Inferring species trees from gene duplication episodes

摘要: Gene tree parsimony, which infers a species that implies the fewest gene duplications across collection of trees, is method for inferring phylogenetic trees from paralogous genes. However, it assumes all are independent, and therefore, does not account large-scale duplication events like whole genome duplications. We describe two methods to infer based on may involve multiple First, episode parsimony seeks possible episodes. Second, adjusted corrects number at each node in by treating largest as single duplication. test both new methods, well using 7,091 representing 7 plant taxa. perform well, returning after an exhaustive search space. By contrast, fails rank true within top third topologies. Furthermore, with randomly permuted leaf labels can imply fewer episodes than correct labels. Adjusted reflects potentially more realistic and, least small data sets, computationally feasible model counting independently or minimizing