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10 results for “contemporary effective population size”
Global contemporary effective population sizes across taxonomic groups
<p>Effective population size (<em>N<sub>e</sub></em>) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum <em>N<sub>e</sub> </em>of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential, respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between <em>N<sub>e</sub></em><sub> </sub>and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced <em>N<sub>e</sub></em> estimates from 3829 unique populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal, and amphibian populations had a <54% probability of reaching = 50 and a <9% probability of reaching = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median than unlisted populations, and this was consistent across all taxonomic groups. was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds, and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on <em>N<sub>e</sub></em> and help prioritize assessment of populations from taxa most at risk of failing to meet conservation thresholds.</p>
Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee
<p>Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (N<sub>e</sub>) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate N<sub>e</sub> variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee <em>Bombus</em> <em>vancouverensis</em> Cresson (Hymenoptera: Apidae: <em>Bombus</em> Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of N<sub>e</sub> through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in N<sub>e</sub>. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. N<sub>e</sub> fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large N<sub>e</sub>. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in N<sub>e</sub> dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.</p>
Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee
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Global contemporary effective population sizes across taxonomic groups
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Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of SNP loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP dataset are unlinked. The approach is applied to an empirical dataset of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci
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Data from: Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens
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Data from: Estimation of contemporary effective population size and population declines using RAD sequence data
Large genomic datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the detection of population-size declines, with declines reliably detected across scenarios approximately 10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP dataset, with 25,000 to 50,000 SNPs required for accurate detection of population trends and at least 20 generations after decline began. The number of samples available and targeted number of RADseq loci are important criteria when choosing between these methods. Neither method suffered any apparent bias due to the effects of allele dropout typical of RAD data. With an understanding of the limitations and biases of these approaches, researchers can make more informed decisions when designing their sampling and analyses. Overall, our results reveal that demographic inference using RADseq data can be successfully applied to infer recent population size change and may be important tools for population monitoring and conservation biology.
Data from: Estimation of contemporary effective population size and population declines using RAD sequence data
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Data from: Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci
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