Department Aquatic Ecology

Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated by combining the diversity and dispersion. ENDP estimates β-variation independently of estimates of within-sample α-variation, although β-and α-estimates could statistically correlate to some extent. This new concept differs from the existing standard where β-diversity is estimated based on the “partition of variation” scheme (beta = gamma − alpha or beta = gamma∕alpha), so that estimates of β-diversity directly depend on the corresponding values of α-diversity. ENDP estimates are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. The analysis is complicated by geographically coexisting cryptic species and the potential mixed-mating system of this hermaphroditic parasite. Analyses with subsampled data demonstrated that ENDP estimates are robust. Number of loci used for genotyping has much stronger effect on variation of point ENDP estimates than sample size.

Host–parasite interactions are influenced by present and past eco-evolutionary interactions and the local environment. An ecological community defines the potential host range of each parasite and the potential parasite diversity of each host species. Past and present processes translate potential to realised interaction niches of parasite and host species. Host–parasite interactions are antagonistic, which may slow the saturation of their interaction niches. Intervality, a property of bipartite networks, measures saturation of interaction niches. Intervality of a community increases as the interaction niches of species of one guild (e.g. hosts) become saturated for their interactions with another guild (e.g. parasites). Characteristics driving intervality in host and parasite communities are largely unknown, as well as the effect of environmental change on intervality of these communities. In our study, we assess if the characteristics 'phylogenetic relatedness' and 'overlap in ecological interactions' explain intervality of rodent host–helminth parasite communities. In addition, we contrast intervality of these communities from habitats that differ in their history of human-driven modification. We performed the analyses for the interaction niches of both parasites and hosts, independently. Our results indicated that host and parasite communities were non-interval or significantly less interval than expected by chance. Phylogenetic relatedness and overlap in ecological interactions did not explain the maximum values of intervality. We speculate that antagonistic coevolution in host–parasite communities may hinder communities to reach saturation, which would explain why it is difficult to find the characteristics that explain intervality of a community. Interestingly, intervality of the interaction niche of parasites (host range) increased with habitat modification (i.e. saturation increased), whereas intervality of the interaction niche of hosts (parasite diversity) decreased as habitat modification increased. These opposite trends suggest that interaction niches of parasites and hosts respond differently to habitat modification.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N_e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N_e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N_e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.