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An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long‐ and short‐term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre‐date the effects of recent drift, and that functional variation in these loci persists despite small short‐term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present‐day levels of variation overestimate the amount of functional genetic diversity present in future populations. [ABSTRACT FROM AUTHOR]

Abstract: Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming. [ABSTRACT FROM AUTHOR]

The success of restoration activities is affected by connectivity with the surrounding landscape. From a genetic perspective, landscape connectivity can influence gene flow, effective size, and genetic diversity of populations, which in turn have impacts on the fitness and adaptive potential of species in restored areas. Researchers and practitioners are increasingly using genetic data to incorporate elements of connectivity into restoration planning and evaluation. We show that genetic studies of connectivity can improve restoration planning in three main ways. First, by comparing genetic estimates of contemporary and historical gene flow and population size, practitioners can establish historical baselines that may provide targets for restoration of connectivity. Second, empirical estimates of dispersal, landscape resistance to movement, and adaptive genetic variance can be derived from genetic data and used to parameterize existing restoration planning tools. Finally, restoration actions can also be targeted to remove barriers to gene flow or mitigate pinch-points in corridors. We also discuss appropriate methods for evaluating the restoration of gene flow over timescales required by practitioners. Collaboration between restoration geneticists, ecologists, and practitioners is needed to develop practical and innovative ways to further incorporate connectivity into restoration practice. [ABSTRACT FROM AUTHOR]

The threat of emerging infectious diseases encourages the investigation of functional loci related to host resilience, such as those belonging to the major histocompatibility complex (MHC). Through careful primer design targeting to conserved regions of MHC class I sequences in birds, we successfully amplified a genomic fragment spanning exons 2-4 in three birds of prey. The identification of a highly conserved region within intron 2 allowed cross-amplifying complete exon 3 sequences in diurnal raptors, owls and New World vultures. We found evidence through PCR and cloning for 1-2 polymorphic class I loci, although this is almost certainly an underestimate. Inferences of diversifying selection in the kestrel MHC revealed that the two major regions of exon 3 exhibiting positive selection mostly agree with those described for the human HLA-A2 molecule. In contrast to passerines, where a high incidence of gene duplications and pseudogenes has been commonly documented, birds of prey emerge as nice model species for the investigation of the evolutionary significance and conservation implications of MHC diversity in vertebrates. [ABSTRACT FROM AUTHOR]

Understanding the selective forces that shape genetic variation in natural populations remains a high priority in evolutionary biology. Genes at the major histocompatibility complex (MHC) have become excellent models for the investigation of adaptive variation and natural selection because of their crucial role in fighting off pathogens. Here we present one of the first data sets examining patterns of MHC variation in wild populations of a bird of prey, the lesser kestrel, Falco naumanni. We report extensive polymorphism at the second exon of a putatively functional MHC class II gene, Fana-DAB*1. Overall, 103 alleles were isolated from 121 individuals sampled from Spain to Kazakhstan. Bayesian inference of diversifying selection suggests that several amino acid sites may have experienced strong positive selection (ω = 4.02 per codon). The analysis also suggests a prominent role of recombination in generating and maintaining MHC diversity (ρ = 4 Nc = 0.389 per codon, θ = 0.017 per codon). Both the Fana-DAB*1 locus and a set of eight polymorphic microsatellite markers revealed an isolation-by-distance pattern across the Western Palaearctic ( r = 0.67; P = 0.01 and r = 0.50; P = 0.04, respectively). Nonetheless, geographical variation at the MHC contrasts with relatively uniform distributions in the frequencies of microsatellite alleles. In addition, we found lower fixation rates in the MHC than those predicted by genetic drift after controlling for neutral mitochondrial sequences. Our results therefore underscore the role of balancing selection as well as spatial variations in parasite-mediated selection regimes in shaping MHC diversity when gene flow is limited. [ABSTRACT FROM AUTHOR]

Despite recent advances in conservation genetics and related disciplines and the growing impact that conservation genetics is having in conservation biology, our knowledge on several key issues in the Weld is still insufficient. Here we identify some of these issues together with addressing several paradoxes which have to be solved before conservation genetics can face new challenges that are appearing in the transitory phase from the population genetics into the population genomics era. Most of these issues, paradoxes and challenges, like the central dogma of conservation genetics, the computational, theoretical and laboratory experiment achievements and limitations in the conservation genetics Weld have been discussed. Further knowledge on the consequences of inbreeding and outbreeding depression in wild populations as well as the capacity of small populations to adapt to local environmental conditions is also urgently needed. The integration of experimental, theoretical and applied conservation genetics will contribute to improve our understanding of methodological and applied aspects of conservation genetics. [ABSTRACT FROM AUTHOR]

During the last decade, the major histocompatibility complex (MHC) has received much attention in the fields of evolutionary and conservation biology because of its potential implications in many biological processes. New insights into the gene structure and evolution of MHC genes can be gained through study of additional lineages of birds not yet investigated at the genomic level. In this study, we characterized MHC class II B genes in five families of birds of prey ( Accipitridae, Pandionidae, Strigidae, Tytonidae, and Falconidae). Using PCR approaches, we isolated genomic MHC sequences up to 1300 bp spanning exons 1 to 3 in 26 representatives of each raptor lineage, finding no stop codons or frameshift mutations in any coding region. A survey of diversity across the entirety of exon 2 in the lesser kestrel Falco naumanni reported 26 alleles in 21 individuals. Bayesian analysis revealed 21 positively selected amino acid sites, which suggests that the MHC genes described here are functional and probably expressed. Finally, through interlocus comparisons and phylogenetic analysis, we also discuss genetic evidence for concerted and transspecies evolution in the raptor MHC. [ABSTRACT FROM AUTHOR]