Balancing Selection in Structured Populations of Three-Spined Sticklebacks

Balancing selection describes evolutionary processes that maintain genetic diversity. To date, the number of impacted genes and underlying biological functions remain elusive. Using 60 three-spined stickleback genomes (Gasterosteus aculeatus) from five recently diverged lake-river population-pairs, we performed genome-wide scans across two levels of organization: population-pairs and populations. We overlapped Tajima’s D and Watterson’s estimator metrics and verified signals with additional summary statistics, and evaluated alternative explanations: neutral evolution, population structure, associated overdominance, or demographic change. Candidate windows exhibiting signals of balancing selection spanned 2.31% (population-pair) and 3.10% (population) of the autosomes. These candidate windows had extended linkage disequilibrium and were enriched in intergenic and non-synonymous SNPs. We identified 715 (population-pair) and 1,010 (population) candidate genes under balancing selection. Importantly, using conservative thresholds, we found a small proportion of candidate genes overlapped with highly differentiated loci or regions of potential associated overdominance. There was little evidence of confounding effects originating from demographic change. Overall, candidate genes under balancing selection were associated with functions related to interactions with the environment (olfaction and receptor signalling pathways). Our results demonstrate selection that maintains standing genetic variation is common and evolves in response to local environmental pressures, playing an important role in adaptation.

Chill coma onset and recovery fail to reveal true variation in thermal performance among populations of Drosophila melanogaster

Species from colder climates tend to be more chill tolerant regardless of the chill tolerance trait measured, but for Drosophila melanogaster, population-level differences in chill tolerance among populations are not always found when a single trait is measured in the laboratory. We measured chill coma onset temperature, chill coma recovery time, and survival after chronic cold exposure in replicate lines derived from multiple paired African and European D. melanogaster populations. The populations in our study were previously found to differ in chronic cold survival ability, which is believed to have evolved independently in each population pair; however, they did not differ in chill coma onset temperature and chill coma recovery time in a manner that reflected their geographic origins, even though these traits are known to vary with origin latitude among Drosophila species and are among the most common metrics of thermal tolerance in insects. While it is common practice to measure only one chill tolerance trait when comparing chill tolerance among insect populations, our results emphasise the importance of measuring more than one thermal tolerance trait to minimize the risk of missing real adaptive variation in insect thermal tolerance.

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European range

The application of demographic history modeling and inference to the study of divergence between species is becoming a cornerstone of speciation genomics. The demographic history is usually reconstructed by analysing a single population from each species, assuming that the divergence history inferred between these populations represents the actual speciation history. However, this assumption is rarely explicitly tested, and it may not be met when species diverge with gene flow. For instance, secondary contact between two species after a range expansion may be confined into a specific geographic region. In this study, we tested to what extent the divergence history inferred from two heterospecific populations would vary depending on their geographic locations, using mound-building red wood ants. The wood ant species Formica polyctena and F. aquilonia have contrasting distributions in Europe and naturally hybridize in Finland. We first performed whole-genome resequencing of 20 individuals sampled in multiple populations across both species ranges. We then reconstructed the divergence histories of distinct heterospecific population pairs using a coalescent-based approach. We found that the analysis of these different population pairs always supported a scenario of divergence with gene flow, suggesting that species divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration stopped (2-19 kya, depending on the population pair considered). However, we found support for contemporary gene flow in the sympatric population pair from Finland, where hybrids have been described. Overall, our results suggest that divergence histories reconstructed from a few individuals may be reliable and applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is heterogeneous across their geographical ranges.

Genetic differentiation between conspecific populations of Merodon avidus A (Diptera, Syrphidae)

Allozyme variability of populations of Merodon avidus A (M i l a n - k o v et al., 2001) from Dubasnica Mountain (Serbia), Morinj Bay (Montenegro) and Pindos Mountain (Greece) was analysed. The influence of gene flow on genetic differentiation among populations from the three biogeographical regions was also investigated. Genetic differentiaiton quantified by the Fst value, which is an inverse function of gene flow between populations, seemed to be correlated to both geographic and genetic distance (D, N e i, 1978), Namely in the population pairs Morinj - Dubasnica (253 km air distance), Morinj - Pindos (390km air distance) genetic differentiation and genetic distance increased with the geographic distance (Fst = 0.133, D = 0.022 and Fst = 0.309, D = 0.052, respectively). The exception was the population pair Dubasnica - Pindos (500 km air distance), where a lower degree of genetic differentiation was observed (Fst = 0.266; D = 0.047) than was expected based solely on the geographic distance. Results of this study suggest that that genetic differentiation among conspecific populations depends not only on the number of migrants (i. e. gene flow), but also on different selection pressure in different habits.