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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.
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The nested Kingman coalescent: speed of coming down from infinity
The nested Kingman coalescent describes the ancestral tree of a population undergoing neutral evolution at the level of individuals and at the level of species, simultaneously. We study the speed at which the number of lineages descends from infinity in this hierarchical coalescent process and prove the existence of an early-time phase during which the number of lineages at time t decays as 2γ/ct^2, where c is the ratio of the coalescence rates at the individual and species levels, and the constant γ ≈ 3.45 is derived from a recursive distributional equation for the number of lineages contained within a species at a typical time.
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- Award ID(s):
- 1707953
- PAR ID:
- 10088922
- Date Published:
- Journal Name:
- The Annals of applied probability
- Volume:
- 29
- Issue:
- 3
- ISSN:
- 1050-5164
- Page Range / eLocation ID:
- 1808-1836
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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