A stable phylogeny of the large-spored Metschnikowia clade.

Draft genomes of 55 strains representing all known large-spored Metschnikowia species were used to construct a robust phylogeny of these yeasts found in association with flower-visiting insects. The genomes were annotated with reference to Clavispora lusitaniae. From 3016 orthologues identified, 1061 were present in all strains with enough overlap to generate alignments of 500 bp or more. We constructed trees for all those alignments and evaluated their accuracy from their ability to resolve each of 22 sets of conspecifics correctly as sister taxa. Neighbour-joining identified species membership better than maximum likelihood, as did trees based on larger gene alignments. However, correct species assignment was not predictive of a gene's ability to resolve deeper topologies, which were more reliably identified by maximum likelihood analyses of large concatenations. Specifically, 14 trees based on independent concatenations ca. 100 kb in length were topologically consistent with a tree based on a single, large concatenation (1 410 065 positions), lending a high degree of confidence to the stability of the phylogeny. A tree based on a concatenation of intergenic regions (112 136 positions) was also congruent. Again, the best predictor of phylogenetic signal quality of a gene was the size of the alignment. Bootstraps were not always good indicators of phylogenetic quality, as they were sometimes affected by clade size. A tree constructed from a presence-absence matrix of all annotated genes was remarkably congruent with sequence-based phylogenies, suggesting that gain or loss of genes is worth exploring further as a phylogenetically significant event.