treatments-xml/data/03/F0/E0/03F0E042C54EFF93FF67F9396317FBB7.xml

<document id="9C42C2E4DA5F1D5FB5B87E2701AB1057" ID-DOI="10.6620/ZS.2023.62-48" ID-ISSN="1810-522X" ID-PMC="PMC10641430" ID-PubMed="37965298" ID-Zenodo-Dep="12828486" IM.bibliography_approvedBy="felipe" IM.illustrations_approvedBy="julia" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.taxonomicNames_approvedBy="felipe" IM.treatments_approvedBy="julia" checkinTime="1721935396705" checkinUser="felipe" docAuthor="Duong, Thuy Yen, Pham, Linh Thi Khanh, Le, Xuyen Thi Kim, Nguyen, Ngoc Tran Thi, Nor, Siti Azizah Mohd &amp; Le, Thanh Hoa" docDate="2023" docId="03F0E042C54EFF93FF67F9396317FBB7" docLanguage="en" docName="ZoolStud.62.48.1-17.pdf" docOrigin="Zoological Studies 62 (48)" docSource="http://dx.doi.org/10.6620/ZS.2023.62-48" docStyle="DocumentStyle:E2601EF9E8BBDC4537EE724C10FF512F.1:ZoolStud.2019-.journal_article" docStyleId="E2601EF9E8BBDC4537EE724C10FF512F" docStyleName="ZoolStud.2019-.journal_article" docStyleVersion="1" docTitle="Pangasiidae Bleeker 1858" docType="treatment" docVersion="1" lastPageNumber="11" masterDocId="FFC9983AC548FF99FFC9FF84626FFFA2" masterDocTitle="Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei." masterLastPageNumber="17" masterPageNumber="1" pageNumber="7" updateTime="1727979283293" updateUser="julia" zenodo-license-document="CC-BY-4.0">
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<mods:title id="1220BAC955907A73CAE761DBF09F53BE">Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei.</mods:title>
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<mods:namePart id="3DAAABDDEB426E5E44F4C95FED798785">Duong, Thuy Yen</mods:namePart>
<mods:affiliation id="F1F769A73307530034C9179DE508ABA7">College of Aquaculture and Fisheries, Can Tho University, 3 / 2 street, Can Tho City, Vietnam. E-mail: thuyyen @ ctu. edu. vn (Duong)</mods:affiliation>
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<mods:namePart id="36CE5C33E3730C1A2E4D5FAC555AA232">Pham, Linh Thi Khanh</mods:namePart>
<mods:affiliation id="117E9758468D4AB0CCCB3919DDB01684">Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., &amp; Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam</mods:affiliation>
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<mods:namePart id="C0DC7370B512AFC94E98410669EF2342">Le, Xuyen Thi Kim</mods:namePart>
<mods:affiliation id="E716F6D122CB9086A84927576FACE84E">Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., &amp; Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam</mods:affiliation>
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<mods:namePart id="2988D4BB565568DA7EDCD0F0D476285A">Nguyen, Ngoc Tran Thi</mods:namePart>
<mods:affiliation id="22EC5514F08F1A2558543E22DAA987A5">College of Aquaculture and Fisheries, Can Tho University, 3 / 2 street, Can Tho City, Vietnam. E-mail: thuyyen @ ctu. edu. vn (Duong)</mods:affiliation>
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<mods:namePart id="DB528C677ABE322F55B209EAED82F47D">Nor, Siti Azizah Mohd</mods:namePart>
<mods:affiliation id="A5DC8C85563258026DC2B54FA828E625">Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: s. azizah @ umt. edu. my (Nor)</mods:affiliation>
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<mods:namePart id="E805E9599868BABCA375678B9A0FB0FF">Le, Thanh Hoa</mods:namePart>
<mods:affiliation id="5579B06B1712C6CB5F30A57D458F64F4">Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., &amp; Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam</mods:affiliation>
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<mods:date id="857A5B937C743AC2D73067F52625D5EB">2023</mods:date>
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Phylogenetic relationships within 
<taxonomicName id="4C592AD7C54EFF9FFD94F9396096F974" ID-CoL="DWM" authorityName="Bleeker" authorityYear="1858" box="[605,761,1725,1750]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
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<paragraph id="8BE65154C54EFF9FFF23F979674DFB94" blockId="6.[174,775,1789,1973]" lastBlockId="6.[850,1455,253,1974]" pageId="6" pageNumber="7">
The complete mtDNA sequence datasets (concatenated 13 PCGs) recovered 
<taxonomicName id="4C592AD7C54EFF9FFD90F89A60BDF897" authorityName="Valenciennes" authorityYear="1840" box="[601,722,1822,1845]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFD90F89A60BDF897" box="[601,722,1822,1845]" italics="true" pageId="6" pageNumber="7">Pangasius</emphasis>
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and 
<taxonomicName id="4C592AD7C54EFF9FFF67F8B9633AF8F7" authorityName="Chevey" authorityYear="1931" box="[174,341,1853,1877]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFF67F8B9633AF8F7" box="[174,341,1853,1877]" italics="true" pageId="6" pageNumber="7">Pangasianodon</emphasis>
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as sister subclades and the 
<taxonomicName id="4C592AD7C54EFF9FFD4EF8B96169F8F7" authorityName="Bleeker" authorityYear="1858" box="[647,774,1853,1877]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
as a monophyletic clade with a 100% bootstrap value (
<figureCitation id="13624DD1C54EFF9FFF7EF8F9636CF837" box="[183,259,1917,1941]" captionStart="Fig" captionStartId="7.[136,167,1470,1489]" captionTargetBox="[136,1416,250,1433]" captionTargetId="figure-6@7.[136,1425,249,1443]" captionTargetPageId="7" captionText="Fig. 2. PhyML-phylogeny of the order Siluriformes, including 32 catfish families (117 sequences) of three suborders, Siluroidei, Loricarioidei, and Diplomystoidei based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of Gonorynchiformes were used as an outgroup. The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X (Kumar et al. 2018). The basal nodes of the three suborders (Diplomystoidei, Loricarioidei, and Siluroidei) as well as the two major “Big Asia” and “Big Africa” groups (background highlighted) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are indicated by stars and with the associated families’ background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Saitoh et al. 2003; Nakatani et al. 2011; Kappas et al. 2016; Zhang et al. 2021; Schedel et al. 2022). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828490" httpUri="https://zenodo.org/record/12828490/files/figure.png" pageId="6" pageNumber="7">Fig. 2</figureCitation>
). The ML tree clarified the monophyly of 
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<emphasis id="B92D8D46C54EFF9FFF67F819630EF817" box="[174,353,1949,1973]" italics="true" pageId="6" pageNumber="7">Pangasianodon</emphasis>
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and 
<taxonomicName id="4C592AD7C54EFF9FFE56F81A6079F817" authorityName="Valenciennes" authorityYear="1840" box="[415,534,1950,1973]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFE56F81A6079F817" box="[415,534,1950,1973]" italics="true" pageId="6" pageNumber="7">Pangasius</emphasis>
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with 88% bootstrap support. The ML tree clarified the monophyly of 
<taxonomicName id="4C592AD7C54EFF9FFCBEFE99665BFE97" authorityName="Chevey" authorityYear="1931" box="[887,1076,285,309]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFCBEFE99665BFE97" box="[887,1076,285,309]" italics="true" pageId="6" pageNumber="7">Pangasianodon</emphasis>
</taxonomicName>
, with 88% bootstrap support. 
