Archaic Adaptive Introgression in Modern Human Reproductive Genes

README:

Modern human genetic data with evidence of adaptive introgression from Neanderthals or Denisovans within circadian rhythm genes. The data was generated from the phased gnomAD 1KGP + HGDP callset (Koenig et al., 2024) and introgressed segments were identified by SPrime (Browning et al., 2018). RAiSD (Alachiotis & Pavlidis, 2018) was used to detect signatures of positive selection within our gene set. Genes of interest were downloaded from Greer et al. (2021). This also includes high resolution images and supplemental tables for Archaic Adaptive Introgression in Modern Human Reproductive Genes. All proper citations can be found on the preprint references listed (available here: https://www.biorxiv.org/content/10.1101/2024.11.06.622331v1).

SPrime ND_Match Files

Raw SPrime identified files that we used for our entire analysis. These were modified to include the archaic allele, archaic allele frequency, and average introgressed segment allele frequency. Note that these have been lifted over (Hinrichs et al., 2006) from GRCh38 (hg38) to GRCh37 (hg19) coordinates to match the genome builds of the archaic samples used in our study. As such, any manually generated variant IDs (chromosome:position:ReferenceAllele_AlternativeAllele naming convention) may no longer match the position they are currently sitting on as they were generated with hg38 coordinates. However, all of these were subsequently filtered out of our final results and any proper SNP IDs (dbSNP labels) will be accurate.

RAiSD Outputs

We used RAiSD (Alachiotis & Pavlidis, 2018) to detect evidence of positive selection within our dataset. Please note these coordinates are mapped to hg38.