Data from: Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.本研究构建了一套全新的灵长类系统发育树，其基于总长度42千碱基对（kb）的分子超级矩阵分析构建，该矩阵包含70%的缺失数据，且覆盖了75%的现生灵长类物种多样性。本研究采用基因分区最大似然法对该超级矩阵进行分析，以获得全面的分子系统发育框架。近期分子研究中得到的所有演化支均在本分析中得到了验证，表明缺失数据并未对本超级矩阵的系统发育推断造成偏倚。随后，本研究采用分子定年法对所得到的系统发育树进行定年，为物种形成事件提供时间尺度。基于宽松分子钟的分析结果与此前采用相同化石校准约束的研究结果一致。该定年后的系统发育树可用于推断灵长类的宏观演化过程。本研究采用SymmeTREE方法和生灭过程模型，分析了灵长类的多样化速率和物种形成速率的演化转变。灵长类整体演化支未检测到显著的演化不对称性，但在7个演化支中发现了多样化速率的显著转变：类人猿亚目（Anthropoidea）、狐猴型下目（Lemuriformes）、狐猴科（Lemuridae）、婴猴科（Galagidae）、狨属（Callithrix）、猕猴亚科（Cercopithecinae）以及亚洲猕猴类（Asian Macaca）。与此前灵长类超级树研究结果对比后发现：(1) 狐猴型下目（Lemuriformes）的基部发生了一次多样化事件；(2) 猴科（Cercopithecidae）和类人猿亚目（Anthropoidea）的多样化速率更高；(3) 猕猴属（Macaca）的多样化速率转变始终被检测到。宏观演化推断结果与灵长类分化时间表明，灵长类的主要多样化事件均发生在古近纪之后，这暗示古老灵长类演化支曾发生过灭绝。