School of Biological Sciences, 348 Manter Hall, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Mol Phylogenet Evol. 2012 Jun;63(3):798-808. doi: 10.1016/j.ympev.2012.02.018. Epub 2012 Mar 2.
Neotropical rivers are home to the largest assemblage of freshwater fishes, but little is known about the phylogeny of these fishes at the species level using multi-locus molecular markers. Here, we present a phylogeny for all known species of the genus Satanoperca, a widespread group of Neotropical cichlid fishes, based on analysis of six unlinked genetic loci. To test nominal and proposed species limits for this group, we surveyed mtDNA sequence variation among 320 individuals representing all know species. Most nominal species were supported by this approach but we determined that populations in the Xingu, Tapajós, and Araguaia+Paraná Rivers are likely undescribed species, while S. jurupari and S. mapiritensis did not show clear genetic distinction. To infer a phylogeny of these putative species, we conducted maximum likelihood and Bayesian non-clock and relaxed clock analyses of concatenated data from three genes (one mitochondrial, two nuclear). We also used a multi-species coalescent model to estimate a species tree from six unlinked loci (one mitochondrial, five nuclear). The topologies obtained were congruent with other results, but showed only minimal to moderate support for some nodes, suggesting that more loci will be needed to satisfactorily estimate the distribution of coalescent histories within Satanoperca. We determined that this variation results from topological discordance among separate gene trees, likely due to differential sorting of ancestral polymorphisms.
新热带地区的河流是最大的淡水鱼类聚居地，但利用多基因座分子标记对这些鱼类的种级系统发育知之甚少。本研究基于对 6 个非连锁遗传座的分析，提供了一个广泛分布于新热带慈鲷鱼类撒旦鲈属所有已知物种的系统发育。为了检验该组群的命名种和提议种的界限，我们对代表所有已知物种的 320 个个体的 mtDNA 序列变异进行了调查。大多数命名种得到了这种方法的支持，但我们确定欣古河、塔帕若斯河和阿拉瓜亚河+巴拉那河流域的种群可能是未描述的物种，而 S. jurupari 和 S. mapiritensis 则没有表现出明显的遗传差异。为了推断这些假定物种的系统发育，我们对来自三个基因（一个线粒体基因和两个核基因）的串联数据进行了最大似然法和贝叶斯非钟和松弛钟分析。我们还使用了一个多物种合并模型，从 6 个非连锁座（一个线粒体基因座和五个核基因座）来估计种系发生树。得到的拓扑结构与其他结果一致，但有些节点的支持度仅为最小到中等，这表明需要更多的基因座才能令人满意地估计撒旦鲈属内合并历史的分布。我们确定这种变异是由于单独基因树之间的拓扑差异造成的，这可能是由于祖先多态性的不同排序造成的。
