Ogilvie, H. A. | Search bioRxiv

bioRxiv2018

Inferring Species Trees Using Integrative Models of Species Evolution

Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.

evolutionary biology↗

bioRxiv2017

Bayesian Inference Of Species Networks From Multilocus Sequence Data

Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network. We assume a multispecies network coalescent (MSNC) prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. We reanalyze a large dataset of genes from closely related spruces, and verify the previously suggested homoploid hybridization event in this clade. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides a general framework for Bayesian inference of reticulate evolution.

evolutionary biology↗