Data from: SimPhy: phylogenomic simulation of gene, locus and species trees

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.本研究提出一款快速且灵活的软件包SimPhy，用于模拟在不完全谱系分选（incomplete lineage sorting）、基因重复与丢失（gene duplication and loss）、水平基因转移（horizontal gene transfer）——这三类过程均可能引发物种树/基因树冲突（species tree/gene tree discordance）——以及基因转换（gene conversion）作用下演化的多基因家族。SimPhy构建了层级系统发育模型（hierarchical phylogenetic model），其中物种、基因座与基因树的演化由全局与局部参数（如全基因组水平、物种特异性、基因座特异性参数）调控，这些参数既可以固定取值，也可以从先验统计分布（a priori statistical distributions）中采样得到。此外，SimPhy整合了全面的谱系间替换率变异模型（无关联松弛分子钟，uncorrelated relaxed clocks），并支持借助INDELible软件，在丰富的替换模型下模拟分区核苷酸、密码子与蛋白质多基因座序列比对。本研究通过理论预期值与其他软件对SimPhy的输出结果进行了验证，并证实其在复杂模型与/或大型树结构下扩展性极佳，运行速度比同类最相近的程序DLCoal-Sim快一个数量级。此外，本研究通过开展模拟实验，刻画了使用标准基因树-物种树整合方法时重复事件时间被系统性高估的特征，以此阐明SimPhy可用于解析不同演化过程间的相互作用。用户可通过https://github.com/adamallo/SimPhy获取SimPhy，该页面提供源代码、预编译可执行文件、详细手册与示例案例。