DOI: 10.5061/dryad.m905qfv4b
title: Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution

description: Chromosomal inversions have been shown to play a major role in local
 adaptation by suppressing recombination between alternative arrangements
 and maintaining beneficial allele combinations. However, so far, their
 importance relative to the remaining genome remains largely unknown.
 Understanding the genetic architecture of adaptation requires better
 estimates of how loci of different effect sizes contribute to phenotypic
 variation. Here, we used three Swedish islands where the marine snail
 Littorina saxatilis has repeatedly evolved into two distinct ecotypes
 along a habitat transition. We estimated the contribution of inversion
 polymorphisms to phenotypic divergence while controlling for polygenic
 effects in the remaining genome using a quantitative genetics framework.
 We confirmed the importance of inversions but showed that contributions of
 loci outside inversions are of similar magnitude, with variable
 proportions dependent on the trait and the population. Some inversions
 showed consistent effects across all sites, whereas others exhibited
 site-specific effects, indicating that the genomic basis for replicated
 phenotypic divergence is only partly shared. The contributions of sexual
 dimorphism as well as environmental factors to phenotypic variation were
 significant but minor compared to inversions and polygenic background.
 Overall, this integrated approach provides insight into the multiple
 mechanisms contributing to parallel phenotypic divergence. 
description: Snails were collected along the Swedish West coast, where Crab
 and Wave habitats frequently come into contact (Figure 1B), in 2013 and
 2014. The sites were Ramsö (58°49’27.8”N11°03’45.3”E), here CZA, Inre
 Arsklovet (58°50’00.5”N 11°08’19.6”E), here CZB, and Yttre Arsklovet
 (58°49’51.3”N11°07’59.0”E), here CZD. At each location snails were
 collected along a transect that started in the wave habitat (exposed
 bedrock) continued to the crab habitat (boulder fields in the centre of a
 bay) and extended into the next wave habitat at the other side of the bay.
 Exact positions of all individuals were recorded in three-dimensional
 space using a Total station (Trimble M3). Positions along the transects
 were then converted to a one-dimensional distance measurement along a
 least-cost path that minimised path length and constrained movement to
 areas of high snail density. The first snail collected along the transect
 path (starting in the Wave habitat) was assigned position 0. Total path
 lengths were: 362.47 m (CZA), 257.00 m (CZB), 270.17 m (CZD).
 Environmental variables were recorded to describe the habitat at 1000-2000
 points for each transect. These included substrate type (bedrock/boulder),
 presence of barnacles as indicator of wave exposure and presence of fucoid
 seaweed (indicator of weak wave action and more sheltered habitats). These
 measurements were then summarised as “habitat PC” by a principal component
 analysis. Sex of each snail was determined by dissection. Weight (wet
 weight of snails including shell), shell length and thickness were
 recorded. Thickness was measured with a thickness gauge (NeoteckDTI
 Digital Dial Indicator Probe, 0.001mm resolution) at the widest point of
 the aperture and the average of three measurements per individual was
 used. Foot area was measured from photos of snails moving inside
 seawater-filled Falcon tubes using the program ImageJ
 (http://imagej.nih.gov/ij/). Foot area (in cm2) was divided by shell
 length to obtain relative foot area. For describing shell shape and
 aperture characteristics, several size-independent parameters
 (height-growth, width-growth, aperture-position, aperture-size,
 aperture-shape) were used, based on a growth model developed by Larsson et
 al. (Larsson et al. 2020; J. R. Soc. Interface 17.). They describe whether
 the shell shape is more elongated with a high spire (small height- and
 width-growth) or globose (large growth parameters). Small values for
 aperture-position and large values for aperture-shape indicate narrow
 apertures, wide apertures have a large aperture-position and small values
 for aperture-shape. Boldness behaviour was measured as Bold Score, which
 is the log-time until an individual crawls out of its shell after
 disturbance (higher Bold Score means individuals are less bold). Each
 individual was measured three times and the average was used as a boldness
 proxy. For inversion genotypes a PCA on all SNPs within previously
 described inversion regions (see Faria et al. 2019, Mol. Ecol.
 28:1375–1393), was applied which resulted in distinct clusters (see Faria
 et al. 2019 for details of this method). Inversion genotypes are coded as
 0 and 2 for homozygotes and 1 for heterozygous.