PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow

Abstract

We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages, or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at https://github.com/cecileane/PhyloCoalSimulations.jl.

Summary tests of introgression are highly sensitive to rate variation across lineages

“…From each scaled network, we simulated 1000 gene trees under the network multispecies coalescent (NMSC) using v0.1.0 [Fogg et al, 2023, Fogg and Ané, 2022], written in [Bezanson et al, 2017]. These simulated gene trees had edge lengths in coalescent units, and had degree-2 nodes to mark each speciation and reticulation event (node in the species network, see Fig.…”