Runs of homozygosity in killer whale genomes provide a global record of
demographic histories
Abstract
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that
are identical by descent from each parent. Length distributions of ROH
are informative about population history; specifically the probability
of inbreeding mediated by mating system and/or population demography.
Here, we investigate whether variation in killer whale (Orcinus orca)
demographic history is reflected in genome-wide heterozygosity and ROH
length distributions, using a global dataset of 26 genomes
representative of geographic and ecotypic variation in this species, and
two F1 admixed individuals with Pacific-Atlantic parentage. We first
reconstruct demographic history for each population as changes in
effective population size through time using the pairwise sequential
Markovian coalescent (PSMC) method. We find a subset of populations
declined in effective population size during the Late Pleistocene, while
others had more stable demography. Genomes inferred to have undergone
ancestral declines in effective population size, were autozygous at
hundreds of short ROH (<1Mb), reflecting high background
relatedness due to coalescence of haplotypes deep within the pedigree.
In contrast, longer and therefore younger ROH (>1.5 Mb)
were found in low latitude populations and populations of known
conservation concern, including a Scottish population, for which 37.8%
of the autosomes comprised of ROH >1.5 Mb in length.