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158 results for “effective population size”
Data from: Measures of effective population size in sea otters reveal special considerations for wide-ranging species
Conservation genetic techniques and considerations of the evolutionary potential of a species are increasingly being applied to species conservation. For example, effective population size (Ne) estimates are useful for determining the conservation status of species, yet accurate estimates of current Ne remain difficult to obtain. The effective population size can contribute to setting federal delisting criteria, as was done for the southern sea otter (Enhydra lutris nereis). After being hunted to near extinction during the North Pacific fur trade, the southern sea otter has recovered over part of its former range, but remains at relatively low numbers, making it desirable to obtain accurate and consistent estimates of Ne. Although theoretical papers have compared the validity of several methods, comparisons of estimators using empirical data in applied conservation settings are limited. We combined thirteen years of demographic and genetic data from 1,006 sea otters to assess multiple Ne estimators, as well as temporal trends in genetic diversity and population genetic structure. Genetic diversity was low and did not increase over time. There was no evidence for distinct genetic units, but some evidence for genetic isolation by distance. Notably, estimates of Ne based on demographic data were much larger than genetic estimates when computed for the entire range of the population, but were similar at smaller spatial scales. The discrepancy between estimates at large spatial scales could be driven by cryptic population structure and/or individual differences in reproductive success. We recommend the development of new delisting criteria for the southern sea otter. We advise the use of multiple estimates of Ne for other wide-ranging species, species with overlapping generations, or with sex biased dispersal, as well as the development of improved metrics of genetic assessments of populations.
Data from: Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective size in a seeded great scallop population (Pecten maximus)
The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.
Data from: Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches
The effective population size (Ne) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating Ne from a single sample of genotypes to trace temporal change in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci, and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both Ne and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (Nb) using Linkage Disequilibrium, Sibship Assignment and Approximate Bayesian Computation methods, and extrapolated these estimates to Ne using the generation interval. The Ne estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of Ne > 50 but short of the long-term minimum viable population goal of Ne > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in Ne probably in the late 1990s and early 2000s. The new single-sample approaches to estimation of Ne provide efficient means for including Ne in monitoring frameworks, and will be of great importance for future management and conservation.
Data from: Effective population size of malaria mosquitoes: large impact of vector control
Malaria vectors in sub-Saharan Africa have proven themselves very difficult adversaries in the global struggle against malaria. Decades of anti-vector interventions have yielded mixed results – with successful reductions in transmission in some areas, and limited impacts in others. These varying successes can be ascribed to a lack of universally effective vector control tools, as well as the development of insecticide resistance in mosquito populations. Understanding the impact of vector control on mosquito populations is crucial for planning new interventions and evaluating existing ones. However, estimates of population size changes in response to control efforts are often inaccurate because of limitations and biases in collection methods. Attempts to evaluate the impact of vector control on mosquito effective population size (Ne) have produced inconclusive results thus far. Therefore, we obtained data for 13-15 microsatellite markers for over 1,500 mosquitoes representing multiple time points for seven populations of three important vector species – Anopheles gambiae, An. melas and An. moucheti in Equatorial Guinea. These populations were subjected to indoor residual spraying or long-lasting insecticidal nets in recent years. For comparison, we also analyzed data from two populations that have no history of organized vector control. We used Approximate Bayesian Computation to reconstruct their demographic history, allowing us to evaluate the impact of these interventions on the effective population size. In six of the seven study populations, vector control had a dramatic impact on the effective population size, reducing Ne between 55-87%, the exception being a single An. melas population. In contrast, the two negative control populations did not experience a reduction in effective population size. This study is the first to conclusively link anti-vector intervention programs in Africa to sharply reduced effective population sizes of malaria vectors.
Data from: Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.
Data from: It takes two: heritable male effects on reproductive timing but not clutch size in a wild bird population
<p>Within-population variation in the traits underpinning reproductive output has long been of central interest to biologists. Since they are strongly linked to lifetime reproductive success, these traits are expected to be subject to strong selection and, if heritable, to evolve. Despite the formation of durable pair bonds in many animal taxa, reproductive traits are often regarded as female-specific, and estimates of quantitative genetic variation seldom consider a potential role for heritable male effects. Yet reliable estimates of such social genetic effects are important since they influence the amount of heritable variation available to selection. Based on a 52-year study of a nestbox-breeding great tit (Parus major) population, we apply 'extended' bivariate animal models in which the heritable effects of both sexes are modelled to assess the extent to which males contribute to heritable variation in seasonal reproductive timing (egg laying date) and clutch size, while accommodating the covariance between the two traits. Our analyses show that reproductive timing is a jointly expressed trait in this species, with (positively covarying) heritable variation for laydate being expressed in both members of a breeding pair, such that the total heritable variance is 50% larger than estimated by traditional models. This result was robust to explicit consideration of a potential male-biased environmental confound arising through sexually dimorphic dispersal. In contrast to laydate, males' contribution to heritable variation in clutch size was limited. Our study thus highlights the contrasting extent of social determination for two major components of annual reproductive success, and emphasises the need to consider the social context of what are often considered individual-level traits.</p>
Data from: Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales
The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89–1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.
Data from: Sex change and effective population size: implications for population genetic studies in marine fish
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.
Data from: Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish
<p>Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (Ne), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had little effect on either fitness correlate, which were determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low Ne and long-term isolation can represent important sources of variation and be capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.</p>
Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.
Data from: Long-term effective population size dynamics of an intensively monitored vertebrate population
Long-term genetic data from intensively monitored natural populations are important for understanding how effective population sizes (Ne) can vary over time. We therefore genotyped 1622 common buzzard (Buteo buteo) chicks sampled over 12 consecutive years (2002–2013 inclusive) at 15 microsatellite loci. This data set allowed us to both compare single-sample with temporal approaches and explore temporal patterns in the effective number of parents that produced each cohort in relation to the observed population dynamics. We found reasonable consistency between linkage disequilibrium-based single-sample and temporal estimators, particularly during the latter half of the study, but no clear relationship between annual Ne estimates (hdy201667e1gif(239)1917) and census sizes. We also documented a 14-fold increase in hdy201667e2gif(239)1917 between 2008 and 2011, a period during which the census size doubled, probably reflecting a combination of higher adult survival and immigration from further afield. Our study thus reveals appreciable temporal heterogeneity in the effective population size of a natural vertebrate population, confirms the need for long-term studies and cautions against drawing conclusions from a single sample.
Supplementary Data - Haplotype-based inference of recent effective population size in modern and ancient DNA samples
<p>This repository contains the simulated data analyzed in our manuscript titled "Haplotype-based Inference of Recent Effective Population Size in Modern and Ancient DNA Samples".The data is split into 7 datasets. </p><p><strong>- demographies.tar.gz</strong>: the simulated demographic models.<br><strong>- modern_data.tar.gz:</strong> simulated SNP-araray data. The genotypes were simulated under 4 demographic histories (see demographies.tar.gz) for 256 samples and under 10 different random seeds (Replicate 1-10). Additionally, Replicates 11 and 12 include simulations at larger sample sizes. Note that the results at lower sample sizes can be obtained by keeping the first N samples of the simulated files.<br><strong>- true_ibd.tar.gz :</strong> This dataset contains the IBD segments from the simulated modern_data (ground truth from ARGON simulator).<br><strong>- ancient_data.tar.gz</strong> dataset contains simulated aDNA data. The dataset contains data simulated at different coverages (MISSING_$M, where $M = exp(-coverage)), sample sizes, demographic models, and random seeds. Split into three parts. See below for instructions on how to reconstruct the dataset. <br><strong>- structure.tar.gz</strong> and<strong> admixture.tar.gz :</strong> contain the data simulated under more complex demographic histories involving 2 isolated populations (structure) or a single population undergoing a recent admixture event (admixtuer.tar.gz). The manuscript provides more details about the demographic histories.<br>- <strong>imputed.tar.gz</strong> dataset contains simulated imputed aDNA data. Each region was simulated independently. Each folder corresponds to a chromosome arm and contains:<br> - data.anc_array.npy: list of the SNPs included in the analysis (simulating a 1240k array)<br> - data.glimpse.vcf.gz: phased ancient population data as phased by GLIMPSE v1<br> - data.glimpse.vcf.gz.csi: index for the above VCF file<br> - data.imputed.vcf.gz: imputed ancient population data (unphased, including dosages and genotype posteriors)<br> - data.imputed.vcf.gz.csi: index file for the above VCF<br> - data.map.gz: genetic map for GLIMPSE (tab-separated format: pos chr cM)<br> - data.ref.tsv.gz: file used for calculating genotype likelihoods with BCFtools mpileup command to use as input for GLIMPSE (format: chromosome position ref_allele,alt_allele)<br> - data.ref.tsv.gz.tbi: index for the above file<br> - data.ref.vcf.gz: simulated sequencing data from the reference panel<br> - data.ref.vcf.gz.csi: index file for the above VCF<br> - data.target_ground_truth.vcf.gz: simulated sequencing data for the ancient population (ground truth)<br> - datalist.txt: list of genotype likelihood files for each target individual (to be used for merging into a single file)<br> - data.temp.map.gz: genetic map for data creation with msprime simulator (format: chr position rate(cM/Mb) cM)<br> - data.tree -> msprime simulator output containing all samples, both reference panel samples and ancient population samples<br> - data.vcf.gz: VCF containing ground truth sequencing data, phased genotypes for reference panel samples and for ancient population samples<br> - dataref.fa.fai: index for reference fasta file used during reads creation</p><p> </p><p>Note that some of the datasets have been split into multiple parts, for example admixed.tar.gz has been split into three different parts admixed.tar.gz-part-aa, admixed.tar.gz-part-ab, and admixed.tar.gz-part-ac<br>You can get the data by typing:</p><p>cat admixed.tar.gz.part-* > admixed.tar.gz</p><p><br> </p>
Data from: Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation
Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree Ne varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single sample estimators of Ne. Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and Ne showed large variation over generations in some populations. Short term Ne estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, Ne estimates were lower when assuming gene flow than when assuming populations were closed. However, attempts to jointly estimate Ne and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single sample estimates of current Ne are generally smaller than the short term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably due to past or ongoing migration. A clearer picture of current and short term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same Ne, they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.
Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations
Currently there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during four years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life-cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only one year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were very low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programs into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.
Comparison of adult census size and effective population size support the need for continued protection of two Solomon Island endemics
<p>Because a population's ability to respond to rapid change is dictated by standing genetic variation, we can better predict a population's long-term viability by estimating and then comparing adult census size (<em>N</em>) and effective population size (<em>N<sub>e</sub></em>). However, most studies only measure <em>N</em> or <em>N<sub>e</sub></em>, which can be misleading. Using a combination of field and genomic sequence data, we here estimate and compare <em>N</em> and <em>N<sub>e</sub></em> in two range-restricted endemics of the Solomon Islands. Two <em>Zosterops</em> White-eye species inhabit the small island of Kolombangara, with a high elevation species endemic to the island (<em>Z. murphyi</em>) and a low elevation species endemic to the Solomon Islands (<em>Z. kulambangrae</em>). Field observations reveal large values of <em>N </em>for both species with <em>Z. kulambangrae</em> numbering at 114,781 ± 32,233 adults, and <em>Z. murphyi</em> numbering at 64,412 ± 15,324 adults. In contrast, genomic analyses reveal that <em>N<sub>e</sub></em> was much lower than <em>N</em>, with <em>Z. kulambangrae</em> estimated at 694.5 and <em>Z. murphyi</em> at 796.1 individuals. Further, positive Tajima's D values for both species suggest that they have experienced a demographic contraction, providing a mechanism for low values of <em>N<sub>e</sub></em>. Comparison of <em>N </em>and <em>N<sub>e</sub></em> suggests that <em>Z. kulambangrae</em> and <em>Z. murphyi</em> are not at immediate threat of extinction but may be at genetic risk. Our results provide important baseline data for long-term monitoring of these island endemics, and argue for measuring both population size estimates to better gauge long-term population viability.</p>
Data and scripts from: Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations, and nonlinearity
<p class="MsoNormal">Theory and analyses of fisheries datasets indicate that harvesting can alter population structure and destabilize nonlinear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of <em>Daphnia magna</em> in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were nonlinear, and nonlinearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via depletion of adults whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases nonlinearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.</p>
Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment
<p>Since the rediscovery of Mendelian genetics over a century ago, there has been much debate about the evolutionary importance of mutations with large phenotypic effects. While population genetic models predict that large-effect mutations will typically contribute to adaptation following an abrupt change in environment, the prediction applies to populations of stable size and overlooks effects of population size change on adaptation (e.g., population decline following habitat loss; growth during range expansion). We evaluate the phenotypic and fitness effects of mutations contributing to adaptation immediately following an abrupt environmental shift that alters both selection and population size dynamics. We show that large-effect mutations are likely to contribute to adaptation in populations declining to a new carrying capacity, somewhat smaller-effect mutations contribute to evolutionary rescue, and small-effect mutations predominate in growing populations. We also show that the relative contributions of positively selected and overdominant mutations to adaptation depend on interactions between the phenotypic effect size distribution for new mutations and the specific form of population size change during adaptation (i.e., growth, decline, or evolutionary rescue). Our results illustrate how population size dynamics can shape the genetic basis of adaptation, which should motivate empirical comparisons of populations adapting in different demographic contexts.</p>
Data from: Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds
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Data from: Nutrient availability and atmospheric CO2 partial pressure modulate the effects of nutrient heterogeneity on the size structure of populations in grassland species
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Data from: Effective population size of malaria mosquitoes: large impact of vector control
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