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Gene Flow02:39

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Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the

John Fogg1, Elizabeth S Allman2, Cécile Ané1,3

  • 1Department of Statistics, University of Wisconsin - Madison, WI, 53706, USA.

Systematic Biology
|May 31, 2023
PubMed
Summary

We introduce a new network coalescent model for simulating gene tree evolution in phylogenetic species networks, accounting for correlated gene flow inheritance. This tool aids simulation studies and inference methods in evolutionary biology.

Keywords:
Admixturegene treegraphhybridizationintrogressionspecies networkspecies tree

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Phylogenetics

Background:

  • Phylogenetic species networks model complex evolutionary histories beyond simple bifurcating trees.
  • The network multispecies coalescent process is crucial for understanding gene tree divergence within these networks.

Purpose of the Study:

  • To introduce a novel network coalescent model incorporating correlated inheritance of gene flow.
  • To generalize existing network coalescent models (independent and common inheritance).

Main Methods:

  • Developed a new network coalescent model with correlated inheritance using a Dirichlet process.
  • Implemented gene tree simulations in the Julia package PhyloCoalSimulations.
  • Utilized PhyloNetworks for species network manipulation and Newick format input/output.

Main Results:

  • The model allows for correlated inheritance of gene flow at reticulation events.
  • Simulated gene trees can preserve information about their embedding within the species network.
  • The software supports input in generations or coalescent units and output in Newick format.

Conclusions:

  • The PhyloCoalSimulations package provides a flexible tool for simulating gene tree evolution under various network coalescent scenarios.
  • This facilitates downstream analyses such as simulating species-specific processes and advancing simulation-based inference methods.