<taxonomicName id="4C592AD7C54EFF9FFC9BFEB9662EFEF7" box="[850,1089,317,341]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="gigas">
<emphasis id="B92D8D46C54EFF9FFC9BFEB9662EFEF7" box="[850,1089,317,341]" italics="true" pageId="6" pageNumber="7">Pangasianodon gigas</emphasis>
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is identified as a sister taxon to a group of 
<taxonomicName id="4C592AD7C54EFF9FFC19FEDA6612FED7" authorityName="Smith" authorityYear="1931" box="[976,1149,350,373]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="sanitwongsei">
<emphasis id="B92D8D46C54EFF9FFC19FEDA6612FED7" box="[976,1149,350,373]" italics="true" pageId="6" pageNumber="7">P. sanitwongsei</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C54EFF9FFB7FFEDA67E4FED7" authorityName="Sauvage" authorityYear="1878" box="[1206,1419,349,373]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54EFF9FFB7FFEDA67E4FED7" box="[1206,1419,349,373]" italics="true" pageId="6" pageNumber="7">Pn. hypophthalmus</emphasis>
</taxonomicName>
(5 mitogenomes), and 
<taxonomicName id="4C592AD7C54EFF9FFBFAFEFA6760FE37" box="[1075,1295,381,405]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="bocourti">
<emphasis id="B92D8D46C54EFF9FFBFAFEFA6760FE37" box="[1075,1295,381,405]" italics="true" pageId="6" pageNumber="7">Pangasius bocourti</emphasis>
</taxonomicName>
(as named in GenBank under no. MN842723) is positioned in the 
<taxonomicName id="4C592AD7C54EFF9FFC9BFE3A664EFE77" authorityName="Sauvage" authorityYear="1878" box="[850,1057,445,469]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54EFF9FFC9BFE3A664EFE77" box="[850,1057,445,469]" italics="true" pageId="6" pageNumber="7">Pn. hypophthalmus</emphasis>
</taxonomicName>
group with 100% bootstrap support. Within the 
<taxonomicName id="4C592AD7C54EFF9FFC1AFE5A6629FE57" authorityName="Valenciennes" authorityYear="1840" box="[979,1094,478,501]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFC1AFE5A6629FE57" box="[979,1094,478,501]" italics="true" pageId="6" pageNumber="7">Pangasius</emphasis>
</taxonomicName>
, 
<taxonomicName id="4C592AD7C54EFF9FFB9FFE5A676EFE57" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[1110,1281,477,501]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C54EFF9FFB9FFE5A676EFE57" box="[1110,1281,477,501]" italics="true" pageId="6" pageNumber="7">P. mekongensis</emphasis>
</taxonomicName>
was recovered as a sister taxon to the Indian 
<taxonomicName id="4C592AD7C54EFF9FFB70FE7A6615FD94" authority="Hamilton-Buchanan, 1822" authorityName="Hamilton-Buchanan" authorityYear="1822" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="pangasius">
<emphasis id="B92D8D46C54EFF9FFB70FE7A67C3FDB7" box="[1209,1452,510,533]" italics="true" pageId="6" pageNumber="7">Pangasius pangasius</emphasis>
Hamilton-Buchanan, 1822
</taxonomicName>
(
<bibRefCitation id="EFC82CA5C54EFF9FFB42FD996705FD94" author="Hossain MY &amp; Rhaman MM &amp; Mollah MFA" box="[1163,1386,541,566]" pageId="6" pageNumber="7" pagination="315 - 316" refId="ref12613" refString="Hossain MY, Rhaman MM, Mollah MFA. 2009. Threatened fishes of the world: Pangasius pangasius Hamilton-Buchanan, 1822 (Pangasiidae). Environ Biol Fishes 84 (3): 315 - 316. doi: 10.1007 / s 10641 - 008 - 9422 - y." type="journal article" year="2009">Hossain et al. 2009</bibRefCitation>
) with a very high bootstrap (100%), while 
<taxonomicName id="4C592AD7C54EFF9FFACBFDBA6719FDF7" authorityName="Fang &amp; Chaux" authorityYear="1949" box="[1282,1398,573,597]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="krempfi">
<emphasis id="B92D8D46C54EFF9FFACBFDBA6719FDF7" box="[1282,1398,573,597]" italics="true" pageId="6" pageNumber="7">P. krempfi</emphasis>
</taxonomicName>
was placed in between 
<taxonomicName id="4C592AD7C54EFF9FFBFBFDDA66D2FDD7" box="[1074,1213,605,629]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="larnaudii">
<emphasis id="B92D8D46C54EFF9FFBFBFDDA66D2FDD7" box="[1074,1213,605,629]" italics="true" pageId="6" pageNumber="7">P. larnaudii</emphasis>
</taxonomicName>
and the two abovementioned 
<taxonomicName id="4C592AD7C54EFF9FFC18FDFA66F1FD37" box="[977,1182,637,661]" pageId="6" pageNumber="7">
<emphasis id="B92D8D46C54EFF9FFC18FDFA662BFD37" box="[977,1092,638,661]" italics="true" pageId="6" pageNumber="7">Pangasius</emphasis>
species
</taxonomicName>
(
<taxonomicName id="4C592AD7C54EFF9FFB78FDFA6733FD37" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[1201,1372,637,661]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C54EFF9FFB78FDFA6733FD37" box="[1201,1372,637,661]" italics="true" pageId="6" pageNumber="7">P. mekongensis</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C54EFF9FFA5EFDFA61D1FD17" authorityName="Hamilton-Buchanan" authorityYear="1822" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="pangasius">
<emphasis id="B92D8D46C54EFF9FFA5EFDFA61D1FD17" italics="true" pageId="6" pageNumber="7">P. pangasius</emphasis>
</taxonomicName>
) with a moderate bootstrap value (68%). The most concerning feature is that 
<taxonomicName id="4C592AD7C54EFF9FFB0DFD3A6719FD77" authorityName="Smith" authorityYear="1931" box="[1220,1398,702,725]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="sanitwongsei">
<emphasis id="B92D8D46C54EFF9FFB0DFD3A6719FD77" box="[1220,1398,702,725]" italics="true" pageId="6" pageNumber="7">P. sanitwongsei</emphasis>
</taxonomicName>
was positioned as a sister taxon to a subgroup of all the 
<taxonomicName id="4C592AD7C54EFF9FFA4EFD5A6199FCB7" authorityName="Sauvage" authorityYear="1878" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54EFF9FFA4EFD5A6199FCB7" italics="true" pageId="6" pageNumber="7">Pn. hypophthalmus</emphasis>
</taxonomicName>
sequences (bootstrap 98%), and was in between this subgroup and 
<taxonomicName id="4C592AD7C54EFF9FFB4DFC9A6682FC97" box="[1156,1261,798,821]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="gigas">
<emphasis id="B92D8D46C54EFF9FFB4DFC9A6682FC97" box="[1156,1261,798,821]" italics="true" pageId="6" pageNumber="7">Pn. gigas</emphasis>
</taxonomicName>
(
<figureCitation id="13624DD1C54EFF9FFB37FC99672BFC94" box="[1278,1348,797,822]" captionStart="Fig" captionStartId="7.[136,167,1470,1489]" captionTargetBox="[136,1416,250,1433]" captionTargetId="figure-6@7.[136,1425,249,1443]" captionTargetPageId="7" captionText="Fig. 2. PhyML-phylogeny of the order Siluriformes, including 32 catfish families (117 sequences) of three suborders, Siluroidei, Loricarioidei, and Diplomystoidei based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of Gonorynchiformes were used as an outgroup. The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X (Kumar et al. 2018). The basal nodes of the three suborders (Diplomystoidei, Loricarioidei, and Siluroidei) as well as the two major “Big Asia” and “Big Africa” groups (background highlighted) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are indicated by stars and with the associated families’ background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Saitoh et al. 2003; Nakatani et al. 2011; Kappas et al. 2016; Zhang et al. 2021; Schedel et al. 2022). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828490" httpUri="https://zenodo.org/record/12828490/files/figure.png" pageId="6" pageNumber="7">Fig. 2</figureCitation>
). Several samples may have been misidentified and, therefore, phylogenetically misplaced. In fact, the sequence named “ 
<taxonomicName id="4C592AD7C54EFF9FFC7DFCF9674DFC37" authorityName="Sauvage" authorityYear="1878" box="[948,1314,893,917]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54EFF9FFC7DFCF9674DFC37" box="[948,1314,893,917]" italics="true" pageId="6" pageNumber="7">Pangasianodon_hypophthalmus</emphasis>
</taxonomicName>
_(BaijinCo-Foshan)-China-MZ286355” is 
<taxonomicName id="4C592AD7C54EFF9FFB70FC1A67CCFC17" box="[1209,1443,925,949]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="larnaudii">
<emphasis id="B92D8D46C54EFF9FFB70FC1A67CCFC17" box="[1209,1443,925,949]" italics="true" pageId="6" pageNumber="7">Pangasius larnaudii</emphasis>
</taxonomicName>
, and the “ 
<taxonomicName id="4C592AD7C54EFF9FFC77FC3A6739FC77" authority="(QingyuanGD)" baseAuthorityName="QingyuanGD" box="[958,1366,957,981]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="bocourti">
<emphasis id="B92D8D46C54EFF9FFC77FC3A66F0FC77" box="[958,1183,957,981]" italics="true" pageId="6" pageNumber="7">Pangasius bocourti</emphasis>
(QingyuanGD)
</taxonomicName>
-China-MN842723” sample is 
<taxonomicName id="4C592AD7C54EFF9FFB98FC5967CBFC57" authorityName="Sauvage" authorityYear="1878" box="[1105,1444,989,1013]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54EFF9FFB98FC5967CBFC57" box="[1105,1444,989,1013]" italics="true" pageId="6" pageNumber="7">Pangasianodon hypophthalmus</emphasis>
</taxonomicName>
. These pangasiid sequences were grouped into their corresponding phylogenetic clades (
<figureCitation id="13624DD1C54EFF9FFB1AFB99677AFB94" box="[1235,1301,1053,1078]" captionStart="Fig" captionStartId="7.[136,167,1470,1489]" captionTargetBox="[136,1416,250,1433]" captionTargetId="figure-6@7.[136,1425,249,1443]" captionTargetPageId="7" captionText="Fig. 2. PhyML-phylogeny of the order Siluriformes, including 32 catfish families (117 sequences) of three suborders, Siluroidei, Loricarioidei, and Diplomystoidei based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of Gonorynchiformes were used as an outgroup. The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X (Kumar et al. 2018). The basal nodes of the three suborders (Diplomystoidei, Loricarioidei, and Siluroidei) as well as the two major “Big Asia” and “Big Africa” groups (background highlighted) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are indicated by stars and with the associated families’ background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Saitoh et al. 2003; Nakatani et al. 2011; Kappas et al. 2016; Zhang et al. 2021; Schedel et al. 2022). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828490" httpUri="https://zenodo.org/record/12828490/files/figure.png" pageId="6" pageNumber="7">Fig. 2</figureCitation>
).
