Data from: MHC variation reflects the bottleneck histories of New Zealand passerines

Most empirical evidence suggests that balancing selection does not counter the effects of genetic drift in shaping post-bottleneck MHC genetic diversity when population declines are severe or prolonged. However, few studies have been able to include data from historical specimens, or to compare populations/species with different bottleneck histories. In this study we examined MHC class II B and microsatellite diversity in four New Zealand passerine (songbird) species that experienced moderate to very severe declines. We compared diversity from historical samples (collected circa 1884-1938) to present day populations. Using a Bayesian framework, we found that the change in genetic diversity from historical to contemporary samples was affected by three main factors: 1) whether the data were based on MHC or microsatellite markers, 2) species (as a surrogate for bottleneck severity) and 3) whether the comparison between historical and contemporary samples was made using historical samples originating from the mainland or using historical samples originating from islands. The greatest losses in genetic diversity occurred for the most severely bottlenecked species, particularly between historical mainland and contemporary samples. Additionally, where loss of diversity occurred, the change was greater for MHC genes compared to microsatellite loci

Data from: Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes

The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response, and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of opposing evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is approximately 15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations

Microsatellite_Genotypes_robins

Microsatellite_Genotypes_robin

MHC_Genotypes_robins_North Island

MHC_Genotypes_robins_North Islan

Microsatellite_Genotypes_Saddlebacks

Microsatellite_Genotypes_Saddleback

MHC_Genotypes_saddlebacks_South Island

MHC_Genotypes_saddlebacks_South Islan

Rscript_univariate models

R script with package MCMCglmm for the univariate-response Bayesian mixed-effects meta-analysis (BMM) models described in Table 2

Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day

Premise of study: Molecular population genetics is a powerful tool to infer how species responded to past environmental change. In the northern hemisphere, interest is increasing in how species responded to changes in ice coverage and temperature during the last glaciation maximum (LGM, between 18000–21000 yr ago) with a common assumption that glacial refugia were located at the southern edge of a species range. Methods: We reconstructed the glacial and postglacial phylogeography of Sabatia kennedyana, a member of the Atlantic Coastal Plains Flora with a current distribution from Nova Scotia (NS) to South Carolina, using both cpDNA and nuclear markers. We also examined clinal variation in morphological traits, in particular relative investment in asexual vs sexual growth. Key results: We find strong evidence that the species did not reside in southern glacial refugia, but rather in primary glacial refugia off the exposed continental shelf extending from Cape Cod and that this area was responsible for the founding of modern populations across the range from Nova Scotia (NS) to the United States. Additionally, based on the finding of higher cpDNA diversity and older cpDNA lineages in NS, we propose that multiple founder events occurred in NS, while only a single lineage gave rise to current populations in the United States. Conclusions: By understanding how S. kennedyana responded to past shifts in climate and by identifying areas of high genetic diversity in the northern range edge, we discuss the potential response of the species to future climate change scenarios