Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population

Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (N(e)) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean N(e) is estimated as 74. We find indications that N(e) varies over time, but there is no obvious temporal trend. We also estimated N(e) using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an N(e) estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (N(b)) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.     

Evaluating the effect of stage-specific survivorship on the N(e)/N ratio

Evaluating effective population size (Ne) and the effective size to census size ratio (Ne/N) in species with Type III survivorship curves is complicated when key demographic parameters [mean (k macro) and variance (V(k)) of family size] are measured during early life stages. The method of Crow & Morton (1955) for scaling demographic data collected at a juvenile stage to expected values at adulthood is extended to consider sequential episodes of random and family correlated survival. Results show the following: (i) The order in which the episodes of random and family-correlated survival occur does not affect N(e) or N(e)/N; (ii) If a population experiences an episode of family-correlated survival, N(e)/N scaled to its expected value in a population of constant size (k macro= 2) is simply the survival rate during the family-correlated stage. If multiple such stages occur, scaled N(e)/N is the product of the survivals during all family-correlated life stages; (iii) Under the assumption of random post-enumeration survival, adjusting the variance effective size to its expected value at k macro= 2 is equivalent to computing the inbreeding effective size at the earlier life stage. Application to experimental data for hatchery populations of Pacific salmon (Oncorhynchus spp.) indicates that nonrandom survival during the marine phase led to estimated reductions in effective size of 0-62 (mean 19) in 12 different cohorts. This approach can provide insights into N(e)/N in highly fecund species, including some marine species in which N(e) has been estimated to be several orders of magnitude less than N.     

Reproductive success and effective population size in woodrats (Neotoma macrotis)

Discrepancies between the census size and the genetically effective size of populations (N(e)) can be caused by a number of behavioural and demographic factors operating within populations. Specifically, strong skew in male reproductive success, as would be expected in a polygynous mating system, could cause a substantial decrease in N(e) relative to census size. Because the mating system of Neotoma macrotis had previously been described as one nearing harem polygyny, I examined the distribution of reproductive success and genetic variation within a population of this species. Combining genetic data and three years of field observations, I show that variance in reproductive success does not deviate from poisson expectations within either sex and variance in success is similar between the sexes. Furthermore, both males and females had multiple partners across litters in addition to some evidence of multiple paternity within litters. Despite a lack of strong skew in reproductive success, an estimate of N(e) based on a number of demographic parameters suggests that the ratio of N(e)/N in this population is 0.48. Although the ratio of N(e)/N suggests that the population is experiencing higher rates of genetic drift than would be expected based on census size alone, the population maintains high levels of genetic diversity. Estimates of neighbourhood size and patterns of recruitment to the study site suggest that immigration plays an important role in this population and may contribute to the maintenance of high levels of genetic diversity.     

Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population

The effective population size (N(e)) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate N(e) are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare N(e) estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias N(e) if not accounted for. Overlapping generations and iteroparity would also upwardly bias N(e) when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of N(e). Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the N(e) estimation.     

Quantifying the variation in the effective population size within a genome

The effective population size (N(e)) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in N(e) is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that N(e) is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species-most genes have an N(e) that is within a few fold of all other genes. Nonetheless we show that this modest variation in N(e) is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of N(e), even taking into account the obvious nonindependence between these measures.     

Life history and environmental variation interact to determine effective population to census size ratio

Successful recovery and sustainability of threatened and exploited species depends in part on retention and maintenance of genetic diversity. Theory indicates that genetic diversity is lost at a rate inversely proportional to the genetically effective population size (N(e)), which is roughly equal to one-half the adult census size (N) in many organisms. However, N(e) has been reported to be up to five orders of magnitude lower than N in species with life histories that result in type III survivorship (high fecundity, but heavy mortality in early life stages, e.g. bony fishes), prompting speculation that low values of N(e) may be a general feature of such organisms despite sometimes vast abundances. Here, we compared N(e) and the ratio N(e)/N across three ecologically similar fish species from the arid southwestern United States, all with type III life histories but with differing expectations of egg and larval survivorship that correlate with the degree of human-imposed habitat fragmentation. Our study indicates that type III life history may be necessary, but this alone is insufficient to account for extraordinarily low values of N(e)/N. Rather, life history interacts with environmentally imposed mortality to determine the rate and magnitude of change in genetic diversity in these desert fish species.     