</paragraph>
<paragraph id="8BE65154C54EFF9FFC46FBB96705F994" blockId="6.[850,1455,253,1974]" pageId="6" pageNumber="7">
Furthermore, using single-gene datasets, we investigated the close phylogenetic relationships between 
<taxonomicName id="4C592AD7C54EFF9FFC7DFBFA664CFB37" authorityName="Valenciennes" authorityYear="1840" box="[948,1059,1150,1173]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFC7DFBFA664CFB37" box="[948,1059,1150,1173]" italics="true" pageId="6" pageNumber="7">Pangasius</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C54EFF9FFB95FBF9676BFB37" authorityName="Chevey" authorityYear="1931" box="[1116,1284,1149,1173]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C54EFF9FFB95FBF9676BFB37" box="[1116,1284,1149,1173]" italics="true" pageId="6" pageNumber="7">Pangasianodon</emphasis>
</taxonomicName>
. Multiple 
<emphasis id="B92D8D46C54EFF9FFAB0FBFA67F1FB37" box="[1401,1438,1150,1173]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 and 
<emphasis id="B92D8D46C54EFF9FFC4BFB1A61CEFB17" box="[898,929,1182,1205]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B barcode sequences are available in GenBank and in previous publications; therefore, we downloaded all 
<emphasis id="B92D8D46C54EFF9FFCB0FB5A61CFFB57" box="[889,928,1246,1269]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 (551 bp) and 
<emphasis id="B92D8D46C54EFF9FFB93FB5A6614FB57" box="[1114,1147,1246,1269]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B (634 bp) sequences and extracted 
<emphasis id="B92D8D46C54EFF9FFC73FB7A61B0FAB7" box="[954,991,1278,1301]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 and 
<emphasis id="B92D8D46C54EFF9FFBE9FB7A6650FAB7" box="[1056,1087,1278,1301]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B, respectively, from the complete mitogenomes (listed in 
<tableCitation id="C6DB64EFC54EFF9FFB95FA9966AEFA94" box="[1116,1217,1309,1334]" captionStart="Table S" captionStartId="16.[850,914,1214,1238]" captionText="Table S3. Accession numbers and country report for the reference cox1 and cytB markers from the GenBank database and those from this study used for the pangasiid comparative phylogenetic studies. (download)" pageId="6" pageNumber="7">Table S3</tableCitation>
). The 
<emphasis id="B92D8D46C54EFF9FFAC5FA9A675DFA97" box="[1292,1330,1310,1333]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 and 
<emphasis id="B92D8D46C54EFF9FFAB0FA9A67F6FA97" box="[1401,1433,1310,1333]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B topologies also revealed that the 
<taxonomicName id="4C592AD7C54EFF9FFB18FAB96738FAF7" authorityName="Bleeker" authorityYear="1858" box="[1233,1367,1341,1365]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
were a sister group to the 
<taxonomicName id="4C592AD7C54EFF9FFBEBFAD966B0FAD7" authorityName="Mo" authorityYear="1991" box="[1058,1247,1373,1397]" family="Austroglanididae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Austroglanididae</taxonomicName>
. All three families (
<taxonomicName id="4C592AD7C54EFF9FFC93FAF9618DFA37" authorityName="Bleeker" authorityYear="1858" box="[858,994,1405,1429]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
, 
<taxonomicName id="4C592AD7C54EFF9FFC26FAF966C7FA37" authorityName="Myers" authorityYear="1931" box="[1007,1192,1405,1429]" family="Cranoglanididae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Cranoglanididae</taxonomicName>
, and 
<taxonomicName id="4C592AD7C54EFF9FFB2CFAF967CBFA37" authorityName="Mo" authorityYear="1991" box="[1253,1444,1405,1429]" family="Austroglanididae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Austroglanididae</taxonomicName>
) together with the 
<taxonomicName id="4C592AD7C54EFF9FFBDFFA1966E6FA17" authorityName="T.N.Gill" authorityYear="1861" box="[1046,1161,1437,1461]" family="Ictaluridae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Ictaluridae</taxonomicName>
formed a large group that was always a sister group to the 
<taxonomicName id="4C592AD7C54EFF9FFB73FA396762FA77" box="[1210,1293,1469,1493]" family="Ariidae" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="family">Ariidae</taxonomicName>
, as discovered in the mitophylogeny constructed based on the complete mitogenome data in our current study and as in the previously reported analysis (
<bibRefCitation id="EFC82CA5C54EFF9FFB44F9996731F994" author="Schedel FDB &amp; Chakona A &amp; Sidlauskas BL &amp; Popoola MO &amp; Usimesa Wingi N &amp; Neumann D &amp; Vreven EJWMN &amp; Schliewen UK" box="[1165,1374,1565,1590]" pageId="6" pageNumber="7" pagination="1171 - 1186" refId="ref14349" refString="Schedel FDB, Chakona A, Sidlauskas BL, Popoola MO, Usimesa Wingi N, Neumann D, Vreven EJWMN, Schliewen UK. 2022. Newphylogenetic insights into the African catfish families Mochokidae and Austroglanididae. J Fish Biol 100 (5): 1171 - 1186. doi: 10.1111 / jfb. 15014." type="journal article" year="2022">Schedel et al. 2022</bibRefCitation>
).
</paragraph>
<paragraph id="8BE65154C54EFF93FC46F9B960D9FDD4" blockId="6.[850,1455,253,1974]" lastBlockId="10.[174,775,253,1045]" lastPageId="10" lastPageNumber="11" pageId="6" pageNumber="7">
The 
<emphasis id="B92D8D46C54EFF9FFC0CF9BA6183F9F7" box="[965,1004,1598,1621]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 phylogenetic tree (
<figureCitation id="13624DD1C54EFF9FFB2CF9B96742F9F4" box="[1253,1325,1597,1622]" captionStart="Fig" captionStartId="8.[174,205,1530,1549]" captionTargetBox="[174,1451,251,1495]" captionTargetId="graphics-265@8.[174,1018,254,1462]" captionTargetPageId="8" captionText="Fig. 3. Detailed PhyML-phylogeny based on the analysis of the partial cox1 sequences (551 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 83 sequences, including 81 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Gymnotiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Karinthanyakit and Jondeung 2012; Tran and Duong 2019; Schedel et al. 2022). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828492" httpUri="https://zenodo.org/record/12828492/files/figure.png" pageId="6" pageNumber="7">Fig. 3</figureCitation>
) indicated that 
<taxonomicName id="4C592AD7C54EFF9FFC4BF9DA6649F9D7" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[898,1062,1629,1653]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C54EFF9FFC4BF9DA6649F9D7" box="[898,1062,1629,1653]" italics="true" pageId="6" pageNumber="7">P. mekongensis</emphasis>
</taxonomicName>
(4 sequences) is a sister taxon to 
<taxonomicName id="4C592AD7C54EFF9FFA51F9DA61D0F937" authorityName="Hamilton-Buchanan" authorityYear="1822" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="pangasius">
<emphasis id="B92D8D46C54EFF9FFA51F9DA61D0F937" italics="true" pageId="6" pageNumber="7">P. pangasius</emphasis>
</taxonomicName>
(8 sequences) with relatively high bootstrap support (88%). In the 
<emphasis id="B92D8D46C54EFF9FFB8EF91A6609F917" box="[1095,1126,1694,1717]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B tree (
<figureCitation id="13624DD1C54EFF9FFB73F9196691F914" box="[1210,1278,1693,1718]" captionStart="Fig" captionStartId="9.[136,167,1645,1664]" captionTargetBox="[206,1344,251,1563]" captionTargetId="graphics-251@9.[206,1031,251,1563]" captionTargetPageId="9" captionText="Fig. 4. Detailed PhyML-phylogeny based on the analysis of the partial cytB sequences (634 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 80 sequences, including 78 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Clupeiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828494" httpUri="https://zenodo.org/record/12828494/files/figure.png" pageId="6" pageNumber="7">Fig. 4</figureCitation>
), this species is sistered with 
<taxonomicName id="4C592AD7C54EFF9FFC24F93A6614F977" authorityName="Hamilton-Buchanan" authorityYear="1822" box="[1005,1147,1726,1749]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="pangasius">
<emphasis id="B92D8D46C54EFF9FFC24F93A6614F977" box="[1005,1147,1726,1749]" italics="true" pageId="6" pageNumber="7">P. pangasius</emphasis>
</taxonomicName>
with 100% nodal support. 
