Endangered Greater One-horned Rhinoceros Carry High Levels of Genetic Variation

Abstract: The population of Rhinoceros unicornis in the Chitwan Valley, Nepal, was reduced to an estimated effective population size (N_e of 21–28 individuals (60–80 total animals) in 1962. Protein electrophoresis shows that heterozygosity remains very high in this population (H_o= 9.9%) despite its near extinction. We attribute this high heterozygosity to large N_e's prior to the population bottleneck, the recent occurrence of the bottleneck, and long generation time. These results illustrate the importance of considering historical demography and life history parameters when evaluating the possible genetic effects of bottlenecks in wild populations. They also offer support to recent arguments that the erosion of genetic diversity attributed to bottlenecks may be overemphasized.     

Effects of Habitat Fragmentation on Effective Population Size in the Endangered Rio Grande Silvery Minnow

Abstract:  We assessed spatial and temporal patterns of genetic diversity to evaluate effects of river fragmentation on remnant populations of the federally endangered Rio Grande silvery minnow ( Hybognathus amarus ). Analysis of microsatellite and mitochondrial DNA detected little spatial genetic structure over the current geographic range, consistent with high gene flow despite fragmentation by dams. Maximum-likelihood analysis of temporal genetic data indicated, however, that present-day effective population size ( N_eV ) of the largest extant population of this species was 78 and the ratio of effective size to adult numbers ( N_eV/N ) was ∼ 0.001 during the study period (1999 to 2001). Coalescent-based analytical methods provided an estimate of historical (river fragmentation was completed in 1975) effective size ( N_eI  ) that ranged between 10⁵ and 10⁶. We propose that disparity between contemporary and historical estimates of N_e and low contemporary N_e/N result from recent changes in demography related to river fragmentation. Rio Grande silvery minnows produce pelagic eggs and larvae subject to downstream transport through diversion dams. This life-history feature results in heavy losses of yearly reproductive effort to emigration and mortality, and extremely large variance in reproductive success among individuals and spawning localities. Interaction of pelagic early life history and river fragmentation has altered demographic and genetic dynamics of remnant populations and reduced N_e to critically low values over ecological time.     

Application of the One-Migrant-per-Generation Rule to Conservation and Management

Abstract:  Endangered species are commonly found in several (partially) isolated populations dispersed on different fragments of a habitat, natural reserve, or zoo. A certain level of connectivity among such populations is essential for maintaining genetic variation within and between populations to allow local and global adaptation and for preventing inbreeding depression. A rule of thumb widely accepted by the conservation community is that one migrant per generation (OMPG) into a population is the appropriate level of gene flow. This rule is based on Wright's study of his island model under a long list of simplifying assumptions. I examined the robustness of the OMPG rule to the violation of each of the many assumptions, quantifying the effect with population genetics theory. I showed that, when interpreted as one effective migrant per generation, OMPG is generally valid for real populations departing from the ideal model in the discrepancies of actual (  N ) and effective (  N_e  ) population sizes and actual ( m ) and effective ( m_e  ) migration rates. I also addressed the issue of converting the effective number of migrants (  M_e= N_em_e  ) into the actual number of migrants ( M = Nm  ) of a certain age and sex. In particular, N_e < N , a case common for natural populations, did not necessarily require M > M_e to maintain a certain level of differentiation among populations. Rather, translating the elusive M_e into the manageable M depends on the specific causes (e.g., biased sex ratio, reproductive skew) that lead to N_e < N .     

Effective Population Size and Lifetime Reproductive Success

The mean and variance of lifetime reproductive success, E_LRS and V_LRS, influence the ratio of effective to census population size, N_e/N_c. Because the complete data needed to calculate E_LRS and V_LRS are seldom available, we provide alternatives for estimating N_e/N_c from incomplete data. These estimates should be useful to conservation biologists trying to compute the effective size of a censused population. An analytical approach makes assumptions regarding the process influencing offspring survival. We provide a method for examining the validity of those assumptions and show that particular violations can result in either over- or underestimates. When the assumptions are violated or when more data are available, we suggest estimating N_e/N_c using computer simulations of models based on individuals. We examine how such simulations can be used to estimate N_e/N_c using an individual-based model for Lesser Snow Geese ( Anser caerulescens ). We demonstrate that such estimates can be biased unless the simulations are based on complete cohorts and samples of known age. We show that because the estimate of N_e/N_c depends on the stage of the reproductive cycle used as a point of reference in the model, the census population size N_c must be based on the same stage to provide unbiased estimates of N_e.     

Genetic Diversity, Population Size, and Fitness in Central and Peripheral Populations of a Rare Plant Lychnis viscaria

Abstract: Genetic diversity is expected to decrease in small and isolated populations as a consequence of bottlenecks, founder effects, inbreeding, and genetic drift. The genetics and ecology of the rare perennial plant Lychnis viscaria (Caryophyllaceae) were studied in both peripheral and central populations within its distribution area. We aimed to investigate the overall level of genetic diversity, its spatial distribution, and possible differences between peripheral and central populations by examining several populations with electrophoresis. Our results showed that the level of genetic diversity varied substantially among populations (  H _exp = 0.000–0.116) and that the total level of genetic diversity (mean H _exp = 0.056) was low compared to that of other species with similar life-history attributes. The peripheral populations of L. viscaria had less genetic variation (mean H _exp = 0.034) than the central ones (0.114). Analysis of genetic structure suggested limited gene flow (mean F _ST = 0.430) and high differentiation among populations, emphasizing the role of genetic drift (  N _e m = 0.33). Isolation was even higher than expected based on the physical distance among populations. We also focused on the association between population size and genetic diversity and possible effects on fitness of these factors. Population size was positively correlated with genetic diversity. Population size and genetic diversity, however, were not associated with fitness components such as germination rate, seedling mass, or seed yield. There were no differences in the measured fitness components between peripheral and central populations. Even though small and peripheral populations had lower levels of genetic variation, they were as viable as larger populations, which emphasizes their potential value for conservation.     

Application of Genetic Bottleneck Testing to the Investigation of Amphibian Declines: a Case Study with Natterjack Toads

Abstract: Declines of amphibians are causing widespread concern and in some cases have been explained by factors such as climate change and the spread of microbial pathogens. A problem remains, however, in the unequivocal demonstration of decline in situations where populations may be undergoing natural fluctuations in abundance. We describe the application of a genetic test for bottlenecks ( Cornuet & Luikart 1996 ) that should distinguish between natural oscillations and true population declines. British natterjack toads (   Bufo calamita  ) provide examples of populations that have not declined in recent decades, populations that have declined, and populations in which trends are unclear. Microsatellite allele frequency data from these populations were tested for heterozygote excess and shifts in allele frequency distributions, and inferences from these computations about bottlenecks (i.e., persistently smaller population sizes than the recent means) were compared with demographic information. The genetic test correctly identified bottlenecks and should therefore prove useful in demonstrating whether amphibian declines have occurred where long-term demographic time series are not available.     

Population Demographics and Genetic Diversity in Remnant and Translocated Populations of Sea Otters

Abstract: The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter ( Enhydra lutris ) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Mitochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size ( r _s = −0.741, p = 0.038) and minimum population size ( r _s = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, although growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.     

Unprecedented Low Levels of Genetic Variation and Inbreeding Depression in an Island Population of the Black-Footed Rock-Wallaby

Abstract: It has been argued that demographic and environmental factors will cause small, isolated populations to become extinct before genetic factors have a significant negative impact. Islands provide an ideal opportunity to test this hypothesis because they often support small, isolated populations that are highly vulnerable to extinction. To assess the potential negative impact of isolation and small population size, we compared levels of genetic variation and fitness in island and mainland populations of the black-footed rock-wallaby ( Petrogale lateralis [Marsupialia: Macropodidae]). Our results indicate that the Barrow Island population of P. lateralis has unprecedented low levels of genetic variation (  H _e = 0.053, from 10 microsatellite loci) and suffers from inbreeding depression (reduced female fecundity, skewed sex ratio, increased levels of fluctuating asymmetry). Despite a long period of isolation ( ∼ 1600 generations) and small effective population size (  N _e ∼ 15), demographic and environmental factors have not yet driven this population to extinction. Nevertheless, it has been affected significantly by genetic factors. It has lost most of its genetic variation and become highly inbred (  F _e = 0.91), and it exhibits reduced fitness. Because several other island populations of P. lateralis also exhibit exceptionally low levels of genetic variation, this phenomenon may be widespread. Inbreeding in these populations is at a level associated with high rates of extinction in populations of domestic and laboratory species. Genetic factors cannot then be excluded as contributing to the extinction proneness of small, isolated populations.     

A Hierarchical View of Genetic Structure in the Rare Annual Plant Clarkia springvillensis

Genetic structure at several spatial scales was examined in the rare California annual, Clarkia springvillensis . Using seven isozyme-encoding loci as genetic markers, we assessed the amount and distribution of genetic variation among three populations and eight subpopulations. Total genetic variation was lower than in species with similar life history traits but equivalent to that of other endemic plants. Spatial autocorrelation showed some evidence for very limited differentiation within subpopulations at a scale of 1–2 m. The subpopulations, separated by tens of meters, were found to be more differentiated from each other ( F _sp = 0.084) on average than were populations ( F,pt = 0.017). This local genetic differentiation was not correlated with physical distance between subpopulations. The low F_pt estimates suggest that substantial gene flow is occurring among populations. However, the lack of correlation between genetic and geographic distances and the significant differentiation of subpopulations suggest that genetic drift is occurring within populations. Therefore, we believe the apparent homogeneity of populations is due to each population's gene frequencies' being an average of several divergent subpopulations. If drift is causing differentiation within populations, it may eventually cause differentiation between populations. The importance of using a hierarchical approach to evaluating genetic structure is clear. Patterns occurring at one spatial scale may not be evident at others. One should not necessarily conclude that gene flow is substantial and that the risk of genetic erosion via drift is negligible just because differentiation between populations is small; the system may not be at equilibrium. This lesson is particularly important when recent changes in climate or land use are apparent.     

Microsatellite Analysis of Population Structure in the Endangered Hawaiian Monk Seal

Abstract: The endangered Hawaiian monk seal breeds at six locations in the northwestern Hawaiian Islands. To determine whether significant genetic differentiation exists among these sites, we used microsatellite loci to examine the monk seal population structure at the five largest breeding colonies. Of 27 loci isolated from other seal species, only 3 were polymorphic in an initial screening of one individual from each breeding site. Only two alleles were found at each of these 3 loci in samples of 46–108 individuals. This extremely low variation is consistent with other measures of genetic variability in this species and is probably the result of a recent severe population bottleneck, combined with a long-term history of small population sizes. Although the smallest monk seal subpopulation in this study ( Kure Atoll) showed some evidence of heterozygote deficit, possibly indicative of inbreeding, the next smallest ( Pearl and Hermes Reef) had an apparent excess of heterozygous individuals. Genetic differentiation was detected between the two subpopulations at extreme ends of the range ( Kure and French Frigate Shoals). This trend was significant only at the microsatellite locus for which we had the largest sample size ( Hg6.3: R _ST = 0.206, p = 0.002; allelic goodness of fit G _h = 15.412, p < 0.005). French Frigate Shoals is the source population for translocated animals that have been released primarily at Kure Atoll. Differentiation between these sites consisted of allele frequency differences (with the same allele predominant in each location at all three loci), rather than the preservation of alternative alleles. Although the translocations have had positive demographic effects, we recommend continued genetic monitoring of both the source and recipient populations because translocated individuals are now entering the breeding population.     

Effects of Population Size, Mating System, and Evolutionary Origin on Genetic Diversity in Spiranthes sinensis and S. hongkongensis

Hong Kong once supported more than 109 species of wild orchids, of which approximately 30% were endemic. Most of the local wild orchids have now become rare or endangered. I conducted a comparative study of genetic diversity in two closely related terrestrial orchids, an allotetraploid, Spiranthes hongkongensis , and its diploid progenitor, S. sinensis , to assess the effects of the population bottleneck associated with the origin of the polyploid and to investigate the relationships between number of breeding individuals, mating system, and level of isozyme variation in their populations. Nearly complete genetic uniformity was observed both within and among populations of S. hongkongensis . In contrast, S. sinensis had high levels of genetic variation for all of the genetic parameters examined. Regression analysis of population size and several components of genetic diversity in S. sinensis revealed that, among various measures of within-population variation, the proportion of polymorphic loci ( P ) and average number of alleles per locus ( A ) or per polymorphic locus ( A _p ) were the most sensitive to population size ( R ² = 0.942, p = 0.001; R ² = 0.932, p = 0.002; and R ² = 0.923, p = 0.002 respectively). The highly negative correlation ( r = −0.999, p < 0.01) between population size and the mean frequency of private alleles in pairwise population comparisons, p (1), indicated that population size may also be used to predict the extent of population differentiation caused by random genetic drift. Conservation of genetic diversity in S. sinensis could be maximized by protecting several of both large and small populations, whereas fewer populations may be needed to achieve this goal for S. hongkongensis.     

Rapid Loss of Genetic Variation in Large Captive Populations of Drosophila Flies: Implications for the Genetic Management of Captive Populations

Levels of variation in eight large captive populations of D. melanogaster (census sizes ∼ 5000) that had been in captivity for periods from 6 months to 23 years (8 to 365 generations) were estimated from allozyme heterozygosities, lethal frequencies, and inversion heterozygosities and phenotypic variances, additive genetic variances ( V _A), and heritabilities ( h ²) for sternopleural bristle numbers. Correlations between all measures of variation except lethal frequencies were high and significant. All measures of genetic variation declined with time in captivity, with those for average heterozygosities, V _A, and h ² being significant. The effective population size ( N _e) was estimated to be 185–253 in these populations, only 0.037–0.051 of census size (N). Levels of allozyme heterozygosities declined rapidly in two large captive populations founded from another wild stock, being reduced by 86% and 62% within 2.5 years in spite of being maintained at sizes of approximately 1000 and 3500. Estimates of N _e/ N for these populations were only 0.016 and 0.004. Two estimates of N _e/ N for captive populations of D. pseudoobscura from data in the literature were also low at 0.036 and 0.012. Consequently, the rate of loss of genetic variation in captive populations and endangered species may be more rapid than hitherto recognized. Merely maintaining captive populations at large census sizes may not be sufficient to maintain essential genetic variation.     

Influence of Fragmentation and Bottlenecks on Genetic Divergence of Wild Turkey Populations

Abstract: There are few empirical studies of the effects of human-induced fragmentation and bottlenecks on the genetic structure of field populations. Assessment of these effects is necessary to evaluate the relevance of predictions obtained from simulation and theoretical models to the management of wild populations. The genetic structure of populations of the Wild Turkey (Meleagris gallopavo), which have been heavily influenced by human activities, was examined using allozyme electrophoresis Allele frequencies at four polymorphic loci were estimated for 27 localities using 461 turkeys The estimated proportion of genetic variation resulting from differences among populations (F_st= 0.102) was one of the highest reported for any avian species and was also much higher than that observed between turkey populations that had not passed through known bottlenecks Almost all of the variation (89%) among populations was accounted for by differences between groups of populations with different histories of manipulation Fragmented distributions and population bottlenecks due to human activities appear to have increased genetic differentiation among populations of wild turkeys. This observation agrees with theoretical predictions concerning the effects of isolation and bottlenecks on the genetic structure of field populations.     

