Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multi-locus or “phylogenomic” data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multi-locus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as OTUs, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.

分类学与物种形成领域的相关文献中，已有大量关于基因树/物种树冲突（gene tree/species tree discordance）潜在成因的深入讨论。学界已提出多种可引发该冲突的机制，包括差异选择（differential selection）、长枝吸引（long-branch attraction）、基因重复（gene duplication）、基因渐渗（genetic introgression）以及不完全谱系分选（incomplete lineage sorting）。对于分化事件新近且快速发生的物种丰富支系而言，受不完全谱系分选的影响，重建真实物种树往往尤为困难。遗憾的是，多座位或“系统基因组学（phylogenomic）”数据集的出现并未彻底解决这一问题，尤其是在采用标准串联分析技术对数据进行处理时更是如此。
在本研究中，我们针对倭狐猴与鼠狐猴所在的鼬狐猴科（Cheirogaleidae）支系开展了一项系统发育研究，其物种采样几乎覆盖了该类群所有已知物种。鼠狐猴属（Microcebus）因其极高的隐存物种多样性，在过去十年间被广泛深入研究；尽管学界对该属内的演化多样性已逐渐形成共识，但对于该类群内部的种间关系仍未达成一致意见。我们通过构建大型多座位数据集，尝试解析鼬狐猴科的系统发育关系，尤其聚焦于鼠狐猴属类群。我们将贝叶斯一致性分析法（Bayesian concordance methods）的结果与标准基因串联分析法的结果进行对比，发现尽管以统计支持度衡量时，串联分析法得到的结果置信度最高，但这类结果实则具有极强的误导性。通过采用将单个等位基因视为操作分类单元（OTUs）的分析策略，我们证实：在串联分析流程中，等位基因的选取会对系统发育分析结果产生显著影响。