Sweeping for Sweeps

Reduction in genomic diversity around a site has been attributed to one of two mechanisms – (1) sites linked to positively selected mutant alleles are often `swept’ to fixation, in a process often called genetic hitchhiking, and/or (2) background selection at sites linked to deleterious mutants are purged (or purified). Recent selective sweeps are thus characterized by long sequences of homozygous sites, and reduced linkage disequilibrium. Ancient sweeps on the other hand, are difficult to characterize – with several methods being proposed to detect them, often using scaled (with respect to a common ancestor) haplotype diversity, Tajima’s D, number of segregating sites, etc  – see Enard et al. (2014) for an excellent recap.
Two recent studies that analyzed human genomes for ancient and recent recurrent selective sweeps revealed some very interesting results.

Quidditch, anyone?

Racimo et al. (2014) propose a method based on ABC (Approximate Bayesian Computation) to detect ancestral selective sweeps that occurred soon after the split of humans and Neanderthals, and apply it to 26 phased human genomes from the 1000 Genomes Project. Scaled diversity (and other statistics) estimated in 0.02 cM windows around non-synonymous mutations, splice sites, 5’ UTR’s, regulatory motif changes show (1) no significant differences in signatures of positive selection between synonymous and non-synonymous sites, 5’ UTR’s, or regulatory motifs, but (2) significantly reduced differences in diversity in splice sites, and (3) failure of sites in favor of positive selection to lie in regions introgressed from Neanderthals.
Dutheil et al. (2014) take a different approach – they analyze regions of the genome (here X chromosome) that show signatures of Incomplete Lineage Sorting (ILS) – i.e. lower divergence, while reconstructing population histories. Low ILS regions thus would be expected to be either under strong background selection, or have experienced strong selective sweeps. Their analyses of reduction in genomic diversity at low-ILS sites from the 1000 genomes data on the X chromosome reveal (1) greater reduction in genomic diversity in non-African X chromosomes, compared to African X chromosomes, and (2) sites with low-ILS, and reduced genomic diversity do not lie in regions introgressed from Neanderthals.
Two studies, similar conclusions, leading into more questions about complex speciation in great apes. A classic clash of brooms. Quidditch, anyone?
Dutheil, Julien Y., et al. “Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation.” bioRxiv (2014): 011601. http://dx.doi.org/10.1101/011601
Enard, David, Philipp W. Messer, and Dmitri A. Petrov. “Genome-wide signals of positive selection in human evolution.” Genome research (2014). http://dx.doi.org/10.1101/gr.164822.113
Racimo, Fernando, Martin Kuhlwilm, and Montgomery Slatkin. “A test for ancient selective sweeps and an application to candidate sites in modern humans.” Molecular biology and evolution 31.12 (2014): 3344-3358. http://dx.doi.org/10.1093/molbev/msu255

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