Generalizing Bayesian phylogenetics to infer shared evolutionary events

Abstract

Many processes of biological diversification can affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a "super-spreading" event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns predicted by such processes, because all phylogenetic methods assume that lineages diverge independently. We introduce a general Bayesian framework to relax the assumption of independent divergences during phylogenetic inference, and test for patterns predicted by processes of diversification that affect multiple evolutionary lineages. Using simulations, we find our new method accurately infers shared divergence events when they occur, and performs as well as current methods when divergnces are independent. We apply our new approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands' landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research.

Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

“…However, when speciation and extinction rates are defined as functions of time and constrained to follow specific functional forms such as the exponential or a biologically motivated function (such as the environmental dependency tested here), speciation and extinction rates remain identifiable [111]. Detecting changes in diversification rates also requires enough statistical power, which might not be attained when inferences are based on small-sized phylogenies [36,112]. The differences observed here in the most likely model depending on whether analyses were run on clades separately or across the entire tree suggests that (i) there is evidence for rate heterogeneity within the subfamily and (ii) the selection of constant-rate model for individual clades might results from weak statistical power.…”

“…Consensus (36) mPTP( 23) mGMYC( 37) sGMYC( 36) ASAP( 36) ABGD (35) sPTP( 36 royalsocietypublishing.org/journal/rspb Proc. R. Soc.…”

“…Model comparison has been increasingly used in diversification studies to investigate alternative scenarios of interplay or independence between local and regional dynamics or the impact of paleoenvironments during species proliferation [33][34][35][36]. By fitting alternative diversification models to empirical phylogenies, the most likely dynamics of species proliferation can be highlighted.…”