The adaptation of marine fish to freshwater environments is a prodigious example of rapid evolution, and yet the underlying ecological causes of genomic and phenotypic differentiation are poorly understood for traits associated with lipid content and composition. Threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized, and adapted to, freshwater habitats across the northern hemisphere. These freshwater populations often show elevated copy number of the fatty acid desaturase 2 gene (FADS2), which increases the biosynthetic capacity of ω-3 long-chain polyunsaturated fatty acids (LC-PUFA). The starkly lower content of LC-PUFA in freshwater compared to marine prey, especially docosahexaenoic acid (DHA), likely imposes strong positive selection on freshwater fish for either increased biosynthesis or greater dietary acquisition of LC-PUFA. The threespine stickleback populations in postglacial coastal lakes of Southern Greenland offer an exceptional opportunity to study how variation in the copy number of FADS2 is related to abiotic and biotic conditions of lakes and their morphometry. As expected, we found strong sexual dimorphism in FADS2 copy number in all populations (19 freshwater, 1 marine, and 1 brackish), and an increased dimorphism in some freshwater populations. We also found that FADS2 copy number was negatively correlated, for both males and females, with the abundance of copepods, which are a DHA-rich food source in the zooplankton community. Overall, our results suggest that the prey community context of lakes might influence the process of metabolic adaptation of marine fish colonizing freshwater ecosystems.

Host-parasite interactions can cause strong demographic fluctuations accompanied by selective sweeps of resistance/infectivity alleles. Both demographic bottlenecks and frequent sweeps are expected to reduce the amount of segregating genetic variation and therefore might constrain adaption during coevolution. Recent studies, however, suggest that the interaction of demographic and selective processes is a key component of coevolutionary dynamics and may rather positively affect levels of genetic diversity available for adaptation. Here, we provide direct experimental testing of this hypothesis by disentangling the effect of demography, selection, and of their interaction in an experimental host-parasite system. We grew 12 populations of unicellular algae (Chlorella variabilis) that experienced either growth followed by constant population sizes (3 populations), demographic fluctuations (3 populations), selection induced by exposure to a virus (3 populations), or demographic fluctuations together with virus-induced selection (3 populations). After 50 days, we conducted whole-genome sequencing of each algal population. We observed more genetic diversity in populations that jointly experienced selection and demographic fluctuations than in populations where these processes were experimentally separated. In addition, in those 3 populations that jointly experienced selection and demographic fluctuations, experimentally measured diversity exceeds expected values of diversity that account for the cultures’ population sizes. Our results suggest that eco-evolutionary feedbacks can positively affect genetic diversity and provide the necessary empirical measures to guide further improvements of theoretical models of adaptation during host-parasite coevolution.

Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic datasets in an increasing number of non-model species. Additionally, this new data provides the opportunity for combining datasets, resulting in larger studies with a broader taxonomic range. Whilst the benefits of new sequencing platforms are obvious, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four-channel to a two-channel system. We caution that when data is combined from these two systems, erroneous guanine base calls that result from the two-channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artifacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever-changing sequencing platform technology.