Considering threats to population viability of the endangered Korean long-tailed goral (Naemorhedus caudatus) using VORTEX

Population viability analysis (PVA) has frequently been used in conservation biology to predict extinction rates for threatened or endangered species. In this study, we used VORTEX to model Korean long-tailed goral (Naemorhedus caudatus) using previously collected ecological data. We focused on modelling population extinction, mean population size and heterozygosity. The minimum viable population size was found to be at least 50 gorals for 100 years, regardless of carrying capacity. However, populations with fewer than 50 gorals could not remain successful in the model. Inbreeding depression, catastrophes and supplementation also affected patterns of population extinction, mean population size and heterozygosity. Supplementation with new individuals had the strongest effect on extinction, mean population size and heterozygosity, followed by initial population size, inbreeding, catastrophes and carrying capacity. These results suggest that a supplementation by extra goral individuals from goral proliferation facilities would be the most helpful means for the restoration programme. More Korean goral-specific information regarding demographic and habitat parameters is needed for further PVA of the species.     

A preliminary population viability analysis of the critically endangered blue‐eyed black lemur (Eulemur flavifrons)

Population viability analysis is an important tool to assess the extinction risk in small populations of highly specialized primates. The blue‐eyed black lemur (Eulemur flavifrons) is critically endangered with a restricted range in the north‐western dry deciduous forest of Madagascar, where habitat fragmentation and loss of forest connectivity threaten its survival. We performed a population viability analysis (PVA) of this lemur in Ankarafa Forest in the Sahamalaza Peninsula National Park, north‐western Madagascar, to determine the demographic parameters most influential for population persistence and to assess extinction probabilities. We conducted PVA analyses using different demographic parameters which characterize the species including reproduction, lifespan and population size using the software VORTEX for six scenarios with 100 iterations and simulated over 100 years. The simulations suggested the first extinction within 13 years when the percentage of habitat destruction increased up to 12%. Severe habitat destruction such as fire and logging was the major cause which led to the risk of population extinction. Conservation strategies, in particular measures to reduce habitat destruction, are proposed to ensure the survival of this critically endangered lemur.     

Loss of genetic variation and effective population size of Kirikuchi charr: implications for the management of small, isolated salmonid populations

Small, isolated populations may face extinction due to a combination of inbreeding depression and other threats. Effective population size ( N _e) is one comprehensive measure that allows us to evaluate the genetic status of a population, and to make management decisions regarding genetic viability. We simulated loss of genetic variation and estimated N _e for two small, isolated populations of Kirikuchi charr Salvelinus leucomaenis japonicus , the endangered, southernmost local populations of the genus Salvelinus in the world, using VORTEX, an individual-based stochastic PVA model. Approximately half of the genetic variation was lost over 200 years regardless of census population size and demographic parameters, and N _e estimates were roughly 50 in each of the two populations, suggesting the possibility of inbreeding depression. The target population size of N _e>500, by securing long-term viability, is several times that of the present size of each of the populations studied, and no local habitats maintaining such a target number are considered to exist. The results strongly indicate a need for recovering natural connections and potential gene flow among local populations. However, the impending threat to these populations from non-native charr widely distributed throughout the drainage has prevented the recovery of the connections. Given the small N _e of the two populations, it would be necessary to retain gene flow artificially within or across local populations. This will be true of many other salmonid populations that have been isolated or fragmented recently.     

漩涡模型及其在白暨豚种群管理中的应用

漩涡模型作为一种用于野生动物种群生存力分析的计算机模拟工具,已在濒危物种的保护和管理方面得到了广泛的应用。本文介绍了漩涡模型的产生和特征,同时使用这一模型完成了长江中白暨豚（Ｌｉｐｏｔｅｓｖｅｘｉｌｌｉｆｅｒ）种群生存力分析。模拟的结果表明,在未来１００年内,白暨豚在高、中死亡率的条件下,种群灭绝概率分别为１．０和０．５左右。但是,在死亡率低和极低的条件下,白暨豚的灭绝过程可能持续１００年以上,或永远也不会灭绝。开始种群大小对白暨豚的平均灭绝时间有一定的影响,但对种群生长率（ｒ）却没有影响。在高、中、和低死亡率条件下,白暨豚种群生长率分别为－０．０７、－０．０４和－０．０２。     

Effectiveness of a reserve network for the conservation of the endemic marsupial Micoureus travassosi in Atlantic Forest remnants in southeastern Brazil

