A time-dependent Poisson random field model for polymorphism within and between two related biological species

TL;DR

This paper introduces a time-dependent Poisson random field model to analyze genetic polymorphisms within and between two related species, accounting for recent common ancestry and allowing for equilibrium or non-equilibrium conditions.

Contribution

It develops a novel Poisson random field framework for population genetics that incorporates time dependence and recent common ancestry, enabling more accurate inference of mutation and selection history.

Findings

Model can handle equilibrium and non-equilibrium scenarios

Provides a method to infer mutation and selection history

Applicable to aligned DNA sequence data

Abstract

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider a random field of Markov chains that describes the fate of a set of individual mutations. This field is approximated by a Poisson random field from which we can make inferences about the amounts of mutation and selection that have occurred in the history of observed aligned DNA sequences.