The authors had conducted a previous study in which they sample 696 adult American lobsters along a gradient of water temperatures (Benestan et al., 2016).
They used a software called Stacks (Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011) to conduct their bioinformatic analysis, which is a package that is popular in population genetics due to its ability to detect single-nucleotide polymorphisms, or SNPs. The authors used version 1.09, which is not available on the authors' website any longer, but fortunately, is available through
Then, they tried to differentiate between subpopulations using several other auxiliary softwares. All of the analysis was based on using the identified single-nucleotide polymorphisms from
Stacks, which may illuminate differences in the population by exposing the hypervariable regions of the genome. They looked at SNPs that were called outliers. They assumed that populations were differentiated by the physical location of the subpopulation. Once outliers were identified, "divergent selection" was claimed if the SNP was an outlier in all three of their geographic subpopulations. SNPs under balancing selection (outlier in multiple, but not all subpopulations; different versions of the allele being maintained) were removed, leaving only neutral and divergent SNPs.
Next, they tried to link spatial structures to the genetic variation that they saw. They used a technique called redundancy analysis (RDA) to check whether there was an effect of some or all of the environmental variables they were testing (spatial distribution, ocean currents, and temperature). This technique is basically just a special form of multiple regression. They also used a Pearson test approach to test the association between environmental variables and the genetic structure. They focused on the very best candidate SNPs to evaluate whether there was spatial structure in the strongest genetic indicators of the population.
- Benestan, L., Quinn, B. K., Maaroufi, H., Laporte, M., Clark, F. K., Greenwood, S. J., … Bernatchez, L. (2016). Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Molecular Ecology, 25(20), 5073–5092.
- Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H. (2011). Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1(3), 171–182.