Correction to: Evolution of immune genes is associated with the Black Death (Nature, (2022), 611, 7935, (312-319), 10.1038/s41586-022-05349-x)

Abstract

Correction to: Naturehttps://doi.org/10.1038/s41586-022-05349-x Published online 19 October 2022 In the version of the article initially published, the genotype likelihood-based allele frequency estimator we used resulted in a biased estimate of allele frequencies, particularly among sites with low coverage data. We have now corrected this by employing a maximum likelihood-based estimator, which offers an unbiased estimate of allele frequencies. To further minimize the risk of erroneous genotype calls, our analyses are now confined to known polymorphic sites, specifically those identified in individuals of European ancestry by the 1000 Genomes Project. Finally, limited by the number of putatively neutral SNPs available for matching, we needed to alter the matching scheme relative to the original publication (see Supplementary Information). Despite these adjustments, the data continue to show increased genetic differentiation at immune loci following the Black Death. The corrected allele frequency estimates result in similar or slightly higher enrichment scores compared to the original results. However, the strength of this evidence is influenced by alternative methods of calculating these enrichments, as discussed in the associated Matters Arising1 and our Reply2. We have updated Fig. 2 and Extended Data Figs. 1 and 2 to reflect these corrected estimates. With the revised allele frequency estimates, the list of outlier candidate loci has changed, but rs2549794 near ERAP1/2 continues to meet all the original criteria as the strongest candidate for positive selection. Consequently, our follow-up analyses, including the estimation of selection coefficients and the section “Functional dissection of candidate loci” (Fig. 3, Extended Figs. 4–6 and 8 and Supplementary Figs. 3 and 4), now focus primarily on this variant and the nearby genes. A comprehensive list of edits, along with the original article for comparison, are provided in the Supplementary Information.