<taxonomicName id="4C592AD7C54EFF9FFC9BF95A6643F957" authorityName="Fang &amp; Chaux" authorityYear="1949" box="[850,1068,1757,1781]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="krempfi">
<emphasis id="B92D8D46C54EFF9FFC9BF95A6643F957" box="[850,1068,1757,1781]" italics="true" pageId="6" pageNumber="7">Pangasius krempfi</emphasis>
</taxonomicName>
, in the 
<emphasis id="B92D8D46C54EFF9FFB45F95A66DCF957" box="[1164,1203,1758,1781]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 tree, was shown to be close to the 
<taxonomicName id="4C592AD7C54EFF9FFBCFF9796693F8B7" box="[1030,1276,1789,1813]" pageId="6" pageNumber="7">
<emphasis id="B92D8D46C54EFF9FFBCFF97966CEF8B7" box="[1030,1185,1789,1813]" italics="true" pageId="6" pageNumber="7">Helicophagus</emphasis>
species
</taxonomicName>
(
<taxonomicName id="4C592AD7C54EFF9FFAD9F9796187F897" authorityName="Ng &amp; Kottelat" authorityYear="2000" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="leptorhynchus">
<emphasis id="B92D8D46C54EFF9FFAD9F9796187F897" italics="true" pageId="6" pageNumber="7">Helicophagus leptorhynchus</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C54EFF9FFBD5F8996743F897" authorityName="Bleeker" authorityYear="1858" box="[1052,1324,1821,1845]" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="waandersii">
<emphasis id="B92D8D46C54EFF9FFBD5F8996743F897" box="[1052,1324,1821,1845]" italics="true" pageId="6" pageNumber="7">Helicophagus waandersii</emphasis>
</taxonomicName>
) with a low bootstrap of 44%, and was placed as a sister taxon in the 
<emphasis id="B92D8D46C54EFF9FFC9BF8DA611EF8D7" box="[850,881,1886,1909]" italics="true" pageId="6" pageNumber="7">cyt</emphasis>
B tree in a non-stable phylogenetic relationship with a 63% bootstrap, to 
<taxonomicName id="4C592AD7C54EFF9FFBE0F8FA66AEF837" authorityName="Bleeker" authorityYear="1850" box="[1065,1217,1918,1941]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="macronema">
<emphasis id="B92D8D46C54EFF9FFBE0F8FA66AEF837" box="[1065,1217,1918,1941]" italics="true" pageId="6" pageNumber="7">P. macronema</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C54EFF9FFB3CF8FA67CAF837" authorityName="Bleeker" authorityYear="1852" box="[1269,1445,1917,1941]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="6" pageNumber="7" phylum="Chordata" rank="species" species="polyuranodon">
<emphasis id="B92D8D46C54EFF9FFB3CF8FA67CAF837" box="[1269,1445,1917,1941]" italics="true" pageId="6" pageNumber="7">P. polyuranodon</emphasis>
</taxonomicName>
. The partial 
<emphasis id="B92D8D46C54EFF9FFC11F81A6191F817" box="[984,1022,1950,1973]" italics="true" pageId="6" pageNumber="7">cox</emphasis>
1 datasets (four sequences, consisting of two from 
<collectingCountry id="F34E11C4C542FF93FE8AFF7963B7FEB7" box="[323,472,253,277]" name="South Africa" pageId="10" pageNumber="11">South Africa</collectingCountry>
, one from 
<collectingCountry id="F34E11C4C542FF93FD91FF7960F1FEB7" box="[600,670,253,277]" name="China" pageId="10" pageNumber="11">China</collectingCountry>
, and one from 
<collectingCountry id="F34E11C4C542FF93FF20FE996337FE97" box="[233,344,285,309]" name="Cambodia" pageId="10" pageNumber="11">Cambodia</collectingCountry>
) and 
<emphasis id="B92D8D46C542FF93FE5DFE9A63DCFE97" box="[404,435,286,309]" italics="true" pageId="10" pageNumber="11">cyt</emphasis>
B datasets (two sequences from 
<collectingCountry id="F34E11C4C542FF93FF67FEB96362FEF7" box="[174,269,317,341]" name="Thailand" pageId="10" pageNumber="11">Thailand</collectingCountry>
and one from 
<collectingCountry id="F34E11C4C542FF93FE60FEB96385FEF7" box="[425,490,317,341]" name="China" pageId="10" pageNumber="11">China</collectingCountry>
) of the correctly identified 
<taxonomicName id="4C592AD7C542FF93FF67FEDA6308FED7" authorityName="Smith" authorityYear="1931" box="[174,359,350,373]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="sanitwongsei">
<emphasis id="B92D8D46C542FF93FF67FEDA6308FED7" box="[174,359,350,373]" italics="true" pageId="10" pageNumber="11">P. sanitwongsei</emphasis>
</taxonomicName>
species placed this taxon into the 
<taxonomicName id="4C592AD7C542FF93FF67FEFA6371FE37" authorityName="Valenciennes" authorityYear="1840" box="[174,286,382,405]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF67FEFA6371FE37" box="[174,286,382,405]" italics="true" pageId="10" pageNumber="11">Pangasius</emphasis>
</taxonomicName>
clade, although with low support (bootstrap 36% and 29%, respectively) (
<figureCitation id="13624DD1C542FF93FE21FE19605EFE14" box="[488,561,413,438]" captionStart="Fig" captionStartId="8.[174,205,1530,1549]" captionTargetBox="[174,1451,251,1495]" captionTargetId="graphics-265@8.[174,1018,254,1462]" captionTargetPageId="8" captionText="Fig. 3. Detailed PhyML-phylogeny based on the analysis of the partial cox1 sequences (551 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 83 sequences, including 81 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Gymnotiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Karinthanyakit and Jondeung 2012; Tran and Duong 2019; Schedel et al. 2022). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828492" httpUri="https://zenodo.org/record/12828492/files/figure.png" pageId="10" pageNumber="11">Figs. 3</figureCitation>
and 
<figureCitation id="13624DD1C542FF93FDACFE1A601AFE14" box="[613,629,414,438]" captionStart="Fig" captionStartId="9.[136,167,1645,1664]" captionTargetBox="[206,1344,251,1563]" captionTargetId="graphics-251@9.[206,1031,251,1563]" captionTargetPageId="9" captionText="Fig. 4. Detailed PhyML-phylogeny based on the analysis of the partial cytB sequences (634 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 80 sequences, including 78 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Clupeiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828494" httpUri="https://zenodo.org/record/12828494/files/figure.png" pageId="10" pageNumber="11">4</figureCitation>
). It should be noted that several 
<taxonomicName id="4C592AD7C542FF93FEBEFE3A6071FE77" authorityName="Smith" authorityYear="1931" box="[375,542,446,469]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="sanitwongsei">
<emphasis id="B92D8D46C542FF93FEBEFE3A6071FE77" box="[375,542,446,469]" italics="true" pageId="10" pageNumber="11">P. sanitwongsei</emphasis>
</taxonomicName>
sequences, including Psan-(PB2)-(
<collectingCountry id="F34E11C4C542FF93FEF7FE5963EAFE57" box="[318,389,477,501]" name="China" pageId="10" pageNumber="11">China</collectingCountry>
)-JN020073 and Psan-(PB1)-CN-JN020086, as well as a 
<taxonomicName id="4C592AD7C542FF93FE0CFE7A602CFDB7" box="[453,579,509,533]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="bocourti">
<emphasis id="B92D8D46C542FF93FE0CFE7A602CFDB7" box="[453,579,509,533]" italics="true" pageId="10" pageNumber="11">P. bocourti</emphasis>
</taxonomicName>
sequence, Pboc-(QingyuanGD)-China-MN842723, were placed in the 
<taxonomicName id="4C592AD7C542FF93FF67FDBA6312FDF7" authorityName="Sauvage" authorityYear="1878" box="[174,381,573,597]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C542FF93FF67FDBA6312FDF7" box="[174,381,573,597]" italics="true" pageId="10" pageNumber="11">Pn. hypophthalmus</emphasis>
</taxonomicName>
cluster, which could be attributed to missampling or misidentification (
<figureCitation id="13624DD1C542FF93FDD5FDD9600AFDD4" box="[540,613,605,630]" captionStart="Fig" captionStartId="8.[174,205,1530,1549]" captionTargetBox="[174,1451,251,1495]" captionTargetId="graphics-265@8.[174,1018,254,1462]" captionTargetPageId="8" captionText="Fig. 3. Detailed PhyML-phylogeny based on the analysis of the partial cox1 sequences (551 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 83 sequences, including 81 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Gymnotiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (Karinthanyakit and Jondeung 2012; Tran and Duong 2019; Schedel et al. 2022). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828492" httpUri="https://zenodo.org/record/12828492/files/figure.png" pageId="10" pageNumber="11">Figs. 3</figureCitation>
and 
<figureCitation id="13624DD1C542FF93FD50FDDA60C6FDD4" box="[665,681,606,630]" captionStart="Fig" captionStartId="9.[136,167,1645,1664]" captionTargetBox="[206,1344,251,1563]" captionTargetId="graphics-251@9.[206,1031,251,1563]" captionTargetPageId="9" captionText="Fig. 4. Detailed PhyML-phylogeny based on the analysis of the partial cytB sequences (634 bp) showing the detailed relationships of the family Pangasiidae and related families (Austroglanididae, Ictaluridae, and Cranoglanididae). In total, 80 sequences, including 78 from Pangasius and Pangasianodon and 2 outgroup sequences from the order Clupeiformes, were included (Table S3). The alignment was performed by MAFFT (Katoh and Standley 2013), curated by BMGE v1.12 (Criscuolo and Gribaldo 2010), the tree was reconstructed in PhyML 3.3 (Guindon et al. 2010) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (Rambaut 2018). The basal nodes of the Pangasiidae and two sister groups (Pangasianodon and (Pangasius + Helicophagus + Pseudolais)) are shown by arrows. The Pangasius mekongensis, Pangasianodon hypophthalmus, and Pangasius krempfi sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from Pangasiidae were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site." figureDoi="http://doi.org/10.5281/zenodo.12828494" httpUri="https://zenodo.org/record/12828494/files/figure.png" pageId="10" pageNumber="11">4</figureCitation>
).
