Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon

An approach frequently used to demonstrate a genetic basis for population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (V(A)) and maternal (V(M)) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.     

Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar . A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.     

Major histocompatibility complex heterozygote advantage and widespread bacterial infections in populations of Chinook salmon (Oncorhynchus tshawytscha)

Despite growing evidence for parasite-mediated selection on the vertebrate major histocompatibility complex (MHC), little is known about variation in the bacterial parasite community within and among host populations or its influence on MHC evolution. In this study, we characterize variation in the parasitic bacterial community associated with Chinook salmon ( Oncorhynchus tshawytscha ) fry in five populations in British Columbia (BC), Canada across 2 years, and examine whether bacterial infections are a potential source of selection on the MHC. We found an unprecedented diversity of bacteria infecting fry with a total of 55 unique bacteria identified. Bacterial infection rates varied from 9% to 29% among populations and there was a significant isolation by distance relationship in bacterial community phylogenetic similarity across the populations. Spatial variation in the frequency of infections and in the phylogenetic similarity of bacterial communities may result in differential parasite-mediated selection at the MHC across populations. Across all populations, we found evidence of a heterozygote advantage at the MHC class II, which may be a source of balancing selection on this locus. Interestingly, a co-inertia analysis indicated only susceptibility associations between a few of the MHC class I and II alleles and specific bacterial parasites; there was no evidence that any of the alleles provided resistance to the bacteria. Our results reveal a complex bacterial community infecting populations of a fish and underscore the importance of considering the role of multiple pathogens in the evolution of host adaptations.     

Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences

Disentangling the effects of natural environmental features and anthropogenic factors on the genetic structure of endangered populations is an important challenge for conservation biology. Here, we investigated the combined influences of major environmental features and stocking with non‐native fish on the genetic structure and local adaptation of Atlantic salmon (Salmo salar) populations. We used 17 microsatellite loci to genotype 975 individuals originating from 34 French rivers. Bayesian analyses revealed a hierarchical genetic structure into five geographically distinct clusters. Coastal distance, geological substrate and river length were strong predictors of population structure. Gene flow was higher among rivers with similar geologies, suggesting local adaptation to geological substrate. The effect of river length was mainly owing to one highly differentiated population that has the farthest spawning grounds off the river mouth (up to 900 km) and the largest fish, suggesting local adaptation to river length. We detected high levels of admixture in stocked populations but also in neighbouring ones, implying large‐scale impacts of stocking through dispersal of non‐native individuals. However, we found relatively few admixed individuals suggesting a lower fitness of stocked fish and/or some reproductive isolation between wild and stocked individuals. When excluding stocked populations, genetic structure increased as did its correlation with environmental factors. This study overall indicates that geological substrate and river length are major environmental factors influencing gene flow and potential local adaptation among Atlantic salmon populations but that stocking with non‐native individuals may ultimately disrupt these natural patterns of gene flow among locally adapted populations.     

Genomic signatures of local adaptation in the Drosophila immune response

As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.     

Distance-based population classification software using mean-field annealing

We describe a distance-based clustering method using a proximity matrix of genetic distances to partition populations into genetically similar groupings. The optimization heuristic mean-field annealing (MFA) was used to find locally optimal solutions where exhaustive search was not possible. To illustrate this method, we analysed both simulated and real data sets. Simulated data indicated that MFA successfully differentiated population groups, even with small F(ST) values, as long as there was separation of within and between group distances. Reanalysis of microsatellite data from various human populations using mean-fields found similar ethnic groups corresponding to major geographic regions reported by Rosenberg et al. (2002) who used the model-based computer program Structure. However, with MFA, the Kalash population was found to group with other Central/South Asian populations instead of being the only member of its own genetic cluster. Europe/Middle East populations formed a separate group from Central/South Asian populations instead of being a single group in the Structure analysis. The MFA analysis determined the greatest genetic distances (largest mean intracluster distance) occurred in native American populations, identifying three groups instead of only one found with Structure. For conservation purposes, it is not only important to identify genetically similar groupings but also to determine the relative level of genetic differentiation captured within these groups. To illustrate this, we compare two separate MFA analyses of Chinook salmon (Oncorhynchus tshawytscha) populations from British Columbia, Canada. The software called PORGS-MFA used in this article can be downloaded from http://www.pac.dfo-mpo.gc.ca/science/facilities-installations/pbs-sbp/mgl-lgm/apps/porgs/index-eng.htm.