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158 results for “Effective population size”
Temporal variability in effective size (Ne) identifies potential sources of discrepancies between mark recapture and close kin mark recapture estimates of population abundance
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Data from: Expansion history and environmental suitability shape effective population size in a plant invasion
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Drivers of strong isolation and small effective population size at a leading range edge of a widespread plant
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Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals
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Simulated genotype data from: Effective population size estimation in large marine populations: Considering current challenges and opportunities when simulating large datasets with high-density genomic information
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Data from: Levels and spatial patterns of effective population sizes in the southern damselfly (Coenagrion mercuriale): On the need to carefully interpret single-point and temporal estimations to set conservation guidelines
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Data from: Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: Challenges and implications for conservation management
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Data from: Dealing with assumptions and sampling bias in the estimation of effective population size: A case study in an amphibian population
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Whole exome sequencing reveals a long-term decline in effective population size of red spruce (Picea rubens)
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Effects of salmon lice on numbers and size distributions of Atlantic salmon populations returning to spawn in Norwegian rivers
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Data from: Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas
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Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest
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Data from: Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Yellowstone grizzly bears
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Data from: Competition among native and invasive Phragmites australis populations: an experimental test of the effects of invasion status, genome size, and ploidy level.
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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: Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)
Quantifying interannual variation in effective adult breeding number (Nb) and relationships between Nb, effective population size (Ne), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long-lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual Nb and generational Ne using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance Nb estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of Nb across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced Nb relative to N on average 36.8% and 16.3%, respectively. Interannual variation in Nb/N ratios (0.27–0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40-fold difference in annual larval production across years (437–16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and Nb/N. Estimates of Ne based on three single-sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of Nb. Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.
Data from: Effective population sizes of a major vector of human diseases, Aedes aegypti
The effective population size (Ne) is a fundamental parameter in population genetics that determines the relative strength of selection and random genetic drift, the effect of migration, levels of inbreeding, and linkage disequilibrium. In many cases where it has been estimated in animals, Ne is on the order of 10-20% of the census size. In this study, we use 12 microsatellite markers and 14,888 single nucleotide polymorphisms (SNPs) to empirically estimate Ne in Aedes aegypti, the major vector of yellow fever, dengue, chikungunya, and Zika viruses. We used the method of temporal sampling to estimate Ne on a global dataset made up of 46 samples of Ae. aegypti that included multiple time points from 17 widely distributed geographic localities. Our Ne estimates for Ae. aegypti fell within a broad range (~25-3,000), and averaged between 400 and 600 across all localities and time points sampled. Adult census size (Nc) estimates for this species range between one and five thousand, so the Ne/Nc ratio is about the same as for most animals. These Ne values are lower than estimates available for other insects and have important implications for the design of genetic control strategies to reduce the impact of this species of mosquito on human health.
Data from: A model-derived short-term estimation method of effective size for small populations with overlapping generations
If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long-lived species. We created an individual-based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life-history parameter combination. The model is freely available as an r-package NEff. The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.
Data from: Comparative analyses of effective population size within and among species: ranid frogs as a case study
It has recently become practicable to estimate the effective sizes (Ne) of multiple populations within species. Such efforts are valuable for estimating Ne in evolutionary modeling and conservation planning. We used microsatellite loci to estimate Ne of 90 populations of four ranid frogs (20 to 26 populations per species, mean n per population = 29). Our objectives were to determine typical values of Ne for populations of each species, compare Ne estimates among the species, and test for correlations between several geographic variables and Ne within species. We used single-sample linkage disequilibrium, approximate Bayesian computation, and sibship assignment methods to estimate contemporary Ne for each population. Three of the species—Rana pretiosa, R. luteiventris, and R. cascadae— have consistently small effective population sizes (<50). Ne in Lithobates pipiens spans a wider range, with some values in the hundreds or thousands. There is a strong east-to-west trend of decreasing Ne in Lithobates pipiens. The smaller effective sizes of western populations of this species may be related to habitat fragmentation and population bottlenecking.
Data from: Patchy distribution and low effective population size raise concern for an at-risk top predator
Aim: Understanding carnivore distribution is important for management decisions that aim to restore naturally-regulated ecosystems and preserve biodiversity. Eastern Wolves, a species at risk in Canada, are centralized in Algonquin Provincial Park and their ability to disperse and establish themselves elsewhere is limited by human-caused mortality associated with hunting, trapping, and vehicle collisions. Here, we refine our understanding of Eastern Wolf distribution and provide the first estimates of their effective population size. Location: Southern Ontario and Gatineau Quebec. Methods: We used noninvasive samples, as well as blood samples archived from other research projects, collected between 2010 – 2014 to generate autosomal microsatellite genotypes at 12 loci for 98 Canis individuals. We utilized Bayesian and multivariate clustering analyses to identify Eastern Wolves in regions that were previously unsampled. Both linkage disequilibrium and temporal approaches were used to estimate effective population size of Eastern Wolves. Results: Assignment tests identified 34 individuals as Eastern Wolves, primarily in or near two provincial parks: Killarney and Queen Elizabeth II Wildlands. Eastern Coyotes were identified in Bon Echo Provincial Park, Frontenac Provincial Park, and Gatineau Park, whereas many of the samples were admixed among the different Canis types. Effective population size (Ne) estimates ranged from 24.3 – 122.1 with a harmonic mean of 45.6. Main Conclusions: The identification of Eastern Wolves in the regions of Killarney and Queen Elizabeth II Wildlands Provincial Parks extends the range of Eastern Wolves north of the French River and southward into previously unidentified regions. The effective population size is low and raises concerns for long-term persistence of this threatened carnivore; values are dangerously close to critical values recommended for short-term persistence. These results provide important information for upcoming Eastern Wolf recovery plans associated with federal and provincial endangered species legislation.
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