Genotyping of marine sticklebacks - Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution

The data provided here was used in the following manuscript:
Predicting future from past: The genomic basis of recurrent and rapid
stickleback evolution Garrett A Roberts Kingman, Deven N Vyas, Felicity C
Jones, Shannon D Brady, Heidi I Chen, Kerry Reid, Mark Milhaven, Thomas S
Bertino, Windsor E Aguirre, David C Heins, Frank A von Hippel, Peter J
Park, Melanie Kirch, Devin M Absher, Richard M Myers, Federica Di Palma,
Michael A Bell*, David M Kingsley*, Krishna R Veeramah* Similar forms
often evolve repeatedly in nature, raising longstanding questions about
the underlying mechanisms. Here we use repeated evolution in sticklebacks
to identify a large set of genomic loci that change recurrently during
colonization of new freshwater habitats by marine fish. The same loci used
repeatedly in extant populations also show rapid allele frequency changes
when new freshwater populations are experimentally established from marine
ancestors. Dramatic genotypic and phenotypic changes arise within 5-7
years, facilitated by standing genetic variation and linkage between
adaptive regions. Both the speed and location of changes can be predicted
using empirical observations of recurrence in natural populations or
fundamental genomic features like allelic age, recombination rates,
density of divergent loci, and overlap with mapped traits. A composite
model trained on these stickleback features can also predict the location
of key evolutionary loci in Darwin’s finches, suggesting similar features
are important for evolution across diverse taxa.