Data_Sheet_1_Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae).ZIP

The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when different sources of molecular data are analyzed. Phylogenetic discordance has previously been hypothesized to be the result of both introgression and incomplete lineage sorting (ILS), but the extent and source of discordance have not yet been evaluated in the context of loci derived from massive sequencing strategies and for a wide representation of the family. Furthermore, no formal methods have been applied to evaluate if the detected phylogenetic discordance among phylogenomic datasets influences phylogenetic dating estimates of the concordant relationships. The objective of this research was to generate a phylogenetic hypothesis of Malvaceae from nuclear genes, specifically we aimed to (1) investigate the presence of major discordance among hundreds of nuclear gene histories of Malvaceae; (2) evaluate the potential source of discordance; and (3) examine whether discordance and loci heterogeneity influence on time estimates of the origin and diversification of subfamilies. Our study is based on a comprehensive dataset representing 96 genera of the nine subfamilies and 268 nuclear loci. Both concatenated and coalescence-based approaches were followed for phylogenetic inference. Using branch lengths and topology, we located the placement of introgression events to directly evaluate whether discordance is due to introgression rather than ILS. To estimate divergence times, concordance and molecular rate were considered. We filtered loci based on congruence with the species tree and then obtained the molecular rate of each locus to distribute them into three different sets corresponding to shared molecular rate ranges. Bayesian dating was performed for each of the different sets of loci with the same parameters and calibrations. Phylogenomic discordance was detected between methods, as well as gene histories. At deep coalescent times, we found discordance in the position of five subclades probably due to ILS and a relatively small proportion of introgression. Divergence time estimation with each set of loci generated overlapping clade ages, indicating that, even with different molecular rate and gene histories, calibrations generally provide a strong prior.

经济意义重大的棉树和可可树科（广义的Malvaceae）长期以来被视为一个单系群。然而，某些亚科之间的关系仍不明确，因为当分析不同来源的分子数据时，不断出现不一致的进化系统发育假说。先前已假设进化系统发育的不一致是由基因渗入和不完全谱系排序（ILS）共同导致的，但尚未在从大规模测序策略衍生出的位点以及该科的广泛代表性中评估不一致的程度和来源。此外，尚未应用正式方法来评估检测到的进化系统发育不一致是否影响了一致关系的进化时间估计。本研究旨在从核基因中生成Malvaceae的进化系统发育假说，具体目标包括：（1）调查Malvaceae数百个核基因历史中是否存在主要的不一致；（2）评估不一致的潜在来源；（3）检查不一致和位点异质性是否影响亚科的起源和多样化时间估计。本研究基于一个综合数据集，该数据集代表九个亚科中的96个属和268个核位点。遵循了串联和合并方法进行进化系统发育推断。通过分支长度和拓扑结构，我们将基因渗入事件的位置定位，以直接评估不一致是否由基因渗入而非ILS引起。为了估计分歧时间，考虑了一致性以及分子速率。基于与物种树的契合度过滤了位点，然后获得了每个位点的分子速率，将它们分配到三个不同的集合中，对应不同的分子速率范围。对于每个位点的不同集合，使用相同的参数和校准进行了贝叶斯时间估计。在深层次的合并时间点上，我们发现五个亚系的定位存在不一致，可能由于ILS和相对较少的基因渗入。使用每个位点的集合进行分歧时间估计产生了重叠的簇年龄，这表明，即使在不同的分子速率和基因历史中，校准通常提供了强大的先验。