#28 · Genomics

Introgression and ancestry tested with sequence-to-function and haplotype analyses

The dominant thread is recovery of admixture history and functional consequences from patterns in genomic variation. In a preprint, AlphaGenome scores 144,139 introgressed SNPs in Papuan genomes, with chromatin predictions matching assays but expression predictions not matching. A second preprint, Restrictome-EVOLVE, applies matched-control haplotype analysis to 30 antiviral restriction-factor loci across 660 genomes and reports reduced population differentiation at these loci. Published work extends the methodological toolkit: a SNP panel of about 1M sites selected for minimal technology-specific bias enables coanalysis of capture and shotgun ancient DNA, and a bivariate marker-effect framework separates large-covariance outlier loci from polygenic background correlation in genetic correlations. A pangenome of 120 Mexican tetra fish addresses recurrent cave-specific deletions, adjacent in scope rather than focused on ancestry. What is new is the sequence-to-function test of introgressed variants, which reveals a modality-dependent gap, alongside matched-control haplotype analysis of restriction-factor loci.