Supporting information for: The frequency and topology of pseudoorthologs

Phylogenetics has long relied on the use of orthologs, or genes related
through speciation events, to infer species relationships. However,
identifying orthologs is difficult because gene duplication can obscure
relationships among genes. Researchers have been particularly concerned
with the insidious effects of pseudoorthologs—duplicated genes that are
mistaken for orthologs because they are present in a single copy in each
sampled species. Because gene tree topologies of pseudoorthologs may
differ from the species tree topology, they have often been invoked as the
cause of counterintuitive results in phylogenetics. Despite these
perceived problems, no previous work has calculated the probabilities of
pseudoortholog topologies, or has been able to circumscribe the regions of
parameter space in which pseudoorthologs are most likely to occur. Here,
we introduce a model for calculating the probabilities and branch lengths
of orthologs and pseudoorthologs, including concordant and discordant
pseudoortholog topologies, on a rooted three-taxon species tree. We show
that the probability of orthologs is high relative to the probability of
pseudoorthologs across reasonable regions of parameter space. Furthermore,
the probabilities of the two discordant topologies are equal and never
exceed that of the concordant topology, generally being much lower. We
describe the species tree topologies most prone to generating
pseudoorthologs, finding that they are likely to present problems to
phylogenetic inference irrespective of the presence of pseudoorthologs.
Overall, our results suggest that pseudoorthologs are less of a problem
for phylogenetics than currently believed, which should allow researchers
to greatly increase the number of genes used in phylogenetic inference.