Population structure and adaptive differentiation in the purple-hinged rock scallop, Crassadoma gigantea
For decades, the shellfish growing community has been interested in cultivating the purple-hinged rock scallop. Although growing methods have been challenged by this species' life history (in particular the cementing behavior of adults), there is renewed interest in developing methods for commercial production.
However, farmed escapes pose genetic risks to populations. If hatchery-produced and wild individuals interbreed, they can cause loss of genetic diversity within and between populations through the production of many offspring from few broodstock and through the movement of animals due to collection of broodstock and transfer of seed. Therefore, it is important to assess parameters related to genetic diversity to inform native shellfish aquaculture management.
A research team led by my PhD adviser Dr. Lorenz Hauser set out to explore population structure and test for local adaptation in the rock scallop, using a multidiscplinary approach. To address several project objectives, I used RAD sequencing to quantify and characterize patterns in population structure, investigate adaptive differentiation, and identify potential drivers of population differentiation. This project was funded by the NOAA Sea Grant Aquaculture Research Program (project R/SFA/N-1)
[1] Quantify and characterize patterns in population structure
[2] Identify putatively adaptive loci and evaluate whether patterns of population structure differ between putatively neutral and adaptive data sets
I extracted, quantified and verified quality of DNA from 7 sites spanning from Alaska to California, and then prepared single-digest RAD libraries using sbfI follwing Etter et al 2011. DNA was sequenced to 150bp at BGI. You can find the library prep protocols in 1_library_prep.
I clustered loci and genotyped individuals using the dDocent pipeline, using a de novo assembly. Genotype data were filtered using vcftools and custom python scripts, such that retained loci passed the following filters:
- minimum minor allele count of 5 reads
- minimum quality score of 20
- minimum genotype depth of 10 reads
- minimum minor allele frequency of 5%
- maximum missing data per locus of 30% across sites
- one SNP per RAD tag, retaining that with the highest minor allele frequency
- in Hardy Weinberg Equilibrium
Individuals were retained if they were successfully genotyped at at least 70% of loci. You can find documentation for my assembly, genotyping, and filtering here.
I used genepop to calculate FST and run exact G tests at global and pairwise scales. We used genepop to calculate expected and observed heterozygosity as well, and used custom python scripts to calculate the proportion of polymorphic loci per site.
I used principal component analysis and dicriminant analysis of principal components to investigate patterns of population differentiation, using the R package adegenet. I used ADMIXTURE to conduct a clustering analysis and the R package poppr to summarize the partitioning of variance among different hierarchical groupings in AMOVAs. You can see the scripts used for population structure analyses here.
A major objective of the grant was to investigate the potential for local adaptation in the species. Reciprocal transplant and common garden experiments were attempted, but ultimately rock scallops would not spawn in ways necessary for the breeding designs needed for those experiments. Alternative projects to address related questions were designed and implemented, such as investigating age at maturity (collaborator Molly Jackson's master's thesis) and
Meanwhile, I leveraged my genomic data to look for signatures of local adaptation. Specifically, I used gene-environment association methods including bayenv2 and redundancy analysis. Additionally, I used FST outlier detection to find additional SNPs putatively under selection. For these methods, I used Bayescan and the R package OutFLANK. You can find scripts and notebooks associated with these analyses here.
I also investigated potential drivers of observed differentiation. Specifically, I tested for isolation by distance using a Mantel test in R. I also compared patterns of differentiation between putatively neutral and putatively adaptive loci. To determine potential biological processes associated with putatively adaptive loci, I used blastx and the UniProt Knowledge Base1 to retrieve GO Slim terms. Files related to potential drivers of population differentiation can be found here.
Data files and all results will be shared publicly here after publication. Below is a DAPC and PCA along with site map, to see general patterns of popuation differentiation. I observed very low levels of population differentiation. Some other results are shared within the readmes per directory of this repo.
This repository contains the protocols, scripts, and notebooks that I used in this project. Here are the quick links:
2_assembly_genotyping_and_filtering