Habitat loss and fragmentation are serious threats to biodiversity conservation in the Atlantic Forest. A network of protected reserves is essential to the protection of native fauna and flora. However, internal and external factors may threaten the preservation of biota, thus population viability analyses (PVA) are important tools in reserve design and management planning. A PVA was carried out, using the computer package VORTEX, to assess the effectiveness of the reserve network of Rio de Janeiro State in Brazil in retaining viable populations of the endemic marsupial Micoureus travassosi. The PVA takes into account demographic, genetic and environmental stochastic events and catastrophes (fire). Rio de Janeiro state has 31 reserves, and 20 of those were considered to retain viable populations for 100 years, whereas eight were predicted to suffer from genetic decay, two from both genetic decay and demographic stochasticity, and one of them probably has an extinct population. The minimum area of suitable habitat needed to maintain a minimum viable population of M. travassosi is estimated at 3600ha. Sensitivity analysis was run for mortality, sex ratio, percentage of reproductive females, inbreeding depression and probability of catastrophes, and suggests that inbreeding depression is important in small population sizes, whereas the effects of catastrophes were significant only for large populations. Although the model indicates that some populations will suffer from demographic and/or genetic stochasticity, the reserve network of Rio de Janeiro state will likely keep M. travassosi's populations for the next 100 years.     

Estimating Minimum Area of Suitable Habitat and Viable Population Size for the Northern Muriqui (Brachyteles hypoxanthus)

A population viability analysis (PVA) using the computer package VORTEX was conducted to assess the minimum viable population (MVP) of the Atlantic Forest endemic primate Brachyteles hypoxanthus. The objectives were: (1) to estimate demographic and genetic MVPs that could be used as quasi-extinction thresholds for future modeling, and (2) to estimate the minimum area of suitable habitat (MASH). The model predicted that populations of 40 and 700 individuals were necessary to achieve demographic and genetic stability, respectively. The model was more sensitive to changes in inbreeding depression, sex ratio and reproduction (percentage of breeding females). MASH estimated to contain genetically viable populations reached 11,570 ha. Muriquis have managed to persist despite severe habitat disturbance, but the results suggest that although most of the extant populations are not threatened by extinction, they are too small to be genetically viable in the long-run, and will loose most of their heterozygosity.     

Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes

Many natural populations fluctuate widely in population size. This is predicted to reduce effective population size, genetic variation, and reproductive fitness, and to increase inbreeding. The effects of fluctuating population size were examined in small populations of Drosophila melanogaster of the same average size, but maintained using either fluctuating ( FPS ) or equal ( EPS ) population sizes.FPS lines were maintained using seven pairs and one pair in alternate generations, and EPS lines with four pairs per generation. Ten replicates of each treatment were maintained. After eight generations, FPS had a higher inbreeding coefficient than EPS (0.60 vs. 0.38), a lower average allozyme heterozygosity (0.068 vs. 0.131), and a much lower relative fitness (0.03 vs. 0.25). Estimates of effective population sizes for FPS and EPS were 3.8 and 7.9 from pedigree inbreeding, and 4.9 vs. 7.1 from changes in average heterozygosities, as compared to theoretical expectations of 3.3 vs. 8.0. Results were generally in accordance with theoretical predictions. Management strategies for populations of rare and endangered species should aim to minimize population fluctuations over generations.     

Patterns of allozyme variation in relation to population size of the threatened plantMegaleranthis saniculifolia (Ranunculaceae) in Korea

Patterns of variation at 27 allozyme loci were investigated in the endangered endemic plantMegaleranthis saniculifolia. Levels of allozyme variation (A = 1.47,P = 40%,He = 0.088) were also compared with other endemic plant species. Genetic divergence between populations was very high (G ^st = 0.271 ), with moderate to high interpopulation differentiation, which probably arose through historical bottlenecks in a landscape of habitat fragmentation and/or human influence. The percentage of polymorphic loci, heterozygosity, and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles in the smaller populations. Individuals in the small and marginal populations (TB, KD, and CJ) showed higher proportions of fixed loci. These ecologically marginal populations were typically more distant from the nearest neighboring population and were more genetically distinct from one another. The genetic structure of the current population ofM. saniculifolia is probably the result of local extinctions of intervening populations. This, in turn, is due to the Pleistocene climatic change and increased habitat destruction. A positive association appears to exist between genetic diversity and population size. Although these small population sizes are more sensitive to stochastic events, securing a certain number of individuals from the three larger populations (SB, JB, and TG) could be accomplished as part of a conservation strategy. In addition, it is important to prioritize populations in different regions in order to limit population declines caused by large-scale environmental catastrophes.     

