Prospects and Limitations of a Genetic Diversity Monitoring in Nature Conservation
Schmid, M., 2014: Prospects and Limitations of a Genetic Diversity Monitoring in Nature Conservation. Master thesis. 62 p.
Schmid M. 2014: Prospects and Limitations of a Genetic Diversity Monitoring in Nature Conservation. Masterarbeit geleitet von Dr. Felix Gugerli (WSL), PD Dr. Janine Bolliger (WSL) und Prof. Frédéric Guillaume (UZH). D-USYS, ETH Zürich.
This master thesis was part of a feasibility study to incorporate the monitoring of neutral genetic diversity into the Biodiversity Monitoring Switzerland (BDM). For this feasibility study, the lepidopteran species Melanargia galathea (Linnaeus, 1758) was chosen as study organism and tissue samples were collected across Switzerland within the BDM program Z7 during the summer 2013. DNA was extracted from 424 individuals at 56 locations, and microsatellite markers were developed for M. galathea on a basis of 454 sequencing data. As microsatellite motifs in lepidopteran frequently share identical or similar flanking sequences, marker development is challenging. Seven microsatellite markers were successfully characterized and applied. Subsequently, measures of genetic diversity were calculated and factors controlling patterns of neutral genetic diversity across Switzerland were estimated.
Across Switzerland, four genetic clusters were detected for M. galathea using a Bayesian clustering approach (STRUCTURE), with single clusters in the Rhine valley, the Rhone valley, the Southern Alps and the North-Western part of Switzerland. These clusters are separated by high mountain ranges that reduce gene flow between clusters and create/maintain genetic differentiation. Genetic clusters are not only created by barriers but also might be shaped by the recolonization process after the last ice age. For instance, we assume that the recolonization process shaped the allelic richness (Nr) within clusters, but additional samples from Southern Europe would be necessary to verify this aspect. While the highest Nr was detected in the Southern Alps cluster, the Rhine valley cluster exhibit the lowest Nr. Comparing the genetic diversity at single locations (with at least ten sampled individuals), no significant difference in Nr between locations was found, although the two locations in the Southern Alps exhibited the highest values of Nr. We can expect that the large scale pattern of genetic diversity has also an impact on the diversity at single locations, together with further factors. One important factor is population size that is positively correlated with Nr under random mating. As the population size cannot be measured correctly with the BDM sampling design, we did not test for this factor. Nevertheless, we conducted a habitat suitability analysis based on genetic data assuming that high population sizes (and therefore high values of Nr) are correlated with suitable habitat. Seven climate and land-use parameters were chosen as potential descriptors of habitat suitability: precipitation, temperature, variation in vegetation height, as well as extensively used grassland, shrubbery, forest and intensively used grassland. Using linear models, we found no significant relationship between allelic richness and habitat parameters. At the individual level, genetic diversity might be represented by the observed heterozygosity (Ho), therefore by the proportion of studied loci with two different alleles. Theory predicts a positive relation between Ho and Nr (in panmixing populations), but such a relationship was not found in our data. One factor that could have shaped Ho considerably is inbreeding, which was detected in two of eighteen locations (based on FIS values). Beside these empirical data, simulation models were used for two different applications in a genetic diversity monitoring. While it was not possible to estimate the dispersal ability of M. galathea from the genetic data, simulation models were useful to estimate the speed of genetic diversity creation. A founder event in the Rhine valley was simulated and the number of generations to reach 80 % of equilibrium diversity (Nr) and differentiation (Dest) were calculated. Both levels of diversity (Nr, Dest) showed an asymptotic increase with time while in average several hundred generations were necessary to reach 80% of the equilibrium values (Nr=763 generations; Dest=445 generations).
Following this procedure, a first step towards a monitoring of genetic diversity was taken. Given that the sampling can be done within an existing monitoring scheme, neutral genetic diversity could be monitored at different hierarchical levels over time with comparatively low financial effort. While it is easily possible to detect large scale and temporal patterns of neutral genetic diversity in Switzerland, it is more difficult to elucidate the causes of them. Furthermore, we have to be aware that microsatellites are measuring neutral genetic diversity and have therefore no direct link to fitness. Adaptive genetic diversity is highly relevant for a species and patterns might differ from the measured neutral ones. But such a monitoring would be connected with a much higher financial effort. As just a small amount of the DNA is used for the microsatellite analysis, the remaining DNA could be analyzed in the future once it becomes affordable to quantify adaptive genetic diversity.