A new special issue of Heredity reflects on the recent advances in environmental genomics (see other posts about eDNA here and here) and highlights the ways NGS can aid in characterizing complex biological systems.
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The cryptic, as well as the rare but active fraction of biodiversity are now accessible to study in all environments. (Joly and Faure 2015)
One of the highlights was the review of E&R (evolve and resequence) by Schlotterer et al. (2015). The authors discuss the use whole genome sequencing of pools of individuals (Pool-Seq).
[The selection for a well-defined trait in a controlled experiment], assures that both the phenotypic and the underlying genomic response are triggered either directly or indirectly by the selection regime applied during the experiment.
The cool thing about this approach is what can be done beyond the characterization of different allele frequencies between two selection regimes (i.e., selected and control populations). It is possible to sample evolving populations at different time points and, thus,
to study the trajectories of the selected alleles and thus elucidate their evolutionary dynamics.
Schlotterer et al. continue with the potential challenges E&R studies face, including experimental design and validation of candidate loci, but conclude that the reliability of E&R interpretation will continue to improve. In time, the method will be extended to a broader range of taxa and species.
References
Joly D and Faure D (2015) Next-generation sequencing propels environmental genomics to the front line of research. Heredity 114 429-430. doi:10.1038/hdy.2015.23
Schlötterer C, Kofler R, Versace E, Tobler R and Franssen SU (2015) Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 114, 431-440. doi:10.1038/hdy.2014.86