DOI: 10.5061/dryad.pvmcvdnjm
title: Genotyping of marine sticklebacks - Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution

description: 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.
description: <strong>SNP discovery and genotyping array design.
  </strong> An Illumina GoldenGate custom SNP
 genotyping array was designed to genotype large numbers of individuals at
 SNPs tagging previously identified adaptive loci that have diverged in
 parallel among marine and freshwater fish throughout the stickleback
 species range (Jones et al 2012). SNPs were selected to tag 72
 "adaptive" genomic regions (235 SNPs) and 50 "random"
 and putatively neutral genomic regions (128 SNPs) defined by
 cyclic-rotation of the bed intervals of the tagged adaptive regions by a
 random integer to ensure roughly equal linkage-disequilibrium among
 adaptive loci and random loci. Tagged SNPs were
 ascertained for the array using variant call data from Illumina short read
 sequencing of 10 marine and 11 freshwater fish (Jones et al, 2012).  For
 targeted adaptive loci, between 3 to 5 SNPs with an allele frequency
 difference &gt;=0.9 and with alternate alleles present in 4 or more
 individuals of each ecotype were selected for each target region.  For
 "random" loci between 2-5 SNPs with a minor allele frequency
 between 0.35 to 0.65 in the combined sample of 21 fish were selected.
 Where possible SNPs with nearby variants in the flanking 60 base pairs
 were excluded, and the SNPs with the highest 'design score' from
 Illumina's design verification process were selected for the
 genotyping array. <strong>Sample collections for
 SNP Genotyping array. </strong> 751, 655 and 237
 marine stickleback fish sampled from Rabbit Slough, Resurrection Bay, and
 Glacier Spit, Alaska respectively, were used for genotyping with a custom
 SNP genotyping array.  <strong>SNP genotyping
 array samples.</strong> DNA from SNP genotyping
 array samples were extracted from clipped spines or fins using overnight
 proteinase K digestion followed by phenol:chloroform isolation as
 previously described previously (Peichel et al, 2001). DNA concentration
 was quantified using a nanodrop spectrophotometer.
 <strong>SNP genotyping. </strong>
 SNP genotyping was performed on 250ng of genomic DNA using
 Illumina GoldenGate 384 custom SNP arrays (Illumina) according to
 manufacturer's protocols. Genotype calls were made using GenomeStudio
 2.0 software (Illumina), with results from each SNP individually inspected
 to verify genotype clusters.<br>  
 <strong>Ancestral Sequence
 imputation.</strong> The ancestral genome
 sequence for Gasterosteus was imputed by comparison of Gasterosteus
 aculeatus with two outgroup species (Gasterosteus wheatllandi and
 Pungitius pungitius). The resulting ancestral genome sequence is available
 here in fasta sequence format. Please see supplementary information for
 more details.
description: The genotyping dataset is in Plink format with gasAcu1-4 genome
 coordinates. The imputed ancestral genome sequence is
 in fasta format.