</paragraph>
<caption id="DF2601DCC54FFF9EFF41FA3A66DEF883" ID-DOI="http://doi.org/10.5281/zenodo.12828490" ID-Zenodo-Dep="12828490" httpUri="https://zenodo.org/record/12828490/files/figure.png" pageId="7" pageNumber="8" startId="7.[136,167,1470,1489]" targetBox="[136,1416,250,1433]" targetPageId="7" targetType="figure">
<paragraph id="8BE65154C54FFF9EFF41FA3A66DEF883" blockId="7.[136,1415,1470,1826]" pageId="7" pageNumber="8">
<emphasis id="B92D8D46C54FFF9EFF41FA3A62AEFA73" bold="true" box="[136,193,1470,1489]" pageId="7" pageNumber="8">Fig. 2.</emphasis>
PhyML-phylogeny of the order 
<taxonomicName id="4C592AD7C54FFF9EFE2BFA3A6020FA73" box="[482,591,1470,1489]" class="Siluriformes" higherTaxonomySource="GBIF" kingdom="Animalia" pageId="7" pageNumber="8" phylum="Chordata" rank="class">Siluriformes</taxonomicName>
, including 32 catfish families (117 sequences) of three suborders, 
<taxonomicName id="4C592AD7C54FFF9EFB45FA3A668DFA73" authorityName="Frizzell &amp; Dante" authorityYear="1965" box="[1164,1250,1470,1489]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="3" phylum="Chordata" rank="subOrder" subOrder="Siluroidei">Siluroidei</taxonomicName>
, 
<taxonomicName id="4C592AD7C54FFF9EFB25FA3A6731FA73" box="[1260,1374,1470,1489]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="12" phylum="Chordata" rank="subOrder" subOrder="Loricarioidei">Loricarioidei</taxonomicName>
, and 
<taxonomicName id="4C592AD7C54FFF9EFF41FA5E6362FA4F" box="[136,269,1498,1517]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="12" phylum="Chordata" rank="subOrder" subOrder="Diplomystoidei">Diplomystoidei</taxonomicName>
based on the complete concatenated nucleotide sequences of all 13 mitochondrial protein coding genes (about 11,408 bp in length) (Table S2). Two sequences of 
<taxonomicName id="4C592AD7C54FFF9EFE59FA72605EF9AB" box="[400,561,1526,1545]" kingdom="Animalia" order="Gonorynchiformes" pageId="7" pageNumber="8" phylum="Chordata" rank="order">Gonorynchiformes</taxonomicName>
were used as an outgroup. The alignment was performed by MAFFT (
<bibRefCitation id="EFC82CA5C54FFF9EFB52FA726713F9AB" author="Katoh K &amp; Standley DM" box="[1179,1404,1526,1545]" pageId="7" pageNumber="8" pagination="772 - 780" refId="ref13062" refString="Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772 - 780. doi: 10.1093 / molbev / mst 010." type="journal article" year="2013">Katoh and Standley 2013</bibRefCitation>
), curated by BMGE v1.12 (
<bibRefCitation id="EFC82CA5C54FFF9EFEAFF996600CF987" author="Criscuolo A &amp; Gribaldo S." box="[358,611,1554,1573]" pageId="7" pageNumber="8" refId="ref11753" refString="Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10: 210. doi: 10.1186 / 1471 - 2148 - 10 - 210." type="journal volume" year="2010">Criscuolo and Gribaldo 2010</bibRefCitation>
), the tree was reconstructed in PhyML 3.3 (
<bibRefCitation id="EFC82CA5C54FFF9EFC11F99666EAF987" author="Guindon S &amp; Dufayard JF &amp; Lefort V &amp; Anisimova M &amp; Hordijk W &amp; Gascuel O." box="[984,1157,1554,1574]" pageId="7" pageNumber="8" pagination="307 - 321" refId="ref12206" refString="Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59 (3): 307 - 321. doi: 10.1093 / sysbio / syq 010." type="journal article" year="2010">Guindon et al. 2010</bibRefCitation>
) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (
<bibRefCitation id="EFC82CA5C54FFF9EFB55F9AA6770F9E3" author="Rambaut A." box="[1180,1311,1582,1601]" pageId="7" pageNumber="8" refId="ref14179" refString="Rambaut A. 2018. FigTree, version 1. 4. 4. http: // tree. bio. ed. ac. uk / software / figtree /." type="url" year="2018">Rambaut 2018</bibRefCitation>
). The nodal bootstrap support values (shown at each node) were interpreted from the concurrently constructed tree using the above MAFFT-BMGE alignment by MEGA X (
<bibRefCitation id="EFC82CA5C54FFF9EFF2EF9E263E6F9DB" author="Kumar S &amp; Stecher G &amp; Li M &amp; Knyaz C &amp; Tamura K." box="[231,393,1638,1658]" pageId="7" pageNumber="8" pagination="1547 - 1549" refId="ref13234" refString="Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35: 1547 - 1549. doi: 10.1093 / molbev / msy 096." type="journal article" year="2018">Kumar et al. 2018</bibRefCitation>
). The basal nodes of the three suborders (
<taxonomicName id="4C592AD7C54FFF9EFD38F9E26116F9DB" box="[753,889,1638,1657]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="12" phylum="Chordata" rank="subOrder" subOrder="Diplomystoidei">Diplomystoidei</taxonomicName>
, 
<taxonomicName id="4C592AD7C54FFF9EFC4AF9E2619AF9DB" box="[899,1013,1638,1657]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="12" phylum="Chordata" rank="subOrder" subOrder="Loricarioidei">Loricarioidei</taxonomicName>
, and 
<taxonomicName id="4C592AD7C54FFF9EFBEAF9E26616F9DB" authorityName="Frizzell &amp; Dante" authorityYear="1965" box="[1059,1145,1638,1657]" class="Actinopterygii" higherTaxonomySource="GBIF" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="3" phylum="Chordata" rank="subOrder" subOrder="Siluroidei">Siluroidei</taxonomicName>
) as well as the two major “Big Asia” and “Big Africa” groups (background highlighted) are shown by arrows. The 
<taxonomicName id="4C592AD7C54FFF9EFCA7F9076652F937" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[878,1085,1666,1685]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C54FFF9EFCA7F9076652F937" box="[878,1085,1666,1685]" italics="true" pageId="7" pageNumber="8">Pangasius mekongensis</emphasis>
</taxonomicName>
, 
<taxonomicName id="4C592AD7C54FFF9EFB80F9066735F937" authorityName="Sauvage" authorityYear="1878" box="[1097,1370,1666,1685]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C54FFF9EFB80F9066735F937" box="[1097,1370,1666,1685]" italics="true" pageId="7" pageNumber="8">Pangasianodon hypophthalmus</emphasis>
</taxonomicName>
, and 
<taxonomicName id="4C592AD7C54FFF9EFF41F91B6349F913" authorityName="Fang &amp; Chaux" authorityYear="1949" box="[136,294,1694,1713]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="krempfi">
<emphasis id="B92D8D46C54FFF9EFF41F91B6349F913" box="[136,294,1694,1713]" italics="true" pageId="7" pageNumber="8">Pangasius krempfi</emphasis>
</taxonomicName>
sequences in this study are indicated by stars and with the associated families’ background highlighted. The taxa were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (
<bibRefCitation id="EFC82CA5C54FFF9EFCFBF95261BCF94B" author="Saitoh K &amp; Miya M &amp; Inoue JG &amp; Ishiguro NB &amp; Nishida M." box="[818,979,1750,1770]" pageId="7" pageNumber="8" pagination="464 - 472" refId="ref14249" refString="Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M. 2003. Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. J Mol Evol 56 (4): 464 - 472. doi: 10.1007 / s 00239 - 002 - 2417 - y." type="journal article" year="2003">Saitoh et al. 2003</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C54FFF9EFC14F95266FDF94B" author="Nakatani M &amp; Miya M &amp; Mabuchi K &amp; Saitoh K &amp; Nishida M." box="[989,1170,1750,1770]" pageId="7" pageNumber="8" refId="ref13754" refString="Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. 2011. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 11 (1): 177. doi: 10.1186 / 1471 - 2148 - 11 - 177." type="journal volume" year="2011">Nakatani et al. 2011</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C54FFF9EFB55F953672BF94B" author="Kappas I &amp; Vittas S &amp; Pantzartzi CN &amp; Drosopoulou E &amp; Scouras ZG" box="[1180,1348,1750,1770]" pageId="7" pageNumber="8" refId="ref12903" refString="Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. 2016. A time-calibrated mitogenome phylogeny of catfish (Teleostei: Siluriformes). PLoS ONE 11 (12): e 0166988. doi: 10.1371 / journal. pone. 0166988." type="journal volume" year="2016">Kappas et al. 2016</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C54FFF9EFA86F9526288F8A7" author="Zhang K &amp; Liu Y &amp; Chen J &amp; Zhang H &amp; Gong L &amp; Jiang L &amp; Liu L &amp; Lu Z &amp; Liu B." pageId="7" pageNumber="8" pagination="677 - 689" refId="ref15191" refString="Zhang K, Liu Y, Chen J, Zhang H, Gong L, Jiang L, Liu L, Lu Z, Liu B. 2021. Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes. Mol Biol Rep 48: 677 - 689. doi: 10.1007 / s 11033 - 020 - 06120 - z." type="journal article" year="2021">Zhang et al. 2021</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C54FFF9EFF38F97663F4F8A7" author="Schedel FDB &amp; Chakona A &amp; Sidlauskas BL &amp; Popoola MO &amp; Usimesa Wingi N &amp; Neumann D &amp; Vreven EJWMN &amp; Schliewen UK" box="[241,411,1778,1798]" pageId="7" pageNumber="8" pagination="1171 - 1186" refId="ref14349" refString="Schedel FDB, Chakona A, Sidlauskas BL, Popoola MO, Usimesa Wingi N, Neumann D, Vreven EJWMN, Schliewen UK. 2022. Newphylogenetic insights into the African catfish families Mochokidae and Austroglanididae. J Fish Biol 100 (5): 1171 - 1186. doi: 10.1111 / jfb. 15014." type="journal article" year="2022">Schedel et al. 2022</bibRefCitation>
