Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny

Paralogy is a pervasive problem in trying to use nuclear gene sequences to infer species phylogenies. One strategy for dealing with this problem is to infer species phylogenies from gene trees using reconciled trees, rather than directly from the sequences themselves. In this approach, the optimal species tree is the tree that requires the fewest gene duplications to be invoked. Because reconciled trees can identify orthologous from paralogous sequences, there is no need to do this prior to the analysis. Multiple gene trees can be analyzed simultaneously; however, the problem of nonuniform gene sampling raises practical problems which are discussed. In this paper the technique is applied to phylogenies for nine vertebrate genes (aldolase, alpha-fetoprotein, lactate dehydrogenase, prolactin, rhodopsin, trypsinogen, tyrosinase, vassopressin, and Wnt-7). The resulting species tree shows much similarity with currently accepted vertebrate relationships.