coalescent simulation (Animalia)

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Method synopsis

Population genetic simulations using coalescent theory to test whether observed allele frequency similarities between species are compatible with neutral genetic drift versus natural selection.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — A genetic polymorphism evolving in parallel in two cell compartments and in two clades (2013), BMC Evolutionary Biology. Implementations in other papers (listed below) may differ.

1. Population genetic simulation
   Used coalescent simulation program 'ms' to simulate symmetric two-allele mutation scenarios with mutations occurring in both ancestral and descendant species. Ran 2×10^7 simulations of 36 sampled sequences for each of two species and each codon polymorphism. Tested probability that variants' frequencies in descendant species would be as similar as observed values under neutral drift.
   Quantities: 2×10^7 simulations per codon polymorphism, 36 sequences per speciesDuration: Not specifiedConditions: Computational simulation with symmetric mutation model
   Equipment: ms coalescent simulation software

Typical Equipment

• ms coalescent simulation software

Output Measurements

• probability values
• null hypothesis tests

Papers Using This Protocol (1)

Species Studied With This Protocol