DOI: 10.5061/dryad.qbzkh18s3
title: SNPs derived from a common garden experiment across the biogeographic range of <em>Kelletia kelletii</em>

description: Signals of natural selection can be quickly eroded in high gene-flow
 systems, severely challenging efforts to understand how and when genetic
 adaptation occurs in the ocean. This long-standing, unresolved topic in
 ecology has renewed importance because rapidly changing environmental
 conditions are driving range expansions that, in many cases, necessitate
 rapid evolutionary responses. Kellet’s whelk expanded its biogeographic
 range in the 1980s and is readily adapting to novel conditions in its
 expanded range. To test for genetic adaptation in a coastal marine species
 with high dispersal potential, we performed a series of crosses on
 Kellet's whelk (Kelletia kelletii) collected from its historical and
 recently colonized range, and conducted RNA-Seq on offspring that we
 reared in a common garden environment. We identified 2,770 differentially
 expressed genes between 54 samples with historical-range and
 expanded-range ancestry. Using SNPs called directly from the
 differentially expressed genes, we revealed parental population structure
 that enabled us to assign “unknown” samples back to their range of origin
 with unprecedented accuracy for a marine species (92.6 to 94.5%). The SNP
 with the highest predictive importance occurred on triosephosphate
 isomerase (TPI), an essential enzyme for glycolysis and glucogenesis,
 which also plays a role in cold stress response. TPI is both highly
 upregulated and contains a non-synonymous mutation in the expanded range,
 where ocean temperatures are colder than in the historical range. Our
 findings pave the way for accurately identifying patterns of dispersal,
 gene flow, and population connectivity in the ocean by demonstrating that
 rapid genetic adaptation can occur even in high gene flow species and that
 experimental transcriptomics can reveal mechanisms for how marine
 organisms respond to changing environmental conditions.
description: Using SCUBA, we collected adult Kellet’s whelks by hand from
 sub-tidal (approximately 15 m depth) locations across California (Figure
 1A, CDFW SCP #8018 to C.W.). Adult whelks from three locations: Monterey
 (MON, north of Point Conception; 36.6181670 N, 121.89 W), Naples (NAP,
 just south of Point Conception; 34.4219670 N, 119.952283 W), and Point
 Loma (POL, Southern California; 32.665333 N, 117.261517 W) were used in
 our main experimental cross (described below). Additionally, adult whelks
 from Diablo Canyon (DIC in the expanded range; 35.22445 N, 120.877483 W)
 were collected and used to validate the results of the main experimental
 cross.   We acclimated 40 individuals each from MON,
 NAP, and POL in common garden aquaria using the flow-through filtered
 seawater system at the California Polytechnic State University Research
 Pier in Avila, California (35.169817 N, 120.740838 W). Additionally, an
 experimental reciprocal cross between MON and NAP was created with 7
 individuals from both sites. The wild-collected adults were acclimated for
 7 to 10 months, fed identical diets of mixed seafood (scallops, shrimp,
 blue mussels, and squid), and then cross-bred within 92-liter common
 aquaria. Because all offspring were reared in a common garden and thus
 environmental conditions were identical, differences in their gene
 expression can largely be attributed to genetic and/or multi-generational
 epigenetic differences between populations (Christie et al., 2016; Roberge
 et al., 2008). A small subset of these differentially expressed genes may
 also be driven by maternal or paternal effects (Mousseau & Fox,
 1998; Wolf & Wade, 2009). In total, these four experimental
 crosses used 134 adult whelks. We separated roughly 500-1000 veliger
 larvae (F1 offspring) from each egg capsule from the maternal egg capsule
 tissue for use in subsequent RNA extraction and sequencing. Thus, each
 “sample” in our analyses represents a pool of larvae from a single egg
 capsule. SNP variants on reads aligned to the de novo transcriptome
 (Daniels et al., 2023) were identified using ANGSD (Korneliussen et al.,
 2014), a maximum likelihood approach to identify major and minor alleles
 (Skotte et al., 2012), the GATK genotyping algorithm (Van der Auwera
 & O’Connor, 2020), and a uniform prior. Bases were only retained
 if they had a Phred-scaled quality score of at least 20. Genotypes with a
 posterior probability of less than 95% and/or a depth of less than 20 in
 an individual or less than 100 across all individuals were removed, and
 only loci genotyped in every individual were retained. Lastly, we removed
 any loci with a minor allele frequency of less than 0.05 in every
 population using the R package snpR/1.2.79 (Hemstrom & Jones,
 2022). Because selection at putatively adaptive loci can often manifest as
 downstream changes in expression, we also identified SNP variants that
 occurred on differentially expressed contigs between MON and NAP. Although
 genetic expression changes are due to changes at nearby cis or distant
 trans regulatory elements, we identified SNPs within the DEGs to search
 for functional (structural) differences in the genes themselves. We called
 122,599 SNPs directly from the RNA-seq data using ANGSD (Korneliussen et
 al., 2014), of which 4,168 were located on DEG contigs (see SI methods and
 Table S1 for filtering details). After SNP calling and filtering (Hemstrom
 et al., 2024), 94,654 SNP loci were identified throughout the
 transcriptome (hereafter “all-SNPs”) with 3,118 loci located on DEG
 contigs (hereafter “DEG-SNPs”).
description: # SNPs derived from a common garden experiment across the biogeographic
 range of *Kelletia kelletii*
 [https://doi.org/10.5061/dryad.qbzkh18s3](https://doi.org/10.5061/dryad.qbzkh18s3) Included here are unfiltered VCF files associated with the publication "Genetic adaptation despite high gene flow in a range-expanding population" in Molecular Ecology. SNPs are called from RNA-Seq reads of samples reared in a common garden.  ## Description of the data and file structure We have provided VCF files for two datasets associated with the study: one for All-SNPs (kw_allsnps.vcf) and one for DEGs-SNPs (kw_degsnps.vcf). The All-SNPs dataset contains SNPs identified throughout the entire transcriptome, representing the full range of genetic variation detected in the samples. In contrast, the DEGs-SNPs dataset includes only the SNPs located within differentially expressed genes (DEGs), which are genes showing significant expression differences between Kellet's whelks from the expanded range versus those from the historical range. These targeted SNPs help focus on genetic variations potentially associated with expression changes linked to range expansion. Associated data for samples can be found in kw_sample_info.csv.  July 2025 versioned changes: added **kw_sample_info.csv**, file with all metadata info for each individual. In this file, the sample names are listed as kwXXX.sorted.bam (which are available at https://www.bco-dmo.org/dataset/945292) #### Sharing/Access information Raw reads can be found in SRA: [https://www.ncbi.nlm.nih.gov/sra/PRJNA1000198.](https://www.ncbi.nlm.nih.gov/sra/PRJNA1000198) #### Code/Software [https://github.com/ChristieLab/kellets_whelk_rnaseq](https://github.com/ChristieLab/kellets_whelk_rnaseq)