Small effective population sizes in two planktonic freshwater copepod species (Eudiaptomus) with apparently large census sizes

In small planktonic organisms, large census sizes (N(c)) suggest large effective population sizes (N(e)), but reliable estimates are rare. Here, we present N(e)/N(c) ratios for two freshwater copepod species (Eudiaptomus sp.) using temporal samples of multilocus microsatellite genotypes and a pseudo-likelihood approach. N(e)/N(c) ratios were very small in both Eudiaptomus species (10(-7)-10(-8)). Although we hypothesized that the species producing resting eggs (E. graciloides) had a larger N(e) than the other (E. gracilis), estimates were not statistically different (E. graciloides: N(e) = 672.7, CI: 276-1949; E. gracilis: N(e) = 1027.4, CI: 449-2495), suggesting that the propagule bank of E. graciloides had no detectable influence on N(e).     

Effective population sizes and migration rates in fragmented populations of an endangered insect (Coenagrion mercuriale: Odonata)

1. Effective population sizes (N(e)) and migration rates (m) are critical evolutionary parameters that impact on population survival and determine the relative influence of selection and genetic drift. While the parameter m is well-studied in animal populations, N(e) remains challenging to measure and consequently is only rarely estimated, particularly in insect taxa. 2. We used demographic and genetic methods to estimate N(e) and m in a fragmented population of the endangered damselfly Coenagrion mercuriale to better understand the contrast between genetic and field estimates of these parameters and also to identify the spatial scale over which populations may become locally adapted. 3. We found a contrast between demographic- and genetic-based estimates of these parameters, with the former apparently providing overestimates of N(e), owing to substantial underestimation of the variance in reproductive success, and the latter overestimating m, because spatial genetic structure is weak. 4. The overall N(e) of sites within the population network at Beaulieu Heath, the largest C. mercuriale site in the UK, was estimated to vary between approximately 60 and 2700. 5. While N(e) was not correlated with either the total numbers of adults (N) or the area of habitat, this parameter was always less than N, because of substantial variance in reproductive success. The ratio N(e)/N varied between 0.006 and 0.42 and was generally larger in smaller populations, possibly representing some 'genetic compensation'. 6. From a simple genetic model and these data on N(e) and m, it seems that populations of C. mercuriale have the potential to respond to localized spatial variation in selection and this would need to be considered for future genetic management of this endangered species.     

Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach

A new genetic estimator of the effective population size (N(e)) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based N(e) estimator (N(eFk)) by using data from simulated populations with known N(e) and real populations. The new likelihood-based estimator (N(eLB)) showed narrower credible intervals and greater accuracy than (N(eFk)) when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., N(e) = 20 for five generations), as few as approximately 10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, approximately 20 loci are required for the same precision when using the classical F-statistic approach. The N(eLB) estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates N(e) than does N(eLB) and thus is less likely to erroneously suggest that a population is large and has a low extinction risk.     

Large global effective population sizes in Paramecium

The genetic effective population size (N(e)) of a species is an important parameter for understanding evolutionary dynamics because it mediates the relative effects of selection. However, because most N(e) estimates for unicellular organisms are derived either from taxa with poorly understood species boundaries or from host-restricted pathogens and most unicellular species have prominent phases of clonal propagation potentially subject to strong selective sweeps, the hypothesis that N(e) is elevated in single-celled organisms remains controversial. Drawing from observations on well-defined species within the genus Paramecium, we report exceptionally high levels of silent-site polymorphism, which appear to be a reflection of large N(e).     

