Scripts from: Ancient stickleback genomes reveal the early stages of parallel adaptation

The parallel evolution of traits and their underlying genetic basis is
well studied; however, studies of the parallel chronology of adaptive
genetic changes remain scarce. The probability of parallel genetic change
should be increased by the clustering of adaptive alleles in regions of
suppressed recombination, particularly for genes that have large fitness
or phenotypic effects. The threespine stickleback is a model system for
studying parallel evolution, here we present genomic data from nine
subfossil stickleback bones dated to 14.8-0.7 KYR BP in age. Comparing the
four highest coverage genomes, which represent different stages along the
marine–freshwater divergence continuum, we find that the accumulation of
freshwater ancestry is clustered rather than randomly distributed
throughout the marine–freshwater divergent regions of the genome. We
consistently find freshwater ancestry on chromosome IV at the early stages
of freshwater adaptation. Regions of chromosome IV contain the greatest
genetic differentiation between marine and freshwater ecotypes and among
the highest density of quantitative trait loci. These include
Ectodysplasin (EDA), a large-effect pleiotropic locus associated with
defensive armor and variation in neurosensory and behavioral traits.
Freshwater ancestry in the subfossils is also consistently found at
inversions and X chromosome early in the adaptive process. Our findings
add to emerging evidence that freshwater adaptation in threespine
stickleback could have a staggered but predictable temporal dynamic.