Department of Biology, Saint Louis University, 3507 Laclede Ave. Saint Louis, MO 63103-2010, USA.
Department of Biology, Saint Louis University, 3507 Laclede Ave. Saint Louis, MO 63103-2010, USA.
Mol Phylogenet Evol. 2010 Apr;55(1):77-98. doi: 10.1016/j.ympev.2009.10.030. Epub 2009 Nov 10.
Members of the genus Cyprinella are abundant and broadly distributed cyprinids in central and eastern rivers of North America. Currently, 30 species are placed in this genus, including seven species restricted to Mexico and three barbeled species formerly placed in different genera (Hybopsis, Erimonax). Phylogenetic analyses were performed for all recognized species of Cyprinella plus species from 14 related genera using complete nucleotide sequences of one mitochondrial (cytochrome b) and one nuclear (Rag1) gene. Cyprinella revealed high levels of genetic divergence between species in both genes compared with species from other related genera examined. Analyses of mitochondrial sequences from 98 specimens of Cyprinella revealed the gene trees of some species as non-monophyletic (i.e., C. venusta, C. lepida, C. nivea, C. lutrensis, C. whipplei). Mitochondrial analyses recovered nine well-supported species groups within a main clade inclusive of most species of Cyprinella, although resolution regarding the monophyly of the genus or its relationships with other genera was poorly resolved, except for C. callistia and C. monacha, two species that are apparently not part of the genus. Analyses of nuclear gene sequences from selected distinctive mitochondrial clades also recovered these nine clades and resulted in shorter branches but greater resolution at more basal nodes. Nuclear data also rejected the inclusion of C. monacha in Cyprinella and indicated that Cyprinella is not monophyletic if Tampichthys and Codoma are recognized as valid genera. A major Clade A (formed by Cyprinella, Tampichthys, Codoma) is more closely related to Pimephales, Opsopoeodus, Hybognathus and some Notropis than to Luxilus and Lythrurus as previously hypothesized. Although mitochondrial data are highly informative phylogenetically, our research revealed fundamental conflicts among mitochondrial and nuclear data for several species of Cyprinella. Interestingly, nuclear trees recovered some species resolved as polyphyletic with mitochondrial variation as monophyletic. While we remain highly supportive of phylogenetic studies using mitochondrial genes and genomes, this study does highlight the utility of nuclear data by identifying issues of possible hybridization or retained ancestral polymorphisms and lineage sorting that can yield erroneous hypothesis in studies using only mit-DNA analyses, while shedding invaluable light on the phylogeny of this controversial group of shiners.
花䱻属的成员是北美的中东部河流中丰富且广泛分布的鲤科鱼类。目前，该属有 30 个种，包括 7 种局限于墨西哥的种和 3 种以前归入不同属的有须种（Hybopsis、Erimonax）。使用一个线粒体（细胞色素 b）和一个核（Rag1）基因的完整核苷酸序列，对所有已识别的花䱻属物种以及来自 14 个相关属的物种进行了系统发育分析。与所研究的其他相关属的物种相比，花䱻属的物种在两个基因中表现出高水平的遗传分化。对来自 98 个花䱻属样本的线粒体序列分析表明，一些物种的基因树为非单系（即，C. venusta、C. lepida、C. nivea、C. lutrensis、C. whipplei）。线粒体分析在一个包含大多数花䱻属物种的主要分支内恢复了 9 个支持良好的物种群，尽管除了 C. callistia 和 C. monacha 这两个显然不属于该属的物种外，关于该属的单系性或与其他属的关系的分辨率很差。从选定的独特线粒体支系的核基因序列分析也恢复了这 9 个支系，并导致在更基础的节点上分支更短但分辨率更高。核数据还排除了 C. monacha 归入花䱻属的可能性，并表明如果坦皮奇斯属和科多玛属被认为是有效的属，那么花䱻属不是单系的。一个主要的 A 类群（由花䱻属、坦皮奇斯属、科多玛属组成）与 Pimephales、Opsopoeodus、Hybognathus 和一些 Notropis 的关系比与 Luxilus 和 Lythrurus 的关系更密切，如以前假设的那样。虽然线粒体数据在系统发育上具有高度信息性，但我们的研究揭示了花䱻属的几个物种的线粒体和核数据之间存在根本冲突。有趣的是，核树恢复了一些以线粒体变异性为单系的多系种。虽然我们仍然高度支持使用线粒体基因和基因组进行系统发育研究，但这项研究确实通过确定可能的杂交或保留的祖先多态性和谱系分类的问题凸显了核数据的实用性，这些问题可能会在仅使用线粒体 DNA 分析的研究中产生错误的假设，同时为这个有争议的鲦鱼群的系统发育提供了宝贵的启示。