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

The effective population size (N(e) ) 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 N(e) from a single sample of genotypes to trace temporal change in N(e) 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 N(e) and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (N(b) ) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to N(e) using the generation interval. The N(e) estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of N(e) > 50 but short of the long-term minimum viable population goal of N(e) > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in N(e) probably in the late 1990s and early 2000s. The new single-sample approaches to the estimation of N(e) provide efficient means for including N(e) in monitoring frameworks and will be of great importance for future management and conservation.     

Determinants of effective population size for loci with different modes of inheritance

Here we report an assessment of the determinants of effective population size (N(e)) in species with overlapping generations. Specifically, we used a stochastic demographic model to investigate the influence of different life-history variables on N(e)/N (where N = population census number) and the influence of sex differences in life-history variables on N(e) for loci with different modes of inheritance. We applied an individual-based modeling approach to two datasets: one from a natural population of savannah baboons (Papio cynocephalus) in the Amboseli basin of southern Kenya and one from a human tribal population (the Gainj of Papua New Guinea). Simulation-based estimates of N(e)/N averaged 0.329 for the Amboseli baboon population (SD = 0.116, 95% CI = 0.172 - 0.537) and 0.786 for the Gainj (SD = 0.184, 95% CI = 0.498 - 1.115). Although variance in male fitness had a substantial impact on N(e)/N in each of the two primate populations, ratios of N(e) values for autosomal and sex-linked loci exhibited no significant departures from Poisson-expected values. In each case, similarities in sex-specific N(e) values were attributable to the unexpectedly high variance in female fitness. Variance in male fitness resulted primarily from age-dependent variance in reproductive success, whereas variance in female fitness resulted primarily from stochastic variance in survival during the reproductive phase.     

The context-dependent effect of multiple paternity on effective population size

Effective population size (N(e)) is important because it describes how evolutionary forces will affect a population. The effect of multiple sires per female on N(e) has been the subject of some debate, at the crux of which is the effects of monandry and multiple-paternity (MP) on male variance in reproductive success. In both mating systems, females mate with several males over their lifetimes, but sire offspring with one male at a time in the former and have several sires per clutch in the latter. First, I theoretically show that whether the annual male variance in reproductive success in an MP population is greater or less than that of a monandrous population depends on the distributions of within-clutch paternity. Then, I simulated different distributions of within-clutch paternity under a range of parameters that characterize natural populations to show that an MP population can have an N(e) smaller or larger than that of a monandrous population with otherwise equal dynamics. The N(e(MP)):N(e(Monandry)) ratio increased with mating frequency and female variance in reproductive success, was equalized by long generation times, and was affected by the distribution of within-clutch paternities. The results of this model provide a unifying framework for the debate.     

Estimation of effective population size and detection of a recent population decline coinciding with habitat fragmentation in a ground beetle

We assess the impact of habitat fragmentation on the effective size (N(e)) of local populations of the flightless ground beetle Carabus violaceus in a small (<25 ha) and a large (>80 ha) forest fragment separated by a highway. N(e) was estimated based on the temporal variation of allele frequencies at 13 microsatellite loci using two different methods. In the smaller fragment, N(e) estimates ranged between 59 and a few hundred, whereas values between 190 and positive infinity were estimated for the larger fragment. In both samples, we detected a signal of population decline, which was stronger in the small fragment. The estimated time of onset of this N(e) reduction was consistent with the hypothesis that recent road constructions have divided a continuous population into several isolated subpopulations. In the small fragment, N(e) of the local population may be so small that its long-term persistence is endangered.     