Genetic Structure of Endangered Clapper Rail (Rallus longirostris) Populations in Southern California

We assessed the genetic structure of two subspecies of endangered Clapper Rails ( Rallus longirostris ) in Southern California using DNA fingerprinting to uncover variation in minisatellite DNA. Minisatellite DNA variation in the Salton Sea population of the R. l. yumanensis subspecies was at a level typical of outbred avian species (average proportion of fragments shared, or S, was 0.33). Variation was extremely low (S from 0.63 to 0.77), however, within four coastal, salt-marsh populations of the subspecies R. l. levipes located along a transect extending about 260 km northwest from the Mexican border. Between-population similarity (S_ij) was also high for the four levipes populations, although individuals of the small, isolated population at Mugu Lagoon consistently clustered separately in phenograms constructed using neighbor-joining or other algorithms. Individuals of yumanensis always clustered as a sister group to all levipes individuals. The minisatellite data were contrasted with the extremely low mtDNA and RAPD variation we found in both subspecies. We propose that variation in these less-mutable markers was lost in a bottleneck that occurred at least 1000 years ago, thus allowing sufficient time for recovery of variation in the rapidly mutating (μ≈} 0.001/gamete/generation) minisatellites (t = 1/μ, or 1000 generations). A second, more-recent bottleneck, or series of bottlenecks within a metapopulation structure, likely resulted in the depauparate variation seen in levipes today. We suggest that translocations from large to small levipes populations could restore important genetic variation to the small populations and would not compromise genetic boundaries.     

Genetic differentiation of Texas Gulf Coast populations of the blue crab Callinectes sapidus

Allelic frequencies at three polymorphic, enzyme-encoding gene loci (GOT-2, EST-1, EST-2) were determined for Callinectes sapidus (Rathbun) megalopae and adults sampled along the Texas coast of the Gulf of Mexico. Significant temporal and spatial variation was observed at all three loci. Primary findings included: (1) megalopal allelic frequencies often differed significantly from those observed among neighboring adult populations; (2) larval allelic frequencies appeared to vary seasonally, with populations showing sharp differences in the summer months but tending to be more homogeneous in winter; (3) allelic frequencies among adult populations were significantly heterogeneous, but only one locus (EST-2) showed significant temporal variation; (4) juvenile and adult crabs sampled within one bay showed no size-specific differences in allelic frequencies. The spatial heterogeneity in allelic frequencies suggests that interpopulation gene flow is not sufficient to overcome population differentiation resulting from genetic drift and/or natural selection. Temporal variation in larval allelic frequencies suggests seasonal changes in larval source populations which may result from population differences in spawning season or developmental times or from seasonal changes in coastal current patterns.     

Genetic Bottlenecks Driven by Population Disconnection

Abstract: Connectivity among populations plays a crucial role in maintaining genetic variation at a local scale, especially in small populations affected strongly by genetic drift. The negative consequences of population disconnection on allelic richness and gene diversity (heterozygosity) are well recognized and empirically established. It is not well recognized, however, that a sudden drop in local effective population size induced by such disconnection produces a temporary disequilibrium in allelic frequency distributions that is akin to the genetic signature of a demographic bottleneck. To document this effect, we used individual‐based simulations and empirical data on allelic richness and gene diversity in six pairs of isolated versus well‐connected (core) populations of European tree frogs. In our simulations, population disconnection depressed allelic richness more than heterozygosity and thus resulted in a temporary excess in gene diversity relative to mutation drift equilibrium (i.e., signature of a genetic bottleneck). We observed a similar excess in gene diversity in isolated populations of tree frogs. Our results show that population disconnection can create a genetic bottleneck in the absence of demographic collapse.     

Predicting the Deleterious Effects of Mutation Load in Fragmented Populations

Abstract:  Human-induced habitat fragmentation constitutes a major threat to biodiversity. Both genetic and demographic factors combine to drive small and isolated populations into extinction vortices. Nevertheless, the deleterious effects of inbreeding and drift load may depend on population structure, migration patterns, and mating systems and are difficult to predict in the absence of crossing experiments. We performed stochastic individual-based simulations aimed at predicting the effects of deleterious mutations on population fitness (offspring viability and median time to extinction) under a variety of settings (landscape configurations, migration models, and mating systems) on the basis of easy-to-collect demographic and genetic information. Pooling all simulations, a large part (70%) of variance in offspring viability was explained by a combination of genetic structure ( F_ST ) and within-deme heterozygosity ( H_S ). A similar part of variance in median time to extinction was explained by a combination of local population size ( N ) and heterozygosity ( H_S ). In both cases the predictive power increased above 80% when information on mating systems was available. These results provide robust predictive models to evaluate the viability prospects of fragmented populations.     

