Data_Sheet_2_Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae).DOCX

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.

经济价值重大的棉属和可可属（广义的 Malvaceae）长期以来被视为一个单系群。然而，一些亚属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。先前已有假设认为，进化系统发育的不一致性可能源于种间杂交以及不完整的谱系排序（ILS），但在广义的 Malvaceae 家族背景下，对于源自大规模测序策略的位点以及广泛的代表性位点，尚未对不一致性的程度和来源进行评估。此外，尚未有正式的方法被应用于评估检测到的进化系统发育不一致性是否影响了协调关系的系统发育年代估计。本研究旨在从核基因生成 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性；（2）评估不一致性的潜在来源；（3）检验不一致性和位点异质性是否影响亚属起源和多样化的时间估计。本研究基于一个综合数据集，该数据集代表了九个亚属中的96个属和268个核位点。本研究遵循了串联和基于合并的进化系统发育推断方法。通过分支长度和拓扑结构，我们将种间杂交事件的位置定位，以直接评估不一致性是由于种间杂交还是由于 ILS。为了估计分化时间，考虑了协调性和分子速率。我们根据与物种树的协调性过滤了位点，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，这些集合对应于共享的分子速率范围。对于每个不同集合的位点，使用相同的参数和校准进行了贝叶斯年代测定。在深层合并时间点，我们发现了五个亚系位置的矛盾，这可能是由于 ILS 和相对较小的种间杂交比例。使用每个位点的集合进行分化时间估计产生了重叠的亚系年龄，这表明，即使在不同的分子速率和基因历史中，校准通常提供强有力的先验。