Genomics and the future of conservation genetics. Nat Rev Genet

University of Montana, Missoula, 59812, USA.
Nature Reviews Genetics (Impact Factor: 36.98). 10/2010; 11(10):697-709. DOI: 10.1038/nrg2844
Source: PubMed


We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for conservation genetics and to recognize limitations in applying genomic tools to conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of conservation.

Full-text preview

Available from:
  • Source
    • "Populations of a species adapted to local environments can therefore present unique conservation and management challenges, wherein each distinct population segment of the species might require special considerations to enable its preservation in the face of environmental perturbation, habitat degradation, and Correspondence: Shawn R. Narum, Fax: 208 837 6047; E-mail: anthropogenic disturbance (Waples 1991; Allendorf et al. 2010; Funk et al. 2012). An understanding of the environmental drivers of such adaptive divergence can thus improve our understanding of how populations evolve and how they may adapt in the face of environmental change (Jump et al. 2006; P€ ortner & Knust 2007; Kovach et al. 2012; Mu~ noz et al. 2015). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, ANOVA P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream-Type Lineage, ANOVA P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, ANOVA P = 0.005), and migration distance (Rangewide, ANOVA P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.
    Molecular Ecology 11/2015; DOI:10.1111/mec.13409 · 6.49 Impact Factor
  • Source
    • "To reveal these underlying differences, marker sets with sufficient sensitivity and resolving power are required to accurately inform conservation and fishery management efforts, but are also necessary in aquaculture applications. Given the availability of such marker sets, genome mapping and association studies are now real possibilities for a number of established species in aquaculture, including quantitative trait locus (QTL) identification and marker assisted selection (MAS; Allendorf et al., 2010; Angeloni et al., 2012; McAndrew and Napier, 2011; Yue, 2013). Genome-wide SNPs are powerful and highly versatile markers capable of addressing this problem, and are gaining broader use in population genomic and phylogenetic investigations, as well as genome structure evaluation and genome wide association studies (Davey et al., 2011; Helyar et al., 2011; Kai et al., 2014; Pool et al., 2010; Rasic et al., 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stockmanagement in bothwild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst =0.046) when visualised with DAPC and an individual network analysis (NetView P),with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD N 192.5). Fst outlier detection revealed 42–62 highly differentiated SNPs (p b 0.02), while case–control association discovered up to 152 SNPs (p b 0.001). Both analyseswere able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.
    Marine Genomics 10/2015; DOI:10.1016/j.margen.2015.10.010 · 1.79 Impact Factor
  • Source
    • "Possible causes for these processes include using just a handful of genetic markers with insufficient genetic information and different marker types due to different modes of inheritance and evolution, leading to difficulties in inferring high-precision population structure and genetic differentiation (Wang et al. 2013). In these circumstances, genomic tools may improve the precision and accuracy of estimating a variety of important population genetic parameters by increasing the number of variable genetic markers, which may be necessary for detecting population subdivision and designating management units for L. polyactis (Allendorf et al. 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent advances in high-throughput sequencing technologies have offered the possibility to generate genome-wide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters, and to evaluate potential adaptive divergence. Here, we identified 27 556 single-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation was identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP dataset of top quality score per contig or neutral loci. However, the two analyzed populations were highly differentiated based on SNP dataset of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST -based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. BLAST2GO annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant BLASTX matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in the present study provided a valuable tool for future population genetics and genomics studies of L. polyactis. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 10/2015; DOI:10.1111/1755-0998.12476 · 3.71 Impact Factor
Show more