Data from: Gene-tree reconciliation with MUL-trees to resolve polyploidy events

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy.多倍化（polyploidy）对物种演化可产生深远影响，且该现象广泛存在，尤其在植物类群中。两类多倍体——同源多倍体（autopolyploids）与异源多倍体（allopolyploids）——的差异，体现在新多倍体谱系中所整合的基因间的分化水平上。由于异源多倍体由杂交事件形成，其内部的同源异位基因拷贝（homoeologous copies of genes）的分化程度至少与形成该异源多倍体的亲本物种间的直向同源基因（orthologs）相当。这意味着，用于推断异源多倍化事件亲本谱系的常规方法并不准确，甚至可能对基因复制与丢失的数量做出错误推论。本研究针对基于拓扑结构的基因树调和（gene-tree reconciliation）算法进行改进，使其可适配多标记树（multi-labeled trees, MUL-trees）。根据定义，MUL-trees的部分末端分支拥有相同的标记，因此其可自然表征多倍体的基因组。借助该改进后的调和算法，我们可实现以下功能：精准将异源多倍化事件定位至系统发育树中；识别参与杂交形成异源多倍体的亲本谱系；区分异源多倍体、同源多倍体（多数场景下）以及无多倍化事件的类群；并准确统计一组基因树中的基因复制与丢失次数。本研究通过模拟包含/不包含多倍化事件的基因树对所提方法进行验证，并重新分析了包含酿酒酵母（baker's yeast）与普通小麦（bread wheat）的演化支中的多倍化历史。针对酵母数据的重新分析验证了该类群此前被认定的异源多倍化起源及其亲本谱系。本研究提出的算法有望在日益增多的具有多倍化演化历史的物种基因组研究中得到广泛应用。