Relationship between population size, allozyme variation, and plant performance in the narrow endemic Cochlearia bavarica

We studied population viability in relation topopulation size and allelic variation in thenarrowly-endemic, monocarpic perennial plantCochlearia bavarica in Bavaria. In 1996,we analysed allelic variation by allozymeelectrophoresis in 24 populations ranging from8–2000 flowering individuals. Fitness-relatedcharacters were investigated in 22 of the 24populations in the field in 1996 (reproductiveand vegetative traits) and 1998 (reproductivetraits only). Differences in allozyme patternwere large between a south-eastern and awestern population group. Genetic diversity,assessed by the Shannon-Wiener diversity index,was low within but high among populations.Small populations had fewer alleles per locus,fewer polymorphic loci, lower observedheterozygosity, and lower genetic diversitythan large populations. Environmentalvariables were not significantly correlatedwith population size or fitness with theexception of light availability, indicatingthat habitat quality was similar for large andsmall populations. Population size showedpositive correlations with number of flowers,fruit set per plant, number of seeds per fruit,and total seed output per plant. Fruit set andnumber of seeds per fruit were positivelycorrelated with the observed heterozygosity andthe proportion of polymorphic loci. We usedpath analyses to study the possible causalrelationships among population size, allelicvariation, and reproductive characters. Thesemodels showed that allelic variation had nodirect influence on reproductive characters,whereas population size did. We conclude thatat present population size reduces viabilityand also reduces allelic variation; but thereduced allelic variation may in the longerterm have negative feed-backs on bothpopulation size and viability.     

Comparative losses of quantitative and molecular genetic variation in finite populations of Drosophila melanogaster

Quantitative genetic variation, the main determinant of the ability to evolve, is expected to be lost in small populations, but there are limited data on the effect, and controversy as to whether it is similar to that for near neutral molecular variation. Genetic variation for abdominal and sternopleural bristle numbers and allozyme heterozygosity were estimated in 23 populations of Drosophila melanogaster maintained at effective population sizes of 25, 50, 100, 250 or 500 for 50 generations, as well as in 19 highly inbred populations and the wild outbred base population. Highly significant negative regressions of proportion of initial genetic variation retained on inbreeding due to finite population size were observed for both quantitative characters (b = -0.67 +/- 0.14 and -0.58 +/- 0.11) and allozyme heterozygosity (b = -0.79 +/- 0.10), and the regression coefficients did not differ significantly. Thus, quantitative genetic variation is being lost at a similar rate to molecular genetic variation. However, genetic variation for all traits was lost at rates significantly slower than predicted by neutral theory, most likely due to associative overdominance. Positive, but relatively low correlations were found among the different measures of genetic variation, but their low magnitudes were attributed to large sampling errors, rather than differences in the underlying processes of loss.     

How do reproductive skew and founder group size affect genetic diversity in reintroduced populations?

Reduced genetic diversity can result in short-term decreases in fitness and reduced adaptive potential, which may lead to an increased extinction risk. Therefore, maintaining genetic variation is important for the short- and long-term success of reintroduced populations. Here, we evaluate how founder group size and variance in male reproductive success influence the long-term maintenance of genetic diversity after reintroduction. We used microsatellite data to quantify the loss of heterozygosity and allelic diversity in the founder groups from three reintroductions of tuatara ( Sphenodon ), the sole living representatives of the reptilian order Rhynchocephalia. We then estimated the maintenance of genetic diversity over 400 years (∼10 generations) using population viability analyses. Reproduction of tuatara is highly skewed, with as few as 30% of males mating across years. Predicted losses of heterozygosity over 10 generations were low (1–14%), and populations founded with more animals retained a greater proportion of the heterozygosity and allelic diversity of their source populations and founder groups. Greater male reproductive skew led to greater predicted losses of genetic diversity over 10 generations, but only accelerated the loss of genetic diversity at small population size (<250 animals). A reduction in reproductive skew at low density may facilitate the maintenance of genetic diversity in small reintroduced populations. If reproductive skew is high and density-independent, larger founder groups could be released to achieve genetic goals for management.     

Genetic differentiation of pink salmon oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 allozyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd- and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation over the allozyme loci, per broodline, were on average 0.43% (GST), while over the microsatellite loci it was 0.26% (the theta(ST) coefficient, F-statistics based on the allele frequency variance), and 0.90% (the rho(ST) coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of Southern Sakhalin Island. Multivariate scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of theta(ST) values were substantially lower than in terms of rho(ST) values. Regional genetic differentiation, mostly expressed at the allozyme loci among the populations from the northern and southern parts of the Sea of Okhotsk (i.e., between the Sakhalin and Kuril populations), was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity,of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the genetic migration coefficient inferred from the "private" allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization and colonization of the range.     

