Accounting for gene flow from unsampled ghost populations while estimating evolutionary history.

ABSTRACT: Gene flow from unsampled or extinct ghost populations leave signatures on the genomes of individuals from extant, sampled populations, often introducing biases, data misinterpretation, and ambiguous results when estimating evolutionary history from population genomic data. Here we establish theoretical expectations for these biases, and then utilize extensive simulations under a variety of ghost topologies to systematically assess biases while accounting, or not accounting for gene flow from ghost populations in (i) population genetics summary statistics such as π, FST, and Tajima's D and (ii) demographic history (mutation-scaled effective population sizes, divergence times, and migration rates) under the Isolation with Migration (IM) model. Estimates of evolutionary history across all sce

SUBMITTER: Sethuraman A 

PROVIDER: S-EPMC12506660 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature