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.     

Genetic changes in Atlantic salmon stocks since historical times and the effective population size of a long-term captive breeding programme

Human-caused genetic changes in two Atlanticsalmon (Salmo salar L.) stocks, from therivers Iijoki and Oulujoki in Finland, wereassessed by comparing the genetic parameters ofthese stocks before and after the hatcherybreeding of several successive generations,corresponding to 40 and 33 years since the wildstate. The changes were also compared withthose observed in a large wild salmon stock inthe River Teno during 56 years. In all, thevariation at seven microsatellite DNA loci wasexamined in 11 Atlantic salmon samplesoriginating from these three rivers. Theeffective population size, N_e, duringbreeding of the Iijoki broodstock and for theTeno salmon was also estimated by the temporalmethod based on allele frequency changes. Forthe Iijoki broodstock, the changes could betracked generation by generation from thefounding of the stock. Statisticallysignificant changes in allele frequencies werecommon in the hatchery stocks (F = 0.029, forIijoki), but not in the wild Teno stock, whichwas temporally very stable (F = 0.007). Allelicrichness decreased statistically significantly(24.8%) in the Oulujoki broodstock, from 62.1to 46.7 alleles at nine loci. On average, therewere 9.7 fewer alleles (15.7%) in thecontemporary broodstocks than in thecorresponding historical stocks. The meanheterozygosity was 6.6% lower in thecontemporary Oulujoki broodstock, but remainedunchanged in the Iijoki broodstock. Theestimated N_e for the Iijoki broodstock wasunder 80 for 4.5 generations from 1962 to 1995and for the wild Teno salmon over 900 for 56years from 1939 to 1995.     

THE INFLUENCE OF MATING SYSTEM AND OVERLAPPING GENERATIONS ON EFFECTIVE POPULATION SIZE

The effective population size (N_e) depends strongly on mating system and generation time. These two factors interact such that, under many circumstances, N_e is close to N/2, where N is the number of adults. This is shown to be the case for both simple and highly polygynous mating systems. The random union of gametes (RUG) and monogamy are two simple systems previously used in estimating N_e, and here a third, lottery polygyny, is added. Lottery polygyny, in which all males compete equally for females, results in a lower N_e than either RUG or monogamy! Given nonoverlapping generations the reduction is 33% for autosomal loci and 25% for sex-linked loci. The highly polygynous mating systems, harem polygyny and dominance polygyny, can give very low values of N_e/N when the generation time (T) is short. However, as T is lengthened, N_e approaches N/2. The influence of a biased sex ratio depends on the mating system and, in general, is not symmetrical. Biases can occur because of sex differences in either survival or recruitment of adults, and the potential for a sex-ratio bias to change N_e is much reduced given a survival bias. The number of juveniles present also has some influence: as the maturation time is lengthened, N_e increases.     

Genetic diversity of four esterase loci in natural populations of Hordeum spontaneum C. Koch from Jordan

Summary The diversity of four esterase loci was studied electrophoretically in 690 individual spikes representing 12 populations of wild barley (Hordeum spontaneum C. Koch.) collected from central, peripheral and marginal regions of its distribution in Jordan. A minimum of 6, 10, 5 and 5 alleles were observed at the Est-1, Est-2, Est-4 and Est-5 loci, respectively. Est-2 and Est-4 were the most diverse loci (H_c=0.53±0.05 and 0.46±0.07, respectively). Est-5 was intermediate (H_c=0.33+0.07) and Est-1 was the lowest (H_c=0.22±0.04). Polymorphism was highest in the central populations (H_e=0.52±0.04), followed by the peripheral (H_e=0.40±0.05) and the marginal (H_e=0.22±0.05) populations. Average allelic diversity between (G_st=0.49) and within (H_s=0.51) populations reflects a high allelic differentiation among these populations. Log-linear analyses revealed that four two-locus terms and two three-locus terms were significantly associated (P<0.05). Geographical distances between populations were not significantly correlated with Nei's genetic similarity index (r=0.16; P<0.19). It is postulated that diversifying selection is a major factor in the population genetic differentiation of these esterase loci.     

Spatial and temporal genetic differentiation and effective population size of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>, L.) in small Danish rivers

The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis of molecular variance (AMOVA) showed that differentiation among populations accounted for a non-significant amount of the genetic differentiation, whereas differentiation among temporal samples within populations was highly significant (0.0244, P<0.001). Estimates of effective population size (N _e) using a maximum-likelihood based implementation of the temporal method, yielded small values (N _e ranging from 33 to 79). When a model was applied that allows for migration among populations, N _e estimates were even lower (24–54), and migration rates were suggested to be high (0.13–0.36). All samples displayed a clear signal of a recent bottleneck, probably stemming from a period of unfavourable conditions due to organic pollution in the 1970–1980’s. By comparison to other estimates of N _e in brown trout, Lake Hald trout represent a system of small populations linked by extensive gene flow, whereas other populations in larger rivers exhibit much higher N _e values and experience lower levels of immigration. We suggest that management considerations for systems like Lake Hald brown trout should focus both on a regional scale and at the level of individual populations, as the future persistence of populations depends both on maintaining individual populations and ensuring sufficient migration links among these populations.     

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.     

Genetic effective size,Ne, tracks density in a small freshwater cyprinid,Pecos bluntnose shiner (Notropis simus pecosensis)

Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (N_eV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (N_eD) for each sample. Estimates of N_e were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch‐per‐unit‐effort), N_eV and N_eD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and N_eV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and N_eD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of N_e and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive‐bred and reared fish. The efficacy of N_e as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.     

Grain protein variability among populations of wild barley (Hordeum spontaneum C. Koch.) from Jordan

Summary Protein content, kernel weight, and genetic diversity in the storage protein hordein, encoded by the Hor 1 and Hor 2 loci, were assessed in 12 populations of wild barley (Hordeum spontaneum C. Koch.) collected from central, peripheral, and marginal areas of its distribution in Jordan. Protein content ranged from 106.3 to 239.1 g kg^-1, and kernel weight ranged from 21.17 to 31.8 mg. Populations with high protein content and heavy kernels have been identified. Electrophoretic analysis of the storage protein hordein showed that the two hordein loci, Hor 1 and Hor 2, are highly polymorphic, having 34 and 38 alleles, respectively. Polymorphism (H_e) was highest in central populations (H_e Hor 1=0.859, H_e Hor 2=0.782), intermediate in peripheral populations (H_e Hor 1=0.566, H_e Hor 2=0.509), and lowest in marginal populations (H_e Hor 1=0.392, H_e Hor 2=0.349). Geographical distances between populations were not indicative of Nei's genetic similarity (NI). NI values averaged 0.209 and ranged from 0.0 to 0.83, supporting the hypothesis of an island population model for the species. The high proportion of allelic diversity, apportioned among populations for Hor 1 (0.584) and Hor 2 (0.495) loci, indicates that these natural populations are a rich reserve of genetic variability for protein. This variability is readily exploitable in breeding.     

Isolation and characterization of microsatellite loci in Swietenia humilis (Meliaceae): an endangered tropical hardwood species

Microsatellites are now firmly established as an informative marker system, with increasing popularity as a tool amongst molecular ecologists. We have developed a method of constructing an enriched microsatellite library for the tropical tree species Swietenia humilis Zucc. (Meliaceae). This method is based on a precloning enrichment of SSRs using synthetic oligonucleotide probes, bound to magnetic beads and hybridizing to complementary microsatellite core sequences in digested genomic DNA. Here we describe the isolation and characterization of 10 microsatellite loci that have been used to survey the genetic diversity within a natural population of S. humilis. A total of 97 alleles were identified with an average of 9.7 alleles over all loci. Very high levels of allelic polymorphism were detected at individual loci, with 23 alleles observed at the most variable. The mean observed heterozygosity was 0.415 (range 0.038-0.815) exceeding levels of diversity detected in related species which used isozymes as the marker system. Subpopulation differentiation at a microgeographical scale was low (F_ST= 0.036) and the values of Nm, calculated from the allelic frequencies, were greater than 1 thus reflecting the extent of gene flow occurring between individual trees.     

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Analysis of linkage disequilibrium (=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N _e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N _e based on for unlinked, diallelic gene loci are sharply biased downwards ( in some cases) if sample size (S) is less than true N _e. The bias is shown to arise from inaccuracies in published formula for when S and/or N _e are small. Empirically derived modifications to for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in % in most cases). The modified method also performs well in estimating N _e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect , but if N has recently increased from a bottleneck can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N _e in natural populations. However, a comprehensive assessment of performance of with highly polymorphic markers such as microsatellites is needed.The US Governmentȁ9s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Effective population size in the captive breeding program of the Lake Victoria cichlid Paralabidochromis chilotes

Microsatellite DNA markers were used to monitor levels of genetic variation in 3 generations of the American Zoo and Aquarium Association [AZA] Species Survival Plan [SSP] captive breeding program for the Lake Victoria cichlid Paralabidochromis chilotes. Temporal changes in the frequency of 15 alleles, across four polymorphic loci, were used to estimate effective population size (N_e). The upper limit of the 95% confidence interval for N_e never exceeded eight individuals, with all of the corresponding N_e/N ratios falling below 0.15. A test of the proportion of expected heterozygous individuals between the F₁ and F₃ generations indicated a significant decline in expected heterozygosity of 5% per generation. Alternative husbandry protocols, including subdividing the captive population, are addressed to reduce the further loss of genetic variation. Zoo Biol 18:215–222, 1999. © 1999 Wiley‐Liss, Inc.     

