Breaking down the jargon

The authors use a lot of terms just in the abstract that might be offputting to someone unfamiliar with population genetics approaches. Here, we'll break down some of those terms and what they mean.

  • loci - specific, comparable locations of the genome. May be a single base or a set of bases called a "locus" and used to track genetic changes.
  • population differentiation - method of comparing groups of organisms and identifying sub-populations
  • Moran's eigenvector map - a mathematical approach to figure out where the variation we see co-occurs locally
  • Euclidean distance matrix - a set of computations for the distance between different identified sites, using the traditional distance metric of Euclidean distance ($\sqrt{x^2 + y^2}$)
  • larval connectivity - whether sites share larvae, that can float freely through the water column, with one another
  • redundancy analysis (RDA) - a multivariate statistical method that enables us to pick out the most important contributors to the variability of interest
  • single nucleotide polymorphisms (SNPs) - variation in genetic information at a single locus, which, in this case, is a single nucleotide/base of DNA in the sequence
  • environmental association (EA) - how genetic varation relates to the available environmental information
  • gene ontology - the "origin" of a gene, in this case finding a meaningful gene equivalent already in a database so that we can better understand what the function of the gene we found might be
  • putative - we think that this is a gene with X function, but we haven't confirmed it yet
  • selection
    • positive (a.k.a. directional) - a new phenotype is favored and selected for in the population (this is the underpinning of collective evolution via natural selection)
    • neutral - selection is not being pushed in any particular direction
    • balancing - multiple versions of the gene/allele are being maintained in the population (but there's not evidence of selection/change - this is often just heterozygosity)
    • divergent - the populations are becoming more different (in this case, all of the sub-populations have a different version of the gene)

(Benestan et al., 2016)

  1. 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.