DOI: 10.5061/dryad.bp25b65
title: Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow

description: Adaptive divergence and speciation may happen despite opposition by gene
 flow. Identifying the genomic basis underlying divergence with gene flow
 is a major task in evolutionary genomics. Most approaches (e.g. outlier
 scans) focus on genomic regions of high differentiation. However, not all
 genomic architectures potentially underlying divergence are expected to
 show extreme differentiation. Here, we develop an approach that combines
 hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency
 change) with system-specific simulations to identify loci inconsistent
 with neutral evolution. We apply this to a genome-wide SNP set from an
 ideally-suited study organism, the intertidal snail Littorina saxatilis,
 which shows primary divergence between ecotypes associated with different
 shore habitats. We detect many SNPs with clinal patterns, most of which
 are consistent with neutrality. Among non-neutral SNPs, most are located
 within three large putative inversions differentiating ecotypes. Many
 non-neutral SNPs show relatively low levels of differentiation. We discuss
 potential reasons for this pattern, including loose linkage to selected
 variants, polygenic adaptation and a component of balancing selection
 within populations (which may be expected for inversions). Our work is in
 line with theory predicting a role for inversions in divergence, and
 emphasises that genomic regions contributing to divergence may not always
 be accessible with methods purely based on allele frequency differences.
 These conclusions call for approaches that take spatial patterns of allele
 frequency change into account in other systems.
description: Cline fitting
 resultsProvides information
 about all SNPs (one SNP per line) that passed filters and where either a
 model of clinal change provided the best fit (Type=Cline), or the allele
 frequency difference between cline ends was &lt; 0.1 / the model of no
 clinal change provided the best fit (Type=NC). - Contig: Reference genome
 contig the SNP is located on - Position: Position of the SNP within the
 contig - Type: Whether SNP showed clinal change (Cline) or no change (NC)
 - Wave: Whether the reference allele is the more common allele in the Wave
 ecotype (1) or not (2) - Centre: Position of the cline centre on the path
 along the shore (in m) - Width: Width of the cline (in m) - p_crab: Allele
 frequency in the Crab ecotype - p_diff: Difference between Crab and Wave
 allele frequency - Var.Ex: Variance explained by the cline model - AIC_NC,
 AIC_cline, AIC_lt, AIC_rt, AIC_bt: AICs for different models (NC, Cline,
 left-tailed cline, right-tailed cline, two-tailed cline) - sel: Whether a
 cline is inconsistent with neutrality, indicating direct or linked
 selection (i.e. whether Var.Ex is &gt; then the threshold [35.69] defined
 by simulations) - LG: Linkage group from genetic map on which SNP is
 located - av: Position on the linkage group where SNP is
 locatedWestramEtAl2018_cline_results_threshold35.69.txtCapture probe sequencesList of all 40,000 capture sequencing probes used in this study. Note that the probe IDs refer to previous L. saxatilis assemblies and are not meaningful with respect to position in the current assembly.WestramEtAl2018_probe_sequences.txtSnail positions and phenotypesProvides information about the sampling coordinates and phenotypes of each snail. - x, y, z: Position of snail on the shore in 3 dimensions - RW1, RW2: Relative warps of geometric morphometric analysis (shell shape) - length_mm: Shell length (in mm) - CS: Centroid size from geometric morphometric analysis - DistAlongPath_m: Position on the path along the shore (in m)WestramEtAl2018_snail_positions_phenotypes.csvLittorina saxatilis genome assemblyL. saxatilis genome assembly used in this study (repeat regions hard-masked).WestramEtAl2018_Littorina_saxatilis_assembly_hard_masked.zip