="[142,266,178,200]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB9FFD193F51098922DFE95" box="[142,266,178,200]" italics="true" pageId="25" pageNumber="283">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
was consistently recovered within the
|
||
<taxonomicName id="EFFC46E6FFB9FFD191981099921CFEBA" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="300" phylum="Chordata" rank="subFamily" subFamily="Microspathodontinae">Microspathodontinae</taxonomicName>
|
||
(not shown). An analysis of their data matrix minus the questionable RAG1 sequence (
|
||
<accessionNumber id="37AFA086FFB9FFD1912210C591E5FF5B" box="[601,706,239,262]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/FJ616676" pageId="25" pageNumber="283">FJ616676</accessionNumber>
|
||
) resolved
|
||
<taxonomicName id="EFFC46E6FFB9FFD193F51127922DFF7E" authorityName="Günther" authorityYear="1862" box="[142,266,269,291]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB9FFD193F51127922DFF7E" box="[142,266,269,291]" italics="true" pageId="25" pageNumber="283">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
as the sister group of
|
||
<emphasis id="1A88E177FFB9FFD19174112791D4FF7E" box="[527,755,269,291]" italics="true" pageId="25" pageNumber="283">
|
||
<taxonomicName id="EFFC46E6FFB9FFD191741127918CFF7E" authorityName="Barlow" authorityYear="1972" box="[527,683,269,291]" class="Actinopterygii" family="Pomacentridae" genus="Stegastes" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="species" species="sensu">
|
||
Stegastes
|
||
<taxonomicNameLabel id="01BB5C0CFFB9FFD191081124918CFF7E" box="[627,683,270,291]" pageId="25" pageNumber="283" sensu="stricto">sensu</taxonomicNameLabel>
|
||
</taxonomicName>
|
||
stricto
|
||
</emphasis>
|
||
(not shown), which matches the results of this study (
|
||
<figureCitation id="B0C721E0FFB9FFD191CC110191D4FF1F" box="[695,755,299,322]" captionStart="FIG" captionStartId="7.[142,170,1900,1920]" captionTargetBox="[194,1477,178,1870]" captionTargetId="figure-1@7.[194,1477,178,1870]" captionTargetPageId="7" captionText="FIG. 1. The phylogenetic relationships of damselfishes (Teleostei: Pomacentridae): (A) outgroup taxa; (B) subfamilies Microspathodontinae and Glyphisodontinae; (C) subfamily Chrominae; (D) subfamily Pomacentrinae (part I); (E) subfamily Pomacentrinae (part II). The phylogeny is based on the maximum-likelihood topology with the best log likelihood score (ln L ¼ –45,4518.728) recovered from ten independent maximum-likelihood analyses of a data matrix composed of 462 taxa and 6,865 nucleotides. Bootstrap values from 1,000 ultrafast replicates are displayed for each node" figureDoi="http://doi.org/10.5281/zenodo.7846740" httpUri="https://zenodo.org/record/7846740/files/figure.png" pageId="25" pageNumber="283">Fig. 1</figureCitation>
|
||
). An analysis that included their sequences of
|
||
<taxonomicName id="EFFC46E6FFB9FFD191D811639002FF02" authorityName="Günther" authorityYear="1862" box="[675,805,329,351]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB9FFD191D811639002FF02" box="[675,805,329,351]" italics="true" pageId="25" pageNumber="283">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
, excluding their RAG1, in our data matrix found their taxon clustered with our representatives of
|
||
<taxonomicName id="EFFC46E6FFB9FFD1911211AF91CCFFC6" authorityName="Günther" authorityYear="1862" box="[617,747,389,411]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB9FFD1911211AF91CCFFC6" box="[617,747,389,411]" italics="true" pageId="25" pageNumber="283">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
(not shown), sister to
|
||
<emphasis id="1A88E177FFB9FFD1921B118E916BFFE4" box="[352,588,420,441]" italics="true" pageId="25" pageNumber="283">
|
||
<taxonomicName id="EFFC46E6FFB9FFD1921B118E9127FFE4" authorityName="Barlow" authorityYear="1972" box="[352,512,420,441]" class="Actinopterygii" family="Pomacentridae" genus="Stegastes" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="species" species="sensu">
|
||
Stegastes
|
||
<taxonomicNameLabel id="01BB5C0CFFB9FFD192B3118E9127FFE4" box="[456,512,420,441]" pageId="25" pageNumber="283" sensu="stricto">sensu</taxonomicNameLabel>
|
||
</taxonomicName>
|
||
stricto
|
||
</emphasis>
|
||
within the
|
||
<taxonomicName id="EFFC46E6FFB9FFD1919811899218FF85" class="Actinopterygii" family="Pomacentridae" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="300" phylum="Chordata" rank="subFamily" subFamily="Microspathodontinae">Microspathodontinae</taxonomicName>
|
||
. All indications are that this single aberrant sequence (
|
||
<accessionNumber id="37AFA086FFB9FFD1927911F5924CFFAB" box="[258,363,479,502]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/FJ616676" pageId="25" pageNumber="283">FJ616676</accessionNumber>
|
||
) produced a misleading topology which resulted in an incorrect classification for
|
||
<taxonomicName id="EFFC46E6FFB9FFD1912D11D791F5FC4E" authorityName="Günther" authorityYear="1862" box="[598,722,509,531]" class="Actinopterygii" family="Pomacentridae" genus="Lepidozygus" kingdom="Animalia" order="Perciformes" pageId="25" pageNumber="283" phylum="Chordata" rank="genus">
|
||
<emphasis id="1A88E177FFB9FFD1912D11D791F5FC4E" box="[598,722,509,531]" italics="true" pageId="25" pageNumber="283">Lepidozygus</emphasis>
|
||
</taxonomicName>
|
||
.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |