Eukaryotic ancestry in a finite world

TL;DR

This paper presents an exact backward-in-time simulation of large diploid populations to study genetic and genealogical ancestry, revealing where theoretical models based on infinite assumptions diverge from finite population realities.

Contribution

It introduces a scalable, exact simulator that models recombination and ancestry without approximations, and compares empirical results with existing theoretical predictions.

Findings

Some theoretical predictions hold in practice

Discrepancies arise between finite and infinite models

Genome structure influences ancestral segment distribution

Abstract

Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large scale is not trivial, as successive recombination events break them into several segments. For this reason, the behavior of the distribution of genetic segments across the ancestral population is not fully understood. Moreover, as individuals transmit only half of their genetic content to their offspring, after a few generations, it is possible that ghosts arise, that is, genealogical ancestors that transmit no genetic material to any individual. While several theoretical predictions exist to estimate properties of ancestral segments or ghosts, most of them rely on simplifying assumptions such as an infinite population size or an infinite chromosome length. It is not clear how well these results hold in a finite universe, and current simulators either make other approximations or cannot handle the scale required to answer these questions. In this work, we use an exact back-in-time simulator of large diploid populations experiencing recombination that tracks genealogical and genetic ancestry, without approximations. We focus on the distinction between genealogical and genetic ancestry and, additionally, we explore the effects of genome structure on ancestral segment distribution and the proportion of genetic ancestors. Our study reveals that some of the theoretical predictions hold well in practice, but that, in several cases, it highlights discrepancies between theoretical predictions assuming infinite parameters and empirical results in finite populations, emphasizing the need for cautious application of mathematical models in biological contexts.