Evolutionary Genomics in Daphnia

For a comprehensive understanding of evolutionary processes and for providing reliable prognoses about the future consequences of environmental change, it is essential to reveal the genetic basis underlying adaptive responses. The importance of this goal increases in light of ongoing climate change, which confronts organisms worldwide with new selection pressures and requires rapid evolutionary change to avoid local extinction. Thereby, freshwater ectotherms like daphnids are particularly threatened. Unraveling the genetic basis of local adaptation is complicated by the interplay of forces affecting patterns of genetic divergence among populations. Due to their key position in freshwater communities, cyclic parthenogenetic mode of reproduction and resting propagules (which form biological archives), daphnids are particularly suited for this purpose. The aim of this thesis was to assess the impact of local thermal selection on the Daphnia longispina complex and to reveal the underlying genetic loci. Therefore, I compared genetic differentiation among populations containing Daphnia galeata, Daphnia longispina and their interspecific hybrids across time, space, and species boundaries. I revealed strongly contrasting patterns of genetic differentiation between selectively neutral and functional candidate gene markers, between the two species, and among samples from different lakes, suggesting (together with a correlation with habitat temperatures) local thermal selection acting on candidate gene TRY5F and indicating adaptive introgression. To reveal the candidate genes’ impact on fitness, I performed association analyses among data on genotypes and phenotypic traits of D. galeata clones from seven populations. The tests revealed a general temperature effect as well as inter-population differences in phenotypic traits and imply a possible contribution of the candidate genes to life-history traits. Finally, utilizing a combined population transcriptomic and reverse ecology approach, I introduced a methodology with a wide range of applications in evolutionary biology and revealed that local thermal selection was probably a minor force in shaping sequence and gene expression divergence among four D. galeata populations, but contributed to sequence divergence among two populations. I identified many transcripts possibly under selection or contributing strongly to population divergence, a large amount thereof putatively under local thermal selection, and showed that genetic and gene expression variation is not depleted specifically in temperature-related candidate genes. In conclusion, I detected signs of local adaptation in the D. longispina complex across space, time, and species barriers. Populations and species remained genetically divergent, although increased gene flow possibly contributed, together with genotypes recruited from the resting egg bank, to the maintenance of standing genetic variation. Further work is required to accurately determine the influence of introgression and the effects of candidate genes on individual fitness. While I found no evidence suggesting a response to intense local thermal selection, the high resilience and adaptive potential regarding environmental change I observed suggest positive future prospects for the populations of the D. longispina complex. However, overall, due to the continuing environmental degradation, daphnids and other aquatic invertebrates remain vulnerable and threatened.