Data_files

Data of 454 sequencing, phenotypes, Kaspar analysis, qPCR analysis for all experiments used in manuscrip

Inferred_haplotypes

Individual haplotypes for each linkage group as inferred from fastPHASE. subpop1=CliffD, subpop2=CliffN, subpop3=IndianD, subpop4=IndianN, subpop5=WebsterD, subpop6=WebsterN, subpop7=EastD, subpop8=EastN, subpop9=TemiscouataD, subpop10=Temiscouata

Genomic_Islands

R code to perform regressions of 90th percentile value of FST as a function of genetic distance from the center of the genomic islands of differentiation. For each lake, the table "Lake_Island_Group.txt" combines FST values at increasing recombination distances (Pos) from the reference position. Map distances were binned into discrete classes (Int) to perform regressions

24sites_lat_long

Geographic coordinates of the sampling location

strata.cucumbers.717ind

strata file with the population numbers used when converting VCF to other format

dapc

Script to perform the DAPC analysi

AEM_weight_all_vectors

AEM vectors used as input for RDA; edge weights used to compute AEM vectors are based on connectivity probabilities between site

dbMEM_straight_all_vectors

dbMEM vectors computed from Euclidean distances between sites used as input for RD

2719neutral_snps_noAK

Allele frequencies across neutral SNPs (excluding Alaska sites) used for spatial eigenfunction analysi

filtered_3699snps_californicus

Filtered dataset consisting of 3,699 SNPs genotyped in 717 giant California sea cucumber individual