Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids

The genetic basis of parallel evolution of similar species is of great
interest in evolutionary biology. In the adaptive radiation of Lake
Victoria cichlid fishes, sister species with either blue or red-back male
nuptial coloration have evolved repeatedly, often associated with
shallower and deeper water, respectively. One such case are blue and
red-backed Pundamilia species, for which we recently showed that a young
species pair may have evolved through “hybrid parallel speciation”.
Coalescent simulations suggested that the older species P. pundamilia
(blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new
“nyererei-like” and “pundamilia-like” species evolved from the admixed
population. Here, we use genome scans to study the genomic architecture of
differentiation, and assess the influence of hybridization on the
evolution of the younger species pair. For each of the two species pairs,
we find over 300 genomic regions, widespread across the genome, which are
highly differentiated. A subset of the most strongly differentiated
regions of the older pair are also differentiated in the younger pair.
These shared differentiated regions often show parallel allele frequency
differences, consistent with the hypothesis that admixture-derived alleles
were targeted by divergent selection in the hybrid population. However,
two thirds of the genomic regions that are highly differentiated between
the younger species are not highly differentiated between the older
species, suggesting independent evolutionary responses to selection
pressures. Our analyses reveal how divergent selection on
admixture-derived genetic variation can facilitate new speciation events.