). The country of origin or geographical regions where the sample was reported are given in full name, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
</paragraph>
</caption>
<caption id="DF2601DCC540FF91FF67FA7E6663F8E0" ID-DOI="http://doi.org/10.5281/zenodo.12828492" ID-Zenodo-Dep="12828492" httpUri="https://zenodo.org/record/12828492/files/figure.png" pageId="8" pageNumber="9" startId="8.[174,205,1530,1549]" targetBox="[174,1451,251,1495]" targetPageId="8" targetType="figure">
<paragraph id="8BE65154C540FF91FF67FA7E6663F8E0" blockId="8.[174,1452,1530,1858]" pageId="8" pageNumber="9">
<emphasis id="B92D8D46C540FF91FF67FA7E6287F9AC" bold="true" box="[174,232,1530,1550]" pageId="8" pageNumber="9">Fig. 3.</emphasis>
Detailed PhyML-phylogeny based on the analysis of the partial 
<emphasis id="B92D8D46C540FF91FCE3FA7F6127F9AF" box="[810,840,1531,1549]" italics="true" pageId="8" pageNumber="9">cox</emphasis>
1 sequences (551 bp) showing the detailed relationships of the family 
<taxonomicName id="4C592AD7C540FF91FF67F9936379F988" authorityName="Bleeker" authorityYear="1858" box="[174,278,1559,1578]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
and related families (
<taxonomicName id="4C592AD7C540FF91FE13F993601BF988" authorityName="Mo" authorityYear="1991" box="[474,628,1559,1578]" family="Austroglanididae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Austroglanididae</taxonomicName>
, 
<taxonomicName id="4C592AD7C540FF91FDB7F99360B1F988" authorityName="T.N.Gill" authorityYear="1861" box="[638,734,1559,1578]" family="Ictaluridae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Ictaluridae</taxonomicName>
, and 
<taxonomicName id="4C592AD7C540FF91FCC6F99361CCF988" authorityName="Myers" authorityYear="1931" box="[783,931,1559,1578]" family="Cranoglanididae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Cranoglanididae</taxonomicName>
). In total, 83 sequences, including 81 from 
<taxonomicName id="4C592AD7C540FF91FAE3F99367EBF98B" authorityName="Valenciennes" authorityYear="1840" box="[1322,1412,1559,1577]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FAE3F99367EBF98B" box="[1322,1412,1559,1577]" italics="true" pageId="8" pageNumber="9">Pangasius</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C540FF91FF67F9B7635CF9E4" authorityName="Chevey" authorityYear="1931" box="[174,307,1587,1606]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FF67F9B7635CF9E4" box="[174,307,1587,1606]" italics="true" pageId="8" pageNumber="9">Pangasianodon</emphasis>
</taxonomicName>
and 2 outgroup sequences from the order 
<taxonomicName id="4C592AD7C540FF91FD5EF9B76170F9E4" authorityName="Berg" authorityYear="1940" box="[663,799,1587,1606]" higherTaxonomySource="CoL" kingdom="Animalia" order="Gymnotiformes" pageId="8" pageNumber="9" phylum="Chordata" rank="order">Gymnotiformes</taxonomicName>
, were included (Table S3). The alignment was performed by MAFFT (
<bibRefCitation id="EFC82CA5C540FF91FABFF9B7633EF9C0" author="Katoh K &amp; Standley DM" pageId="8" pageNumber="9" pagination="772 - 780" refId="ref13062" refString="Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772 - 780. doi: 10.1093 / molbev / mst 010." type="journal article" year="2013">Katoh and Standley 2013</bibRefCitation>
), curated by BMGE v1.12 (
<bibRefCitation id="EFC82CA5C540FF91FDF6F9CB6152F9C0" author="Criscuolo A &amp; Gribaldo S." box="[575,829,1615,1634]" pageId="8" pageNumber="9" refId="ref11753" refString="Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10: 210. doi: 10.1186 / 1471 - 2148 - 10 - 210." type="journal volume" year="2010">Criscuolo and Gribaldo 2010</bibRefCitation>
), the tree was reconstructed in PhyML 3.3 (
<bibRefCitation id="EFC82CA5C540FF91FB7CF9CB670DF9C0" author="Guindon S &amp; Dufayard JF &amp; Lefort V &amp; Anisimova M &amp; Hordijk W &amp; Gascuel O." box="[1205,1378,1615,1634]" pageId="8" pageNumber="9" pagination="307 - 321" refId="ref12206" refString="Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59 (3): 307 - 321. doi: 10.1093 / sysbio / syq 010." type="journal article" year="2010">Guindon et al. 2010</bibRefCitation>
) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (
<bibRefCitation id="EFC82CA5C540FF91FA95F9EF62B1F938" author="Rambaut A." pageId="8" pageNumber="9" refId="ref14179" refString="Rambaut A. 2018. FigTree, version 1. 4. 4. http: // tree. bio. ed. ac. uk / software / figtree /." type="url" year="2018">Rambaut 2018</bibRefCitation>
). The basal nodes of the 
<taxonomicName id="4C592AD7C540FF91FE0CF9036040F938" authorityName="Bleeker" authorityYear="1858" box="[453,559,1671,1690]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
and two sister groups (
<taxonomicName id="4C592AD7C540FF91FCC0F90361FCF938" authorityName="Chevey" authorityYear="1931" box="[777,915,1671,1690]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FCC0F90361FCF938" box="[777,915,1671,1690]" italics="true" pageId="8" pageNumber="9">Pangasianodon</emphasis>
</taxonomicName>
and (
<taxonomicName id="4C592AD7C540FF91FC03F9036649F93B" authorityName="Valenciennes" authorityYear="1840" box="[970,1062,1671,1689]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FC03F9036649F93B" box="[970,1062,1671,1689]" italics="true" pageId="8" pageNumber="9">Pangasius</emphasis>
</taxonomicName>
+ 
<taxonomicName id="4C592AD7C540FF91FB88F90366D3F938" authorityName="Bleeker" authorityYear="1858" box="[1089,1212,1671,1690]" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FB88F90366D3F938" box="[1089,1212,1671,1690]" italics="true" pageId="8" pageNumber="9">Helicophagus</emphasis>
</taxonomicName>
+ 
<taxonomicName id="4C592AD7C540FF91FB11F9036756F938" authorityName="Vaillant" authorityYear="1902" box="[1240,1337,1671,1690]" family="Pangasiidae" genus="Pseudolais" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C540FF91FB11F9036756F938" box="[1240,1337,1671,1690]" italics="true" pageId="8" pageNumber="9">Pseudolais</emphasis>
</taxonomicName>
)) are shown by arrows. The 
<taxonomicName id="4C592AD7C540FF91FEF5F9276062F914" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[316,525,1699,1718]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C540FF91FEF5F9276062F914" box="[316,525,1699,1718]" italics="true" pageId="8" pageNumber="9">Pangasius mekongensis</emphasis>
</taxonomicName>
, 
<taxonomicName id="4C592AD7C540FF91FDD3F9276140F914" authorityName="Sauvage" authorityYear="1878" box="[538,815,1699,1718]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C540FF91FDD3F9276140F914" box="[538,815,1699,1718]" italics="true" pageId="8" pageNumber="9">Pangasianodon hypophthalmus</emphasis>
</taxonomicName>
, and 
<taxonomicName id="4C592AD7C540FF91FCABF927666BF914" authorityName="Fang &amp; Chaux" authorityYear="1949" box="[866,1028,1699,1718]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="species" species="krempfi">
<emphasis id="B92D8D46C540FF91FCABF927666BF914" box="[866,1028,1699,1718]" italics="true" pageId="8" pageNumber="9">Pangasius krempfi</emphasis>
</taxonomicName>
sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from 
<taxonomicName id="4C592AD7C540FF91FCB4F93B618CF970" authorityName="Bleeker" authorityYear="1858" box="[893,995,1727,1746]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="8" pageNumber="9" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies (
<bibRefCitation id="EFC82CA5C540FF91FC16F973677CF8A8" author="Karinthanyakit W &amp; Jondeung A." box="[991,1299,1783,1802]" pageId="8" pageNumber="9" pagination="2549 - 2570" refId="ref12952" refString="Karinthanyakit W, Jondeung A. 2012. Molecular Phylogenetic Relationships of Pangasiid and Schilbid Catfishes in Thailand. J Fish Biol 80: 2549 - 2570. doi: 10.1111 / j. 1095 - 8649.2012.03303. x." type="journal article" year="2012">Karinthanyakit and Jondeung 2012</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C540FF91FAD4F97362B4F884" author="Tran TML &amp; Duong TY" pageId="8" pageNumber="9" pagination="116 - 120" refId="ref14573" refString="Tran TML, Duong TY. 2019. Differentiation of two Pangasius species, Pangasius krempfi and Pangasius mekongensis using inter-sequence simple repeat markers. Int J Fish Aquat Stud 7 (4): 116 - 120." type="journal article" year="2019">Tran and Duong 2019</bibRefCitation>
; 
