Yang Lei, Mayden Richard L, Naylor Gavin J P
Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA.
Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
Biology (Basel). 2024 Dec 20;13(12):1072. doi: 10.3390/biology13121072.
Fishes in the cypriniform family Catostomidae (suckers) are evolutionary tetraploids. The use of nuclear markers in the phylogenetic study of this important group has been greatly hindered by the challenge of identifying paralogous copies of genes. In the present study, we used two different methods to separate the gene copies of five single-copy nuclear genes (i.e., RAG1, EGR2B, EGR3, IRBP2, and RAG2). For each gene, all sequences of Copy I formed a clade that was sister to the clade formed by all sequences of Copy II in the phylogenetic trees. The maternal and paternal progenitor of the tetraploid ancestor of the Catostomidae could not be determined. We also constructed a mitochondrial tree to reflect the maternal relationships among major catostomid lineages. Our data appear to support a sister relationship between Catostominae and a monophyletic group composed of Myxocyprininae, Cycleptinae, and Ictiobinae. However, within Catostominae, there is significant conflict between mitochondrial and nuclear data regarding the relationships among Erimyzonini, Catostomini, and Moxostomatini/Thoburnini. Many indels, unexpected stop codons, and possible gene loss were identified in one gene copy of RAG1, RAG2, and IRBP2. We believe that additional nuclear genome data are needed to better resolve the phylogenetic relationships within the family Catostomidae.
鲤形目吸口鲤科（吸盘鱼）的鱼类是进化四倍体。在这个重要类群的系统发育研究中，由于难以识别基因的旁系同源拷贝，核标记的使用受到了极大阻碍。在本研究中，我们使用了两种不同方法来分离五个单拷贝核基因（即RAG1、EGR2B、EGR3、IRBP2和RAG2）的基因拷贝。对于每个基因，在系统发育树中，拷贝I的所有序列形成一个分支，该分支是拷贝II的所有序列形成的分支的姐妹分支。吸口鲤科四倍体祖先的母本和父本祖先无法确定。我们还构建了一个线粒体树，以反映主要吸口鲤科谱系之间的母系关系。我们的数据似乎支持吸口鲤亚科与一个由粘鲤亚科、环口鲤亚科和牛尾鱼亚科组成的单系群之间的姐妹关系。然而，在吸口鲤亚科内部，关于埃氏鲤族、吸口鲤族和牛鼻鲤族/托伯恩鲤族之间的关系，线粒体和核数据存在显著冲突。在RAG1、RAG2和IRBP2的一个基因拷贝中发现了许多插入缺失、意外的终止密码子和可能的基因丢失。我们认为，需要更多的核基因组数据来更好地解析吸口鲤科内部的系统发育关系。
