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 ...多倍体化（polyploidy）对物种演化具有显著影响，且是一种极为常见的演化现象，尤其在植物界中广泛存在。两类多倍体——同源多倍体（autopolyploids）与异源多倍体（allopolyploids）——的核心差异，在于整合至新多倍体谱系中的基因之间的分化水平有所不同。由于异源多倍体通过杂交过程形成，其内部的基因部分同源拷贝（homoeologous copies）的分化程度，至少与参与杂交形成该异源多倍体的亲本物种中的直系同源基因（orthologs）相当。这一特性使得常规的异源多倍化事件亲本谱系推断方法并不准确，进而可能导致对基因复制与丢失次数的错误推论。本研究对基于拓扑结构的基因树协调（gene-tree reconciliation）算法进行了适配，使其可应用于多标记树（multi-labeled trees，简称MUL树）。根据定义，多标记树存在若干标签相同的末端节点，这使其能够自然表征多倍体的基因组。借助这一全新的协调算法，我们可以实现：准确地……