Data from: The ‘heritability’ of domestication and its functional partitioning in the pig

We propose to estimate the proportion of variance explained by regression
on genome-wide markers (or genomic heritability) when wild/domestic status
is considered the phenotype of interest. This approach differs from the
standard Fst in that it can accommodate genetic similarity between
individuals in a general form. We apply this strategy to complete genome
data from 47 wild and domestic pigs from Asia and Europe. When we
partitioned the total genomic variance into components associated to
subsets of single nucleotide polymorphisms (SNPs) defined in terms of
their annotation, we found that potentially deleterious non-synonymous
mutations (9566 SNPs) explained as much genetic variance as the whole set
of 25 million SNPs. This suggests that domestication may have affected
protein sequence to a larger extent than regulatory or other kinds of
mutations. A pathway-guided analysis revealed ovarian steroidogenesis and
leptin signaling as highly relevant in domestication. The genomic
regression approach proposed in this study revealed molecular processes
not apparent through typical differentiation statistics. We propose that
at least some of these processes are likely new discoveries because
domestication is a dynamic process of genetic selection, which may not be
completely characterized by a static metric like Fst. Nevertheless, and
despite some particularly influential mutation types or pathways, our
analyses tend to rule out a simplistic genetic basis for the domestication
process: neither a single pathway nor a unique set of SNPs can explain the
process as a whole.