Coalescent models derived from birth-death processes

Theor Popul Biol. 2021 Dec;142:1-11. doi: 10.1016/j.tpb.2021.09.003. Epub 2021 Sep 24.

Abstract

A coalescent model of a sample of size n is derived from a birth-death process that originates at a random time in the past from a single founder individual. Over time, the descendants of the founder evolve into a population of large (infinite) size from which a sample of size n is taken. The parameters and time of the birth-death process are scaled in N0, the size of the present-day population, while letting N0→∞, similarly to how the standard Kingman coalescent process arises from the Wright-Fisher model. The model is named the Limit Birth-Death (LBD) coalescent model. Simulations from the LBD coalescent model with sample size n are computationally slow compared to standard coalescent models. Therefore, we suggest different approximations to the LBD coalescent model assuming the population size is a deterministic function of time rather than a stochastic process. Furthermore, we introduce a hybrid LBD coalescent model, that combines the exactness of the LBD coalescent model model with the speed of the approximations.

Keywords: Bernoulli sampling; Conditioned reconstructed process; Founder population; Kingman coalescence; Variable population size coalescence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genetics, Population*
  • Models, Genetic*
  • Population Density
  • Sample Size
  • Stochastic Processes