Temporal genetic stability and high effective population size despite fisheries-induced life-history trait evolution in the North Sea sole

Heavy fishing and other anthropogenic influences can have profound impact on a species' resilience to harvesting. Besides the decrease in the census and effective population size, strong declines in mature adults and recruiting individuals may lead to almost irreversible genetic changes in life-history traits. Here, we investigated the evolution of genetic diversity and effective population size in the heavily exploited sole (Solea solea), through the analysis of historical DNA from a collection of 1379 sole otoliths dating back from 1957. Despite documented shifts in life-history traits, neutral genetic diversity inferred from 11 microsatellite markers showed a remarkable stability over a period of 50 years of heavy fishing. Using simulations and corrections for fisheries induced demographic variation, both single-sample estimates and temporal estimates of effective population size (N(e) ) were always higher than 1000, suggesting that despite the severe census size decrease over a 50-year period of harvesting, genetic drift is probably not strong enough to significantly decrease the neutral diversity of this species in the North Sea. However, the inferred ratio of effective population size to the census size (N(e) /N(c) ) appears very small (10(-5) ), suggesting that overall only a low proportion of adults contribute to the next generation. The high N(e) level together with the low N(e) /N(c) ratio is probably caused by a combination of an equalized reproductive output of younger cohorts, a decrease in generation time and a large variance in reproductive success typical for marine species. Because strong evolutionary changes in age and size at first maturation have been observed for sole, changes in adaptive genetic variation should be further monitored to detect the evolutionary consequences of human-induced selection.     

Estimation of effective population size for the long-lived darkblotched rockfish Sebastes crameri

We report the variance effective population size (Ne) in darkblotched rockfish (Sebastes crameri) utilizing the temporal method for overlapping generations, which requires a combination of age-specific demography and genetic information from cohorts. Following calculations of age-specific survival and reproductive success from fishery data, we genotyped a sample (n = 1087) comprised by 6 cohorts (from 1995 to 2000) across 7 microsatellite loci. Our Ne estimate (Ne) plus 95% confidence interval was (Ne) = 9157 [6495-12 215], showing that the breeding population number could be 3-4 orders of magnitude smaller than the census population size (N) = 24 376 210). Our estimates resemble closely those found for fishes with similar life history, suggesting that the small (Ne)/(N) ratio for S. crameri is most likely explained by a combination of high variance in reproductive success among individuals, genetic structure, and demographic perturbations such as historical fishing. Because small (Ne)/(N) ratios have been commonly associated with potential loss of genetic variation, our estimates need careful consideration in rockfish management and conservation.     

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.     

Maturation,growth and fecundity of Arctic charr, <Emphasis Type="Italic">Salvelinus alpinus</Emphasis> (L.), life-history variants co-existing in lake systems of Southern Baffin Island,Nunavut, Canada

Two life-history variants of Arctic charr (Salvelinus alpinus), anadromous and lake-resident, have been previously identified in lakes of Southern Baffin Island, Nunavut, Canada. In accordance with classical life-history theory, it is hypothesised that anadromous charr will delay maturation in both size and age, and have increased fecundity (per spawning event) in comparison with lake-resident charr. Sagittal otoliths and biological data were collected for both life-history variants within the three studied lakes: Iqalugaarjuit, Qasigiat and Qinngu. Sagittal otoliths were embedded in epoxy resin, cross-sectioned for age determination, and imaged for back-calculation (size and age). Back-calculated data in each lake were fit to von Bertalanffy growth models for each life-history variant and compared via analysis of residual sums of squares. Anadromous charr had greater mean size at maturity and experienced a delay in mean age at maturity in comparison with lake-residents. The relationship between size and fecundity or egg diameter did not differ between the two life-history variants. Growth models indicate that the overall growth coefficients of lake-resident and anadromous charr were different in all three studied lakes. The Brody growth coefficient for all lake-resident charr populations was greater than anadromous individuals indicating that maximum length was reached at a rapid rate, resulting in a smaller asymptotic length. Indirect evidence suggests that anadromous and lake-resident charr belong to one reproductive population. Future genetic analysis is necessary to further determine the degree of divergence between the life-history variants.