This is a project analyzing population structure and genetic adaptation of Kellet's whelks (Kelletia kelletii) --- a range expanding marine species with high gene flow potential. We performed a series of crosses on Kellet's whelks collected from its historical and recently colonized range, and conducted RNA-Seq on 70 offspring that we reared in a common garden environment. We also used transcriptome derived SNPs to examine population structure and genetic adaptation.
Corresponding article https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17511
Code for the project are split up into directories:
- Study system. R code associated with figure 1.
- Sequence processing. Process RNA transcripts and conduct DEG analysis
- SNP calling. Contains for SNP variant calling using ANGSD
- Population structure and population assignment. R codes analyszing transcriptome-derived SNPs using snpR (Figure 2)
- Candidate loci driving differntiation. R codes analyszing transcriptome-derived SNPs using snpR, population assignment using rubias and ranger (Figure 3). R code analyzing the TPI gene (Figure 4)
- Gene Ontology and WGCNA. R codes associated with analyses of expression data (Supplemental)
All raw data and sample metadata generated for this project are stored in the NCBI Short Read Archive (SRA) under project PRJNA1000198 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1000198). VCF files for the all-SNPs and DEG-SNPs datasets are deposited in Dryad (https://doi.org/10.5061/dryad.qbzkh18s3).