Reply to Barton et al: signatures of natural selection during the Black Death.

ABSTRACT: Barton et al.¹ raise several statistical concerns regarding our original analyses² that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high F_ST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10^-5

SUBMITTER: Vilgalys TP 

PROVIDER: S-EPMC10104142 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature