Contemporary effective population size and predicted maintenance of genetic diversity in the endangered kea (Nestor notabilis)

Population size and the potential for maintenance of genetic diversity are critical information for the monitoring of species of conservation concern. However, direct estimates of population size are not always feasible, making indirect genetic approaches a valuable alternative. We estimated contemporary effective population size (N_e) in the endangered kea (Nestor notabilis) using three different methods. We then inferred the census size (N_C) using published N_e/N_C ratios and modelled the future maintenance of genetic diversity assuming a number of demographic parameters. Short-term N_e was small with a range-wide N_e?N_C was within the range of the current estimate (c. 1000–5000). Forward simulations showed low probability of retaining 90% of rare alleles without immigration. However, the probability of maintaining genetic diversity was high with immigration, juvenile survival of?≥?30%, and an initial sex ratio of c. 0.5–0.6. Despite the low N_e in kea, predator control and/or artificial immigration might be sufficient to maintain the present genetic diversity.     

Low effective population size and survivorship in a grassland grouse

Assessments of census size (N _c) and effective population size (N _e) are necessary for the conservation of species exhibiting population declines. We examined two populations (Oklahoma and New Mexico) of the lesser prairie-chicken (Tympanuchus pallidicinctus), a declining lek-breeding bird, in which one population (Oklahoma) has larger clutch size and more nesting attempts per year but lower survival caused by human changes to the landscape. We estimated demographic and genetic estimates of N _e for each population and found that both populations have low N _e estimates with a risk of inbreeding depression. Although Oklahoma females produce a larger number of offspring, the proportion of females successfully reproducing is not higher than in New Mexico. Higher reproductive effort has likely reached a physiological limit in Oklahoma prairie-chickens but has not led to a higher N _e or even a larger N _c than New Mexico. We propose that future conservation efforts focus on maximizing survivorship and decreasing the variance in reproductive success because these factors are more likely than increasing reproductive output alone to yield population persistence in lek-breeding species.     

Do estimates of contemporary effective population size tell us what we want to know?

Estimation of effective population size (N_e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N_e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N_e such as inbreeding (N_eI), variance (N_eV), additive genetic variance (N_eAV), linkage disequilibrium equilibrium (N_eLD), eigenvalue (N_eE) and coalescence (N_eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N_e‐estimators target N_eV or N_eLD of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N_eI) and additive genetic variance (N_eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation.  The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.     

Accounting for missing data in the estimation of contemporary genetic effective population size (Ne)

Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N_e) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N_e). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N_e and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed‐inverse variance‐weighted harmonic mean) consistently performed the best for both single‐sample and two‐sample (temporal) methods of estimating N_e and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per‐locus sample size components.     

Making sense of genetic estimates of effective population size

The last decade has seen an explosion of interest in use of genetic markers to estimate effective population size, N_e. Effective population size is important both theoretically (N_e is a key parameter in almost every aspect of evolutionary biology) and for practical application (N_e determines rates of genetic drift and loss of genetic variability and modulates the effectiveness of selection, so it is crucial to consider in conservation). As documented by Palstra & Fraser ( 2012 ), most of the recent growth in N_e estimation can be attributed to development or refinement of methods that can use a single sample of individuals (the older temporal method requires at least two samples separated in time). As with other population genetic methods, performance of new N_e estimators is typically evaluated with simulated data for a few scenarios selected by the author(s). Inevitably, these initial evaluations fail to fully consider the consequences of violating simplifying assumptions, such as discrete generations, closed populations of constant size and selective neutrality. Subsequently, many researchers studying natural or captive populations have reported estimates of N_e for multiple methods; often these estimates are congruent, but that is not always the case. Because true N_e is rarely known in these empirical studies, it is difficult to make sense of the results when estimates differ substantially among methods. What is needed is a rigorous, comparative analysis under realistic scenarios for which true N_e is known. Recently, Gilbert & Whitlock ( 2015 ) did just that for both single‐sample and temporal methods under a wide range of migration schemes. In the current issue of Molecular Ecology, Wang ( 2016 ) uses simulations to evaluate performance of four single‐sample N_e estimators. In addition to assessing effects of true N_e, sample size, and number of loci, Wang also evaluated performance under changing abundance, physical linkage and genotyping errors, as well as for some alternative life histories (high rates of selfing; haplodiploids). Wang showed that the sibship frequency (SF) and linkage disequilibrium (LD) methods perform dramatically better than the heterozygote excess and molecular coancestry methods under most scenarios (see Fig. 1, modified from figure 2 in Wang 2016 ), and he also concluded that SF is generally more versatile than LD. This article represents a truly Herculean effort, and results should be of considerable value to researchers interested in applying these methods to real‐world situations.     

Multiple estimates of effective population size for monitoring a long‐lived vertebrate: an application to Yellowstone grizzly bears

Effective population size (N_e) is a key parameter for monitoring the genetic health of threatened populations because it reflects a population's evolutionary potential and risk of extinction due to genetic stochasticity. However, its application to wildlife monitoring has been limited because it is difficult to measure in natural populations. The isolated and well‐studied population of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem provides a rare opportunity to examine the usefulness of different N_e estimators for monitoring. We genotyped 729 Yellowstone grizzly bears using 20 microsatellites and applied three single‐sample estimators to examine contemporary trends in generation interval (GI), effective number of breeders (N_b) and N_e during 1982–2007. We also used multisample methods to estimate variance (N_eV) and inbreeding N_e (N_eI). Single‐sample estimates revealed positive trajectories, with over a fourfold increase in N_e (≈100 to 450) and near doubling of the GI (≈8 to 14) from the 1980s to 2000s. N_eV (240–319) and N_eI (256) were comparable with the harmonic mean single‐sample N_e (213) over the time period. Reanalysing historical data, we found N_eV increased from ≈80 in the 1910s–1960s to ≈280 in the contemporary population. The estimated ratio of effective to total census size (N_e/N_c) was stable and high (0.42–0.66) compared to previous brown bear studies. These results support independent demographic evidence for Yellowstone grizzly bear population growth since the 1980s. They further demonstrate how genetic monitoring of N_e can complement demographic‐based monitoring of N_c and vital rates, providing a valuable tool for wildlife managers.     

Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin

There is an increasing awareness that the long-term viability of endemic island populations is negatively affected by genetic factors associated with population bottlenecks and/or persistence at small population size. Here we use contemporary samples and historic museum specimens (collected 1888–1938) to estimate the effective population size (N _e) for the endangered yellow-eyed penguin (Megadyptes antipodes) in South Island, New Zealand, and evaluate the genetic concern for this iconic species. The South Island population of M. antipodes—constituting almost half of the species’ census size—is thought to be descended from a small number of founders that reached New Zealand just a few hundred years ago. Despite intensive conservation measures, this population has shown dramatic fluctuations in size over recent decades. We compare estimates of the harmonic mean N _e for this population, obtained using one moment and three likelihood based-temporal methods, including one method that simultaneously estimates migration rate. Evaluation of the N _e estimates reveals a harmonic mean N _e in the low hundreds. Additionally, the inferred low immigration rates (m = 0.003) agree well with contemporary migration rate estimates between the South Island and subantarctic populations of M. antipodes. The low N _e of South Island M. antipodes is likely affected by strong fluctuations in population size, and high variance in reproductive success. These results show that genetic concerns for this population are valid and that the long-term viability of this species may be compromised by reduced adaptive potential.     

Reconciling Genetic and Demographic Estimators of Effective Population Size in the Anuran Amphibian Bufo Calamita

We used genetic and demographic methods to estimate the variance effective population sizes (N _e) of three populations of natterjack toads Bufo calamita in Britain. This amphibian breeds in temporary pools where survival rates can vary among families. Census population sizes (N) were derived from spawn string counts. Point and coalescent-based maximum likelihood estimates of N _e based on microsatellite allele distributions were similar. N _e/N ratios based on genetic estimates of N _e ranged between 0.02 and 0.20. Mean demographic estimates of N _e were consistently higher (2.7–8.0-fold) than genetic estimates for all three populations when variance in breeding success was evaluated at the point where females no longer influence their progeny. However, discrepancies between genetic and demographic estimators could be removed by using a model that included extra variance in survivorship (above to Poisson expectations) among families. The implications of these results for the estimation of N _e in wild populations are discussed.     