Comparison of allozyme,RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen

We examined genetic variation in allozyme loci, nuclear DNA restriction fragment length polymorphisms (RFLPs), and random amplified polymorphic DNAs (RAPDs) in 130 trembling aspen (Populus tremuloides) and 105 bigtooth aspen (P. grandidentata) trees. In trembling aspen 10 out of 13 allozyme loci assayed (77%) were polymorphic (P), with 2.8 alleles per locus (A) and an expected heterozygosity (H_e) of 0.25. In contrast, bigtooth aspen had a much lower allozyme genetic variability (P=29%; A=1.4; H_e=0.08). The two species could be distinguished by mutually exclusive alleles at Idh-1, and bigtooth aspen has what appears to be a duplicate 6PG locus not present in trembling aspen. We used 138 random aspen genomic probes to reveal RFLPs in HindIII digests of aspen DNA. The majority of the probes were from sequences of low copy number. RFLP results were consistent with those of the allozyme analyses, with trembling aspen displaying higher genetic variation than bigtooth aspen (P=71%, A=2.7, and H_e=0.25 for trembling aspen; P=65%, A=1.8, and H_e=0.13 for bigtooth aspen). The two species could be distinguished by RFLPs revealed by 21 probes (15% of total probes assayed). RAPD patterns in both species were studied using four arbitrary decamer primers that revealed a total of 61 different amplified DNA fragments in trembling aspen and 56 in bigtooth aspen. Assuming a Hardy-Weinberg equilibrium, estimates of P=100%, A=2, and H_e=0.30 in trembling aspen and P=88%, A=1.9, and H_e=0.31 in bigtooth aspen were obtained from the RAPD data. Five amplified DNA fragments were species diagnostic. All individuals within both species, except for 2 that likely belong to the same clone, could be distinguished by comparing their RAPD patterns. These results indicate that (1) RFLPs and allozymes reveal comparable patterns of genetic variation in the two species, (2) trembling aspen is more genetically variable than bigtooth aspen at both the allozyme and DNA levels, (3) one can generate more polymorphic and species-specific loci with DNA markers than with allozymes in aspen, and (4) RAPDs provide a very powerful tool for fingerprinting aspen individuals.     

High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)

The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria × ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (H_e or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12–17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.Communicated by J. Dvorak     

Enzyme and colour variation in the hoplonemertean Tetrastemma nigrifrons from the Sea of Japan

Five sympatric colour varieties of the hoplonemertean Tetrastemma nigrifrons (var. pallidum, var. bicolor, var. purpureum, var. punctata, var. albino) were found in Vostok Bay (the Sea of Japan). The taxonomic status of the varieties, some of which have been known for almost a century, was uncertain. Starch gel electrophoresis was used to compare allele frequencies of these varieties at 19 isozyme loci. Neither fixed allelic differences nor statistically significant differences in allele frequencies between different colour varieties was revealed. It was concluded therefore that all the colour varieties studied are conspecific. As estimated from the electrophoretic screening of 24 isozyme loci, the species is highly variable at the molecular level. It has high mean values of observed and expected heterozygosity estimates, H _o =0.313 ± 0.049 and H _e =0.323 ± 0.050, and is one of the most variable species among invertebrates.     

Genetic Variability Assessed by Microsatellites in a Breeding Program of Pacific White Shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>)

Genetic diversity in a shrimp-breeding program was monitored for 2 generations by microsatellite DNA markers (Pvan1578 and Pvan1815) to establish levels of variation and proceed with a selection program. An increase in the number and frequencies of some alleles in both microsatellite loci from G₀ to G₂ was induced by foreign sire contributions. Most common alleles and high heterozygosities (around 70% in both loci) were maintained through the generations, indicating that there had not been a significant loss of genetic variability in the breeding program. However, when compared with variability in other wild and cultured stocks, the presence of 4 main alleles at both loci may be an indication that a certain reduction in variability already was present in the line used as founder stock (G₀). Therefore, it is recommended that additional genetic variability be introduced to the breeding stock by crossing it with a different line.     

EFFECTIVE POPULATION SIZE AND GENETIC DRIFT IN TRISTYLOUS EICHHORNIA PANICULATA (PONTEDERIACEAE)