<bibRefCitation id="EFC82CA5C540FF91FF2DF89763E5F884" author="Schedel FDB &amp; Chakona A &amp; Sidlauskas BL &amp; Popoola MO &amp; Usimesa Wingi N &amp; Neumann D &amp; Vreven EJWMN &amp; Schliewen UK" box="[228,394,1811,1830]" pageId="8" pageNumber="9" pagination="1171 - 1186" refId="ref14349" refString="Schedel FDB, Chakona A, Sidlauskas BL, Popoola MO, Usimesa Wingi N, Neumann D, Vreven EJWMN, Schliewen UK. 2022. Newphylogenetic insights into the African catfish families Mochokidae and Austroglanididae. J Fish Biol 100 (5): 1171 - 1186. doi: 10.1111 / jfb. 15014." type="journal article" year="2022">Schedel et al. 2022</bibRefCitation>
). The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
</paragraph>
</caption>
<paragraph id="8BE65154C541FF90FDA8F9C26008F9F2" box="[609,615,1606,1616]" pageId="9" pageNumber="10">0</paragraph>
<paragraph id="8BE65154C541FF90FDAFF9C26005F9F2" box="[614,618,1606,1616]" pageId="9" pageNumber="10">.</paragraph>
<paragraph id="8BE65154C541FF90FDA1F9C2601AF9F2" box="[616,629,1606,1616]" pageId="9" pageNumber="10">05</paragraph>
<caption id="DF2601DCC541FF90FF41F9E96351F816" ID-DOI="http://doi.org/10.5281/zenodo.12828494" ID-Zenodo-Dep="12828494" httpUri="https://zenodo.org/record/12828494/files/figure.png" pageId="9" pageNumber="10" startId="9.[136,167,1645,1664]" targetBox="[206,1344,251,1563]" targetPageId="9" targetType="figure">
<paragraph id="8BE65154C541FF90FF41F9E96351F816" blockId="9.[136,1414,1645,1972]" pageId="9" pageNumber="10">
<emphasis id="B92D8D46C541FF90FF41F9E962ADF922" bold="true" box="[136,194,1645,1664]" pageId="9" pageNumber="10">Fig. 4.</emphasis>
Detailed PhyML-phylogeny based on the analysis of the partial 
<emphasis id="B92D8D46C541FF90FCCDF9EA6172F922" box="[772,797,1646,1664]" italics="true" pageId="9" pageNumber="10">cyt</emphasis>
B sequences (634 bp) showing the detailed relationships of the family 
<taxonomicName id="4C592AD7C541FF90FF41F90D629FF93E" authorityName="Bleeker" authorityYear="1858" box="[136,240,1673,1692]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
and related families (
<taxonomicName id="4C592AD7C541FF90FE7DF90D6021F93E" authorityName="Mo" authorityYear="1991" box="[436,590,1673,1692]" family="Austroglanididae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Austroglanididae</taxonomicName>
, 
<taxonomicName id="4C592AD7C541FF90FD91F90D60D7F93E" authorityName="T.N.Gill" authorityYear="1861" box="[600,696,1673,1692]" family="Ictaluridae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Ictaluridae</taxonomicName>
, and 
<taxonomicName id="4C592AD7C541FF90FD20F90D6112F93E" authorityName="Myers" authorityYear="1931" box="[745,893,1673,1692]" family="Cranoglanididae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Cranoglanididae</taxonomicName>
). In total, 80 sequences, including 78 from 
<taxonomicName id="4C592AD7C541FF90FACDF90E6731F93E" authorityName="Valenciennes" authorityYear="1840" box="[1284,1374,1674,1692]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FACDF90E6731F93E" box="[1284,1374,1674,1692]" italics="true" pageId="9" pageNumber="10">Pangasius</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C541FF90FF41F9216361F91A" authorityName="Chevey" authorityYear="1931" box="[136,270,1701,1720]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FF41F9216361F91A" box="[136,270,1701,1720]" italics="true" pageId="9" pageNumber="10">Pangasianodon</emphasis>
</taxonomicName>
and 2 outgroup sequences from the order 
<taxonomicName id="4C592AD7C541FF90FDB0F9216080F91A" box="[633,751,1701,1720]" higherTaxonomySource="CoL" kingdom="Animalia" order="Clupeiformes" pageId="9" pageNumber="10" phylum="Chordata" rank="order">Clupeiformes</taxonomicName>
, were included (Table S3). The alignment was performed by MAFFT (
<bibRefCitation id="EFC82CA5C541FF90FA99F9216344F976" author="Katoh K &amp; Standley DM" pageId="9" pageNumber="10" pagination="772 - 780" refId="ref13062" refString="Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772 - 780. doi: 10.1093 / molbev / mst 010." type="journal article" year="2013">Katoh and Standley 2013</bibRefCitation>
), curated by BMGE v1.12 (
<bibRefCitation id="EFC82CA5C541FF90FDD0F9456178F976" author="Criscuolo A &amp; Gribaldo S." box="[537,791,1729,1748]" pageId="9" pageNumber="10" refId="ref11753" refString="Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10: 210. doi: 10.1186 / 1471 - 2148 - 10 - 210." type="journal volume" year="2010">Criscuolo and Gribaldo 2010</bibRefCitation>
), the tree was reconstructed in PhyML 3.3 (
<bibRefCitation id="EFC82CA5C541FF90FB46F9456753F976" author="Guindon S &amp; Dufayard JF &amp; Lefort V &amp; Anisimova M &amp; Hordijk W &amp; Gascuel O." box="[1167,1340,1729,1749]" pageId="9" pageNumber="10" pagination="307 - 321" refId="ref12206" refString="Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59 (3): 307 - 321. doi: 10.1093 / sysbio / syq 010." type="journal article" year="2010">Guindon et al. 2010</bibRefCitation>
) using a maximum likelihood method and 1000 bootstrap resamplings, and the output Newick tree was extracted and visualized using FigTree v1.4.4 (
<bibRefCitation id="EFC82CA5C541FF90FAFEF95962D7F8AE" author="Rambaut A." pageId="9" pageNumber="10" refId="ref14179" refString="Rambaut A. 2018. FigTree, version 1. 4. 4. http: // tree. bio. ed. ac. uk / software / figtree /." type="url" year="2018">Rambaut 2018</bibRefCitation>
). The basal nodes of the 
<taxonomicName id="4C592AD7C541FF90FE56F97D6066F8AE" authorityName="Bleeker" authorityYear="1858" box="[415,521,1785,1804]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
and two sister groups (
<taxonomicName id="4C592AD7C541FF90FD2AF97D6102F8AE" authorityName="Chevey" authorityYear="1931" box="[739,877,1785,1804]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FD2AF97D6102F8AE" box="[739,877,1785,1804]" italics="true" pageId="9" pageNumber="10">Pangasianodon</emphasis>
</taxonomicName>
and (
<taxonomicName id="4C592AD7C541FF90FC6DF97E666FF8AE" authorityName="Valenciennes" authorityYear="1840" box="[932,1024,1786,1804]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FC6DF97E666FF8AE" box="[932,1024,1786,1804]" italics="true" pageId="9" pageNumber="10">Pangasius</emphasis>
</taxonomicName>
+ 
<taxonomicName id="4C592AD7C541FF90FBD5F97D66F8F8AE" authorityName="Bleeker" authorityYear="1858" box="[1052,1175,1785,1804]" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FBD5F97D66F8F8AE" box="[1052,1175,1785,1804]" italics="true" pageId="9" pageNumber="10">Helicophagus</emphasis>
</taxonomicName>
+ 
<taxonomicName id="4C592AD7C541FF90FB7BF97D677CF8AE" authorityName="Vaillant" authorityYear="1902" box="[1202,1299,1785,1804]" family="Pangasiidae" genus="Pseudolais" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C541FF90FB7BF97D677CF8AE" box="[1202,1299,1785,1804]" italics="true" pageId="9" pageNumber="10">Pseudolais</emphasis>
</taxonomicName>
)) are shown by arrows. The 
<taxonomicName id="4C592AD7C541FF90FEDFF8926388F88A" authorityName="Gustiano, Teugels &amp; Pouyaud" authorityYear="2003" box="[278,487,1813,1832]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="species" species="mekongensis">
<emphasis id="B92D8D46C541FF90FEDFF8926388F88A" box="[278,487,1813,1832]" italics="true" pageId="9" pageNumber="10">Pangasius mekongensis</emphasis>
</taxonomicName>
, 
<taxonomicName id="4C592AD7C541FF90FE3DF8916166F88A" authorityName="Sauvage" authorityYear="1878" box="[500,777,1813,1832]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C541FF90FE3DF8916166F88A" box="[500,777,1813,1832]" italics="true" pageId="9" pageNumber="10">Pangasianodon hypophthalmus</emphasis>
</taxonomicName>
, and 
<taxonomicName id="4C592AD7C541FF90FCF5F89261B1F88A" authorityName="Fang &amp; Chaux" authorityYear="1949" box="[828,990,1813,1832]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="species" species="krempfi">
<emphasis id="B92D8D46C541FF90FCF5F89261B1F88A" box="[828,990,1813,1832]" italics="true" pageId="9" pageNumber="10">Pangasius krempfi</emphasis>
</taxonomicName>
sequences in this study are bolded. The taxonmisidentified sequences were added with a question mark at the end. The taxa from 
<taxonomicName id="4C592AD7C541FF90FC9EF8B561D2F8E6" authorityName="Bleeker" authorityYear="1858" box="[855,957,1841,1860]" family="Pangasiidae" kingdom="Animalia" order="Siluriformes" pageId="9" pageNumber="10" phylum="Chordata" rank="family">Pangasiidae</taxonomicName>
were shortened and those from other related families were presented with their full names. The abbreviations of the isolates are given in brackets, including the geographical origin or voucher records of each sequenced specimen (where available), which were retrieved from the previous studies. The country of origin or where the sample was reported is given in full or in brackets, if available. Accession numbers are given at the end of each sequence label. The scale bar represents the number of substitutions per site.