Estimating effective population size from linkage disequilibrium: severe bias in small samples

Effective population size (N _e) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, fixation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of N _e from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of N _e using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small (<‰100) and below the true N _e. This is probably due to the linkage disequilibrium generated by the sampling process itself and the inadequate correction for this phenomenon in the method. Results suggest that N _e estimates derived using this method should be regarded with caution in many cases. To improve the method’s reliability and usefulness we propose a way to determine whether a given sample size exceeds the population N _e and can therefore be used for the computation of an unbiased estimate.     

Evaluating methods for estimating local effective population size with and without migration

Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate N_e from genetic data have been developed that take advantage of various approaches for inferring N_e. The ability of these methods to accurately estimate N_e, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating N_e from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of N_e can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves N_e estimates.     

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 (N_b) and relationships between N_b, effective population size (N_e), 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 N_b and generational N_e 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 N_b 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 N_b across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced N_b relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N_b/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 N_b/N. Estimates of N_e based on three single‐sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N_b. 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.     

Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation

Effective population size (N_e) is a key parameter to understand evolutionary processes and the viability of endangered populations as it determines the rate of genetic drift and inbreeding. Low N_e can lead to inbreeding depression and reduced population adaptability. In this study, we estimated contemporary N_e using genetic estimators (LDNE, ONeSAMP, MLNE and CoNe) as well as a demographic estimator in a natural insular house sparrow metapopulation. We investigated whether population characteristics (population size, sex ratio, immigration rate, variance in population size and population growth rate) explained variation within and among populations in the ratio of effective to census population size (N_e/N_c). In general, N_e/N_c ratios increased with immigration rates. Genetic N_e was much larger than demographic N_e, probably due to a greater effect of immigration on genetic than demographic processes in local populations. Moreover, although estimates of genetic N_e seemed to track N_c quite well, the genetic N_e‐estimates were often larger than N_c within populations. Estimates of genetic N_e for the metapopulation were however within the expected range (<N_c). Our results suggest that in fragmented populations, even low levels of gene flow may have important consequences for the interpretation of genetic estimates of N_e. Consequently, further studies are needed to understand how N_e estimated in local populations or the total metapopulation relates to actual rates of genetic drift and inbreeding.     

Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia

Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F _ST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N _e) ranged from seven to 228 and were significantly correlated with those of historical N _e but not with lake size. A census size (N _C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N _e (i.e. N _e/N _C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.     

Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.)

Temporal genetic data may be used forestimating effective population size (N _e) and for addressing the `temporal stability' of population structure, two issues of central importance for conservation and management. In this paper we assess the amount of spatio-temporal genetic variation at 17 di-allelic allozyme loci and estimate current N _e in two populations of stream resident brown trout (Salmo trutta) using data collected over 20 years. The amount ofpopulation divergence was found to bereasonably stable over the studied time period.There was significant temporal heterogeneitywithin both populations, however, and N _e was estimated as 19 and 48 for the twopopulations. Empirical estimates of theprobability of detecting statisticallysignificant allele frequency differencesbetween samples from the same populationseparated by different numbers of years wereobtained. This probability was found to befairly small when comparing samples collectedonly a few years apart, even for theseparticular populations that exhibit quiterestricted effective sizes. We discuss someimplications of the present results for browntrout population genetics and conservation, andfor the analysis of temporal genetic change inpopulations with overlapping generations ingeneral.     

Considerations for monitoring population trends of colonial waterbirds using the effective number of breeders and census estimates

Detecting trends in population size fluctuations is a major focus in ecology, evolution, and conservation biology. Populations of colonial waterbirds have been monitored using demographic approaches to determine annual census size (N_a). We propose the addition of genetic estimates of the effective number of breeders (N_b) as indirect measures of the risk of loss of genetic diversity to improve the evaluation of demographics and increase the accuracy of trend estimates in breeding colonies. Here, we investigated which methods of the estimation of N_b are more precise under conditions of moderate genetic diversity, limited sample sizes and few microsatellite loci, as often occurs with natural populations. We used the wood stork as a model species and we offered a workflow that researchers can follow for monitoring bird breeding colonies. Our approach started with simulations using five estimators of N_b and the theoretical results were validated with empirical data collected from breeding colonies settled in the Brazilian Pantanal wetland. In parallel, we estimated census size using a corrected method based on counting active nests. Both in simulations and in natural populations, the approximate Bayesian computation (ABC) and sibship assignment (SA) methods yielded more precise estimates than the linkage disequilibrium, heterozygosity excess, and molecular coancestry methods. In particular, the ABC method performed best with few loci and small sample sizes, while the other estimators required larger sample sizes and at least 13 loci to not underestimate N_b. Moreover, according to our N_b/N_a estimates (values were often ≤0.1), the wood stork colonies evaluated could be facing the loss of genetic diversity. We demonstrate that the combination of genetic and census estimates is a useful approach for monitoring natural breeding bird populations. This methodology has been recommended for populations of rare species or with a known history of population decline to support conservation efforts.     

