Genomics and the future of conservation genetics. Nat Rev Genet

University of Montana, Missoula, 59812, USA.
Nature Reviews Genetics (Impact Factor: 39.79). 10/2010; 11(10):697-709. DOI: 10.1038/nrg2844
Source: PubMed

ABSTRACT 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.

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    • "The goal of many conservation genetic, and now conservation genomic, studies is to identify genetic contributions to fitness differences within and among populations (Allendorf et al. 2010; Ouborg et al. 2010; Angeloni et al. 2012; Funk et al. 2012; McMahon et al. 2014), possibly narrowing genetic effects down to causative loci. Frequently used analytical approaches include outlier analyses (Namroud et al. 2008; Nosil et al. 2012), detection of inbreeding through heterozygosity fitness correlations (HFCs; Grueber et al. 2008; Szulkin et al. 2010; Miller and Coltman 2014), and identifying adaptive genetic variation or evolutionary potential (Funk et al. 2012; Hansen et al. 2012; Harrisson et al. 2014). "
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    ABSTRACT: Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D′, and χ′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
    Ecology and Evolution 08/2015; 5(16):3401-3412. DOI:10.1002/ece3.1612 · 1.66 Impact Factor
    • "NGS techniques can be broadly divided in three types: array-based SNP genotyping platforms, reduced-representation sequencing (i.e., sequencing of a subset of the genome), and whole-genome sequencing (Allendorf et al. 2010). A modified protocol of DNA capture, a method of reduced-representation sequencing that enriches the sample to be sequenced in endogenous DNA, has been tested with success using non-invasive chimpanzees DNA samples (Perry et al. 2010). "
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    ABSTRACT: Non-human primates are among the world’s most threatened taxa and are especially sensitive to extinction by anthropogenic disturbance. Conservation genetics aims to mitigate extinction by genetic processes and conserve species’ adaptive potential. Primate populations often become reduced and fragmented as a result of deforestation and hunting. In small and isolated populations stochastic effects become important for their long-term persistence and evolution. Genetic drift and inbreeding contribute to loss of genetic diversity and reproductive fitness. The use of PCR, molecular markers and non-invasive sampling has allowed genetic surveys of wild primates to become common. A set of individual-based analytical tools is available to study dispersal patterns at different geographical scales and the effect of landscape features on gene flow. Genome data obtained from non-invasive sources will allow more accurate estimations of key population parameters and enable studies of local genetic adaptation.
    International Encyclopedia of Primatology, Edited by Augustin Fuentes, 08/2015: chapter Primate Conservation Genetics; in press., ISBN: in press
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    • "However, the validity of estimates produced by these methods is similarly constrained by the number and allelic diversity of the markers available (Wang 2006). A more useful approach would be to direct resources into whole genome sequencing or at least constructing large SNP panels for non-model organisms, the benefits of which would extend far beyond the measurement of inbreeding (Allendorf et al. 2010). Until those data are available, conservation managers interested in detecting inbreeding depression in species with low genetic diversity would perhaps be best served by investing resources in long term behavioural monitoring (combined with comprehensive genetic sampling), which would also reap multiple benefits for conservation (Clutton-Brock and Sheldon 2010). "
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    ABSTRACT: Pedigrees are frequently recommended for estimating inbreeding coefficients (F PED ), but are error-prone due to missing behavioural data in wild populations. Genetic marker-based pedigrees have been suggested as a remedy to this problem, but their accuracy depends on the number and polymorphism of loci available, and the completeness of population sampling. We used simulations to examine how accuracy of marker-based pedigrees varies with number of loci and sampling regime when allelic diversity is low (2.2–4 alleles per locus in founders), as is often the case in threatened species. We also examined the impact of pedigree errors on the validity of F PED estimated from marker-based pedigrees. Our results indicate that accurate parentage assignments are only feasible if genotypes are available for all individuals that ever existed in the population, and that accuracy does not improve past 40 loci. Errors in marker-based pedigrees resulted in underestimation of F PED by up to 27 % and overestimation of the variance in F PED by up to 182 %. At least 80 % pedigree accuracy was required to produce unbiased estimates of F PED , which were still highly imprecise. Given the degree of sampling required, it is not currently feasible to measure inbreeding in wild populations of threatened species with a pedigree based solely on microsatellite data. Resources may be better directed towards developing more robust genetic tools (whole genome sequencing and large SNP panels) to facilitate direct estimation of inbreeding coefficients without a pedigree. Where this is not possible, long-term monitoring projects will be required to accurately estimate inbreeding coefficients via a combination of behavioural and genetic data.
    Conservation Genetics 08/2015; 16(4). DOI:10.1007/s10592-015-0709-1 · 1.85 Impact Factor
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