A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation

The detection of adaptive loci in the genome is essential as it gives the possibility of understanding what proportion of a genome or which genes are being shaped by natural selection. Several statistical methods have been developed which make use of molecular data to reveal genomic regions under selection. In this paper, we propose an approach to address this issue from the environmental angle, in order to complement results obtained by population genetics. We introduce a new method to detect signatures of natural selection based on the application of spatial analysis, with the contribution of geographical information systems (GIS), environmental variables and molecular data. Multiple univariate logistic regressions were carried out to test for association between allelic frequencies at marker loci and environmental variables. This spatial analysis method (SAM) is similar to current population genomics approaches since it is designed to scan hundreds of markers to assess a putative association with hundreds of environmental variables. Here, by application to studies of pine weevils and breeds of sheep we demonstrate a strong correspondence between SAM results and those obtained using population genetics approaches. Statistical signals were found that associate loci with environmental parameters, and these loci behave atypically in comparison with the theoretical distribution for neutral loci. The contribution of this new tool is not only to permit the identification of loci under selection but also to establish hypotheses about ecological factors that could exert the selection pressure responsible. In the future, such an approach may accelerate the process of hunting for functional genes at the population level.     

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.     

Why are fruit traits of Cistus ladanifer (Cistaceae) so variable: A multi-level study across the western Mediterranean region

Variation is the raw material for evolution. Differences among populations in the expression of traits related to plant fitness may result from natural selection, phenotypic plasticity (in response to local conditions), and developmental instability (manifested as high intra-individual variation in repeated patterns or characters). Cistus ladanifer is a highly polymorphic plant distributed in the Mediterranean and the only species in the family (Cistaceae, 180 species) with a variable number of valves per fruit. We herein analysed the variation in the number of valves (5–12) and seeds (318–1185) per fruit in 36 populations (607 individuals, 1821 fruits) at different levels: temporal, geographical, ecogeographical, taxonomic, and phylogeographical. In addition, we tested whether an increased number of fruit valves influences pre-dispersal seed predation. Large variation in the number of valves and seeds per fruit among populations, individuals, and years was reported. The number of ovules and seeds per valve increased with a higher number of fruit valves. Geographical and taxonomic variables did not significantly explained this fruit variation. On the contrary, we found a negative relationship between the number of fruit valves and altitude and a positive relationship with precipitation. We argue that ecogeographical factors, in addition to some phylogeographical and phylogenetic signals, are involved in the multiplication of carpels during the development of the ovary wall. This, coupled with the results of the evolutionary history of Cistus in previous studies, indicates active evolutionary processes in C. ladanifer populations.