genome-wide genelaogy - senecio7の日記

Speidel L, Forest M, Shi S & Myers SR 2019 A method for genome-wide genealogy estimation for thousands of samples. Nat Genet 51:1321-1329.

all populations show a remarkable increase in inferred population size, often to >1,000,000, in the recent past
it is straightforward to explore the relative mutation rate of particular classes of mutations through time
as reported previously²⁵, this confirms a strong elevation in the rate of mutation types including TCC->TTC tri ucleotide changes in West Eurasian groups, which we date to 5,000-30,000 YBP

caution should be exerted when interpreting polygenic adaptation
a selection signal associated to a particular trait may not necessarily imply a phenotypic change in the same effect direction
for example, selection could have occurred to counter-act a large change in phenotype caused by another mutation

East Asians have the fewest selection signals and no enrichment of low p-values (Supplementary Figure 7) which may partly be explained by their stronger population bottleneck

Relate-based trees are able to capture evolutionary processes that are themselves evolving through time
evolution of evolution
changes through time in mutation rates, population size, migration, and archaic admixture, are simultaneously inferred, as are population-specific signals of natural selection

in common with previous studies, we find a relatively small (<40) number of clear signals of strong, ongoing selection across multiple human populations
we see an enrichment of selection evidence at loci shown to associate with human phenotypes in GWAS studies
these findings appear highly consistent with the polygenic nature of most human phenotypes - which are expected to impose very weak selection, but on a large collection of loci

if for example a selective sweep has fixed a single SNP of major effect [...], then selection might be acting on other SNPs to compensate this change
we only utilise the direction of association signals in testing for selection evidence

Relate is able to provide age estimates for mutations and other events in the tree
these estimates enable us to construct initial statistics to understand ancient migration and admixture events, as well as evidence for natural selection either on individual mutations or collections of mutations
we regard the selection statistics applied here as initial approaches along a path towards a richer inference framework
it should be straightforward to develop related approaches to target e.g. background selection, full selective sweeps, or balancing selection