Effects of a Population Bottleneck on Whooping Crane Mitochondrial DNA Variation

Abstract: The Whooping Crane ( Grus americana ) is an endangered bird that suffered a severe population bottleneck; only 14 adults survived in 1938. We assessed the genetic effect of this human-caused bottleneck by sequencing 314 base pairs ( bp) of the mitochondrial DNA control region from cranes that lived before, during, and after this bottleneck. The maximum length of DNA amplifiable from museum specimens was negatively correlated with age, and only 10 of 153 specimens yielded the entire 314 bp sequence. Six haplotypes were present among the prebottleneck individuals sequenced, and only one of these persists in the modern population. The most common modern haplotype was in low frequency in the prebottleneck population, which demonstrates the powerful effect of genetic drift in changing allele frequencies in very small populations. By combining all available data, we show that no more than one-third of the prebottleneck haplotypes survived the human-caused population bottleneck. High levels of variation of substitution rates among nucleotide sites prevented us from estimating the prebottleneck population size. Our data will be incorporated into the captive breeding program to allow better management decisions regarding the preservation of current genetic diversity. These data offer the first glimpse into the genetic toll this species has paid for human activities.     

Temporal genetic variation in subpopulations of bicolor damselfish (Stegastes partitus) inhabiting coral reefs in the Florida Keys

In 1986 we observed significant genetic heterogeneity among samples of bicolor damselfish (Stegastes partitus) from geographically proximate coral reefs in the Florida Keys. This result was in contrast to results of virtually all previous studies of coral reef fishes. To assess temporal stability of localized genetic differentiation, we resampled reefs in 1989. Within approximately two generations, allele frequencies at the most differentiated locus,ACO-1 ^*, had changed by as much as 0.65, resulting in almost complete homogeneity between previously differentiated subpopulations. Estimates of 10.78 migrants per generation suggested that high gene flow is the most likely factor responsible for the significant change in allele frequencies. We attribute the original genetic differentiation to a population bottleneck, possibly caused by environmental perturbations such as hurricanes and consequent genetic drift. For reef fishes with pelagic egg and/or larval stages, a growing body of data suggests that: (1) populations are geographically extensive gene pools, and (2) rates of dispersal appear to be high enough to allow for continual repopulation of isolated and/or perturbed coral reef communities.     

Modeling Problems in Conservation Genetics Using Captive Drosophila Populations: Consequences of Equalization of Family Sizes

Equalization of family sizes is recommended for use in captive breeding programs, as it is predicted to double effective population sizes, reduce inbreeding, and slow the loss of genetic variation. The effects of maintaining small captive populations with equalization of family sizes versus random choice of parents on levels of inbreeding genetic variation, reproductive fitness, and effective population sizes ( N _e) were evaluated in 10 lines of each treatment maintained with four pairs of parents per generation. The mean inbreeding coefficient ( F ) increased at a significantly slower rate with equalization than with random choice (means of 0.35 and 0.44 at generation 10). Average heterozygosities at generation 10, based on six polymorphic enzyme loci, were significantly higher with equalization (0.149) than with random choice (0.085), compared to the generation 0 level of 0.188. The competitive index measure of reproductive fitness at generation 11 was more than twice as high with equalization as with random choice, both being much lower than in the outbred base population. There was considerable variation among replicate lines within treatments in all the above measures and considerable overlap between lines from the two treatments. Estimates of N _e for equalization were greater than those for random choice, whether estimated from changes in average heterozygosities or from changes in F. Equalization of family sizes can be unequivocally recommended for use in the genetic management of captive populations.