Wu Meng, Kostyun Jamie L, Hahn Matthew W, Moyle Leonie C
Department of Biology, Indiana University, Bloomington, Indiana.
Department of Plant Biology, University of Vermont, Burlington, Vermont.
Mol Ecol. 2018 Jun 28. doi: 10.1111/mec.14780.
Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon-dubbed "hemiplasy"-is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here, we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar colour, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and to introgression events among the well-supported subclades. As both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit colour evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit colour variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.
性状进化的系统发育分析可以深入了解引发和推动表型多样化的进化过程。然而，最近的系统基因组学研究揭示了广泛的基因树与物种树不一致现象，如果仅使用单一物种树进行分析，这可能导致对性状进化的错误推断。这种被称为“半似性”的现象在分析快速辐射类群的性状进化时尤其需要考虑，因为在这些类群中不一致现象很普遍。在这里，我们生成了全转录组数据，用于对茄属植物的姐妹分支——Jaltomata属的14个物种进行系统发育分析，该属最近经历了快速的性状进化，包括果实和花蜜颜色以及花的大小和形状。与其他辐射类群一致，我们发现了由于不完全谱系分选（ILS）以及在得到充分支持的亚分支之间的基因渗入事件而导致的大量基因树不一致的证据。由于ILS和基因渗入都会增加半似性的概率，我们进行了几项分析，在识别可能有助于表型进化的基因时考虑了不一致性。尽管存在不一致性，但Jaltomata属果实颜色进化的历史仍可高度自信地推断出来，并且我们发现了与果实颜色变异相关的个别基因发生从头适应性进化的证据。相比之下，半似性似乎强烈影响了对Jaltomata属花性状转变的推断，并且我们识别出了可能源于多个谱系特异性替代或现存祖先多态性的候选基因座。我们的分析提供了一个可推广的例子，说明了在识别辐射谱系中与性状进化相关的基因座时如何处理不一致性。
