Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity.

ABSTRACT: Statistical methods to identify Neanderthal ancestry in modern human genomes rest on varying assumptions and inputs. Nonetheless, most studies of introgression use only a single method to define Neanderthal ancestry. Due to a lack of "ground truth," we have a limited understanding of the accuracy, comparative strengths and weaknesses, and the sensitivity of downstream conclusions for these methods. Here, we performed large-scale comparisons of genome-wide introgression maps from 12 representative Neanderthal introgression detection algorithms. These span methods that consider archaic and human reference genomes not from Africa (ArchaicSeeker2, CRF, DICAL-ADMIX), only archaic genomes (S*, Sprime, HMM, SARGE, ARGWeaver-D), only human reference genomes, including from Africa (IBDmix), or simu

SUBMITTER: Chen Y 

PROVIDER: S-EPMC12485899 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature