Its evolutionary history and its extraordinary phenotypic diversity made it appropriate for studying the genetic changes that underlie adaptation to new environments. Moreover, recent advances in genome biology and next generation sequencing techniques allowed addressing questions about evolutionary processes acting at a genomic scale in natural populations.
In this paper (“Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags”) of Hohenlohe et al. 2010 the main goal was to assess whether the rapid adaptation of freshwater populations and their phenotypic similarities might be due to parallel genetic evolution. Therefore, 100 individuals from two oceanic and three freshwater populations have been assessed implementing Illumina-sequenced libraries of restriction-site associated DNA (RAD) tags.
Using RAD Tags has many advantages because it discovers, proves and investigates markers simultaneously. By generating a high amount of single nucleotide polymorphisms (SNP) it is also most likely to cover a large proportion of the linkage disequilibrium (LD) blocks involved in stickleback adaptation and thus to detect even private alleles in natural populations. Interestingly, Hohenlohe et al. 2010 did not find any private alleles in the freshwater populations. Therefore, the author suggested that selection in freshwater populations has acted on haplotypes that were extremely rare in the oceanic. This is in consistency with the hypothesis that genetic variability in freshwater populations is mainly the result of selection on standing genetic variation present in the oceanic stock.
Signatures of selection have been found across six different linkage groups and have been confirmed by previous QTL mapping, like the lateral plate phenotype. Moreover, signs of balancing selection on regions that were implicated in pathogen resistance and immune responses have also been unravelled. Hohenlohe et al. 2010 argued that the loss of armor in all three independently derived populations confirms a parallel genetic evolution. However, parallel evolution is the development of a same trait in two distinct species. This article focused on populations coming from the same species. Therefore, it remains ambiguous to affirm parallel evolution in threespine stickleback even though it seems most likely.
Although, this article was not the easiest one and in some points repetitive, I find that the results are striking. This study is one of the first using RAD Tags for whole genome sequencing in natural populations and gives a lot of ideas for future research. Especially for researchers who do not work on model organisms RAD Tags seem to deliver reliable results because even without a reference genome huge amounts of SNPs can be found. Further on those can be used for genome-wide association studies and the search for candidate genes.Hohenlohe, P., Bassham, S., Etter, P., Stiffler, N., Johnson, E., & Cresko, W. (2010). Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags PLoS Genetics, 6 (2) DOI: 10.1371/journal.pgen.1000862