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (N_e) and a simple capture-recapture estimator of abundance (N) to quantify the size and trend of stable or declining populations (true N = 100–10,000), using simulated Wright–Fisher populations. Neither method accurately or precisely estimated abundance at sample sizes of S = 30 individuals, regardless of true N. However, if larger samples of S = 60 or 120 individuals were collected, these methods provided useful insights into abundance and trends for populations of N = 100–500. At small population sizes (N = 100 or 250), precision of the N_e estimates was improved slightly more by a doubling of loci sampled than by a doubling of individuals sampled. In general, monitoring N_e proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space we explored, and performance of the N_e estimator is further enhanced if the N_e/N ratio is low. However, at the largest population size (N = 10,000), N estimation outperformed N_e. Both methods generally required ≥ 5 generations to pass between sampling events to correctly identify population trend.     

Genetic diversity through time and space: diversity and demographic history from natural history specimens and serially sampled contemporary populations of the threatened Gouldian finch (<Emphasis Type="Italic">Erythrura gouldiae</Emphasis>)

Declines in population size can compromise the viability of populations by reducing the effective population size (N_e), which may result in loss of genetic diversity and inbreeding. Temporal population genetic data can be a powerful tool for testing the presence and severity of reductions in N_e. The Gouldian finch (Erythrura gouldiae) is a flagship for conservation of Australian monsoonal savanna species. This species underwent severe population declines in the twentieth century due to land use changes associated with European colonization. Microsatellite and mitochondrial genetic data from Gouldian finch samples sourced from natural history collections prior to land use changes were compared with contemporary samples to estimate the severity of decline in effective population size and to detect changes in gene flow. These data show that Gouldian finch decline was not as severe as some sources suggest, and that population genetic connectivity has not changed following land use changes in the twentieth century. Multiple estimators of current N_e using genetic data from consecutive years suggest the Gouldian finch N_e is likely between a few hundred and a few thousand individuals, with some estimates within the range considered of conservation concern. This work has identified the need to genetically characterize populations in Queensland, and to understand critical demographic parameters (e.g. lifespan) in the Gouldian finch. Understanding these factors is vital to further improve genetic estimates of population size, key to the formation of appropriate conservation management of this species.     

Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (N_e), although N_e is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables. Location Yosemite National Park, California, USA. Methods I estimated F_ST, D_ps and N_e using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between N_e and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation. Results I found substantial variation in genetic distances between populations (F_ST = 0.004–0.396, D_ps = 0.045–0.839) and in effective population sizes (N_e = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with N_e. Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.     

Small effective population sizes of two remnant ocelot populations (<Emphasis Type="Italic">Leopardus pardalis albescens</Emphasis>) in the United States

Threatened populations are vulnerable to the effects of genetic drift and inbreeding, particularly when gene flow is low and the effective population size is small. Estimates of effective population size (N _e ) provide important information on the status of endangered populations that have experienced severe fragmentation and serve as indicators of genetic viability. Genetic data from microsatellite loci were used to estimate N _e for the 2 remaining populations of the endangered ocelot (Leopardus pardalis albescens) occurring in the United States. Several methods were used to calculate N _e , resulting in estimates ranging from N _e  = 8.0 (95% CI: 3.2–23.1) to 13.9 (95% CI: 7.7–25.1) for the population located at the Laguna Atascosa Wildlife Refuge in Cameron County, Texas. The ocelot population in Willacy County, Texas, had N _e estimates of 2.9 (95% CI: 1.7–5.6) and 3.1 (95% CI: 1.9–13.5), respectively. Estimates of N _e in both populations were below the critical value recommended for short-term viability.     

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 (N_b) and the generational effective population size (N_e) 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 N_e estimates, suggesting that mature male parr are significantly increasing N_b and N_e over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.