During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome-wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation-with-gene-flow mechanism.

Genotypes_5_Lakes_3438_MarkersGenotypes at 3438 RAD markers (in Arlequin format), for 195 individual collected in 5 lakes. Each lake comprises a dwarf and a normal whitefish sample.5_Lakes_Mapped_2734_FSTMapped FST values (dwarf/normal) for 2734 polymorphic RAD markers in each lake.Genomic_IslandsR 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.Inferred_haplotypesIndividual 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=TemiscouataN