</paragraph>
</caption>
<paragraph id="8BE65154C542FF93FF23FDFA6317FBB7" blockId="10.[174,775,253,1045]" pageId="10" pageNumber="11">
In both the 
<emphasis id="B92D8D46C542FF93FE49FDFA63C7FD37" box="[384,424,638,661]" italics="true" pageId="10" pageNumber="11">cox</emphasis>
1 and 
<emphasis id="B92D8D46C542FF93FE33FDFA6072FD37" box="[506,541,638,661]" italics="true" pageId="10" pageNumber="11">cyt</emphasis>
B phylogenies, the 
<taxonomicName id="4C592AD7C542FF93FF67FD196336FD17" authorityName="Chevey" authorityYear="1931" box="[174,345,669,693]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF67FD196336FD17" box="[174,345,669,693]" italics="true" pageId="10" pageNumber="11">Pangasianodon</emphasis>
</taxonomicName>
was clearly resolved as a sister to the 
<taxonomicName id="4C592AD7C542FF93FF67FD3A6372FD77" authorityName="Valenciennes" authorityYear="1840" box="[174,285,702,725]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF67FD3A6372FD77" box="[174,285,702,725]" italics="true" pageId="10" pageNumber="11">Pangasius</emphasis>
</taxonomicName>
with medium nodal support (bootstrap: 86% for 
<emphasis id="B92D8D46C542FF93FF11FD5A6291FD57" box="[216,254,734,757]" italics="true" pageId="10" pageNumber="11">cox</emphasis>
1 and 52% for 
<emphasis id="B92D8D46C542FF93FE62FD5A63A4FD57" box="[427,459,734,757]" italics="true" pageId="10" pageNumber="11">cyt</emphasis>
B). While the monophyletic 
<taxonomicName id="4C592AD7C542FF93FF67FD796330FCB7" authorityName="Chevey" authorityYear="1931" box="[174,351,765,789]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF67FD796330FCB7" box="[174,351,765,789]" italics="true" pageId="10" pageNumber="11">Pangasianodon</emphasis>
</taxonomicName>
was resolved with its two members (
<taxonomicName id="4C592AD7C542FF93FF7EFC9A634EFC97" box="[183,289,798,821]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="gigas">
<emphasis id="B92D8D46C542FF93FF7EFC9A634EFC97" box="[183,289,798,821]" italics="true" pageId="10" pageNumber="11">Pn. gigas</emphasis>
</taxonomicName>
was the sister taxon to 
<taxonomicName id="4C592AD7C542FF93FDF8FC9A6168FC97" authorityName="Sauvage" authorityYear="1878" box="[561,775,797,821]" family="Pangasiidae" genus="Pangasianodon" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="hypophthalmus">
<emphasis id="B92D8D46C542FF93FDF8FC9A6168FC97" box="[561,775,797,821]" italics="true" pageId="10" pageNumber="11">Pn. hypophthalmus</emphasis>
</taxonomicName>
in both the 
<emphasis id="B92D8D46C542FF93FEE2FCBA633FFCF7" box="[299,336,830,853]" italics="true" pageId="10" pageNumber="11">cox</emphasis>
1 and the 
<emphasis id="B92D8D46C542FF93FE74FCBA63B3FCF7" box="[445,476,830,853]" italics="true" pageId="10" pageNumber="11">cyt</emphasis>
B phylogenetic topologies), the 
<taxonomicName id="4C592AD7C542FF93FF11FCDA6327FCD7" authorityName="Valenciennes" authorityYear="1840" box="[216,328,862,885]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF11FCDA6327FCD7" box="[216,328,862,885]" italics="true" pageId="10" pageNumber="11">Pangasius</emphasis>
</taxonomicName>
cluster included not only 
<taxonomicName id="4C592AD7C542FF93FDA2FCDA60B4FCD7" authorityName="Valenciennes" authorityYear="1840" box="[619,731,862,885]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FDA2FCDA60B4FCD7" box="[619,731,862,885]" italics="true" pageId="10" pageNumber="11">Pangasius</emphasis>
</taxonomicName>
but 
<taxonomicName id="4C592AD7C542FF93FF67FCF9632BFC37" authorityName="Bleeker" authorityYear="1858" box="[174,324,893,917]" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FF67FCF9632BFC37" box="[174,324,893,917]" italics="true" pageId="10" pageNumber="11">Helicophagus</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C542FF93FEB7FCF96023FC37" box="[382,588,893,917]" pageId="10" pageNumber="11">
<emphasis id="B92D8D46C542FF93FEB7FCF9639AFC37" box="[382,501,893,917]" italics="true" pageId="10" pageNumber="11">Pseudolais</emphasis>
species
</taxonomicName>
as well. Though they had low bootstrap values (28% for 
<emphasis id="B92D8D46C542FF93FDA2FC1A60FFFC17" box="[619,656,926,949]" italics="true" pageId="10" pageNumber="11">cox</emphasis>
1 and 29% for 
<emphasis id="B92D8D46C542FF93FF13FC3A6294FC77" box="[218,251,958,981]" italics="true" pageId="10" pageNumber="11">cyt</emphasis>
B phylogeny), 
<taxonomicName id="4C592AD7C542FF93FE64FC396023FC77" authorityName="Bleeker" authorityYear="1858" box="[429,588,957,981]" family="Pangasiidae" genus="Helicophagus" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="genus">
<emphasis id="B92D8D46C542FF93FE64FC396023FC77" box="[429,588,957,981]" italics="true" pageId="10" pageNumber="11">Helicophagus</emphasis>
</taxonomicName>
and 
<taxonomicName id="4C592AD7C542FF93FD40FC39636EFC57" pageId="10" pageNumber="11">
<emphasis id="B92D8D46C542FF93FD40FC396168FC77" box="[649,775,957,981]" italics="true" pageId="10" pageNumber="11">Pseudolais</emphasis>
species
</taxonomicName>
were grouped as sister taxa to some of the 
<taxonomicName id="4C592AD7C542FF93FF67FC7A6317FBB7" box="[174,376,1021,1045]" family="Pangasiidae" genus="Pangasius" kingdom="Animalia" order="Siluriformes" pageId="10" pageNumber="11" phylum="Chordata" rank="species" species="undetermined">
<emphasis id="B92D8D46C542FF93FF67FC7A6372FBB7" box="[174,285,1022,1045]" italics="true" pageId="10" pageNumber="11">Pangasius</emphasis>
species.
</taxonomicName>
</paragraph>
</subSubSection>
</treatment>
</document>