Populations of the tristylous, annual Eichhornia paniculata are markedly differentiated with respect to frequency of mating types. This variation is associated with evolutionary changes in mating system, from predominant outcrossing to high self-fertilization. To assess the potential influence of genetic drift acting on this variation, we estimated effective population size in 10 populations from northeastern Brazil using genetic and demographic methods. Effective size (N_e) was inferred from temporal changes in allele frequency at two to eight isozyme loci and also calculated using five demographic variables: 1) the number of flowering individuals (N); 2) temporal fluctuations in N; 3) variance in flower number; 4) frequency of mating types; and 5) selfing rate. Average N_e based on isozyme data was 15.8, range 3.4–70.6, and represented a fraction (mean N_e/N = 0.106) of the census number of individuals (mean N = 762.8; range: 30.5–5,040). Temporal variation in N and variance in flower number each reduced N_e to about a half of N whereas mating type frequencies and selfing rate caused only small reductions in N_e relative to N. All estimates of N_e based on demographic variables were considerably larger than those obtained from genetic data. The two kinds of estimates were in general agreement, however, when all demographic variables were combined into a single measure. Monte Carlo simulations indicated that effective size must be fewer than about 40 for drift to overcome the frequency-dependent selection that maintains the polymorphism for mating type. Applying the average N_e/N value to 167 populations censused in northeastern Brazil indicated that 72% had effective sizes below this number. This suggests that genetic drift is likely to play a dominant role in natural populations of E. paniculata.     

Population genetics of the American eel (Anguilla rostrata): FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

We performed population genetic analyses on the American eel (Anguilla rostrata) with three main objectives. First, we conducted the most comprehensive analysis of neutral genetic population structure to date to revisit the null hypothesis of panmixia in this species. Second, we used this data to provide the first estimates of contemporary effective population size (N_e) and to document temporal variation in effective number of breeders (N_b) in American eel. Third, we tested for statistical associations between temporal variation in the North Atlantic Oscillation (NAO), the effective number of breeders and two indices of recruit abundance. A total of 2142 eels from 32 sampling locations were genotyped with 18 microsatellite loci. All measures of differentiation were essentially zero, and no evidence for significant spatial or temporal genetic differentiation was found. The panmixia hypothesis should thus be accepted for this species. N_b estimates varied by a factor of 23 among 12 cohorts, from 473 to 10 999. The effective population size N_e was estimated at 10 532 (95% CI, 9312–11 752). This study also showed that genetically based demographic indices, namely N_b and allelic richness (Ar), can be used as surrogates for the abundance of breeders and recruits, which were both shown to be positively influenced by variation during high (positive) NAO phases. Thus, long‐term genetic monitoring of American glass eels at several sites along the North American Atlantic coast would represent a powerful and efficient complement to census monitoring to track demographic fluctuations and better understand their causes.     

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.     

Genetic Structure of Wild Rice Oryza Glumaepatula Populations in Three Brazilian Biomes Using Microsatellite Markers

The existence of Oryza glumaepatula is threatened by devastation and, thus, the implementation of conservation strategies is extremely relevant. This study aimed to characterize the genetic variability and estimate population parameters of 30 O. glumaepatula populations from three Brazilian biomes using 10 microsatellite markers. The levels of allelic variability for the SSR loci presented a mean of 10.3 alleles per locus and a value of 0.10 for the average allelic frequency value. The expected total heterozygosity (H_e) ranged from 0.63 to 0.86. For the 30 populations tested, the mean observed (H_o) and expected heterozygosities (H_e) were 0.03 and 0.11within population, respectively, indicating an excess of homozygotes resulting from the preferentially self-pollinating reproduction habit. The estimated fixation index ( _IS ) was 0.79 that differed significantly from zero, indicating high inbreeding within each O. glumaepatula population. The total inbreeding of the species (_IT ) was 0.98 and the genetic diversity indexes among populations, _ST and _ST, were 0.85 and 0.90, respectively, indicating high genetic variability among them. Thus, especially for populations located in regions threatened with devastation, it is urgent that in situ preservation conditions should be created or that collections be made for ex situ preservation to prevent loss of the species genetic variability.     

neogen: A tool to predict genetic effective population size (Ne) for species with generational overlap and to assist empirical Ne study design

Molecular genetic estimates of population effective size (N_e) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic N_e for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user‐specified age‐structured sampling schemes. neogen provides a population simulation and genetic power analysis framework that simulates the demographics, genetic composition, and N_e, from species‐specific life history, mortality, population size, and genetic priors. neogen guides the user to establish a tractable sampling regime and to determine the numbers of samples and microsatellite or SNP loci required for accurate and precise genetic N_e estimates when sampling a natural population. neogen is useful at multiple stages of a study's life cycle: when budgeting, as sampling and locus development progresses, and for corroboration when empirical N_e estimates are available. The underlying model is applicable to a wide variety of iteroparous species with overlapping generations (e.g., mammals, birds, reptiles, long‐lived fishes). In this paper, we describe the neogen model, detail the workflow for the point‐and‐click software, and explain the graphical results. We demonstrate the use of neogen with empirical Australian east coast zebra shark (Stegostoma fasciatum) data. For researchers wishing to make accurate and precise genetic N_e estimates for overlapping generations species, neogen facilitates planning for sample and locus acquisition, and with existing empirical genetic N_e estimates neogen can corroborate population demographic and life history properties.