朱鹮(Nipponia nippon)种群生存力分析

到目前为止,只有一个野生朱鹮群体幸存下来,而且它的种群大小自1981年重新发现以来,一直在20只以下波动。本文应用种群生存力分析的方法,借助漩涡模型,根据朱鹮14年的种群数据,总结和预测了其种群动态,并着重研究了朱鹮的濒危程度。结果显示,按过去10余年的生存状况,朱鹮在50年内绝灭的可能性是98.5%,平均绝灭时间为15.72 年。现存种群数量很低,所以种群统计随机性对其命运有很大影响。灵敏度分析表明,当前的朱鹮种群对意外死亡和生存环境的波动较为敏感。保护工作的优先项目是对猎杀和天敌的控制以及从各个方面提高朱鹮的生活质量。     

朱■（Nipponianippon）种群生存力分析

到目前为止,只有一个野生朱群体幸存下来,而且它的种群大小自１９８１年重新发现以来,一直在２０只以下波动。本文应用种群生存力分析的方法,借助漩涡模型,根据朱１４年的种群数据,总结和预测了其种群动态,并着重研究了朱的濒危程度。结果显示,按过去１０余年的生存状况,朱在５０年内绝灭的可能性是９８．５％,平均绝灭时间为１５．７２年。现存种群数量很低,所以种群统计随机性对其命运有很大影响。灵敏度分析表明,当前的朱种群对意外死亡和生存环境的波动较为敏感。保护工作的优先项目是对猎杀和天敌的控制以及从各个方面提高朱的生活质量     

Extremely low levels of genetic diversity in the terrestrial orchid Epipactis thunbergii (Orchidaceae) in South Korea: implications for conservation

Levels of allozyme variation, population genetic structure, and fine-scale genetic structure (FSGS) of the rare, both sexually and clonally reproducing terrestrial orchid Epipactis thunbergii were examined for eight ( N  = 734) populations in a 20 × 20-km area in South Korea. Twenty-three putative allozyme loci resolved from 15 enzyme systems were used. Extremely low levels of allozyme variation were found within populations: the mean frequency of polymorphic loci was 3.8% [isocitrate dehydrogenase ( Idh-2 ) with two alleles was polymorphic across populations], the mean number of alleles per locus was 1.04, and the mean expected heterozygosity was 0.013. The overall fixation index was not significantly different from zero ( F _IS = 0.069), although the species is self-compatible. However, a significantly high degree of population differentiation was found between populations at Idh-2 ( F _ST = 0.388) in the studied area. Furthermore, spatial autocorrelation analyses revealed a significant FSGS (up to 3 m) within populations. These observations suggest that the main explanatory factors for the extremely low levels of genetic diversity and the shaping of the population genetic structure of E. thunbergii are genetic drift as a result of a small effective population size, a restricted gene flow, and the isolation of populations. Considering the current genetic structure of E. thunbergii , three guidelines are suggested for the development of conservation strategies for the species in South Korea: (1) protection of habitats of standing populations; (2) prohibition by law of any collection of E. thunbergii ; and (3) protection of nearby pollinator populations, given the fact that fruit set in natural habitats is very low.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 161–169.     

A morphologic and genetic analysis of Littorina saxatilis (Prosobranchia) from Venice, and on the problem of saxatilis—rudis nomenclature

Shell morphology and allozyme patterns of 17 enzymes are analysed within the isolated population of L. saxatilis Olivi (1792) from Venice, the type locality of the species. The shell morphology is compared to three different L. saxatilis phenotypes from Sweden, and showed to be similar to the brackish water 'tenebrosa' type. The Venice population is genetically more distant from British and Swedish populations than are the latter from each other. Less variability (heterozygosity) within the Venice compared to the Atlantic populations is probably a consequence of random genetic drift during a period of small population size.
The nomenclature of L. saxatilis in the Atlantic is discussed and it is suggested that until the exact taxonomic relationship between the Mediterranean and the Atlantic populations has been confirmed by, for example, cross-breeding experiments, the name 'saxatilis' should be kept for the non-Venetian populations (described by Maton (1797) under the name 'rudis').     

Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution,Population Size and Extinction Risk

The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km². During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation.     

Context-Dependent Survival Differences among Electrophoretic Genotypes in Natural Populations of the Marine Bivalve Spisula Ovalis

We investigated the relationships between allozyme genotypes at nine polymorphic loci and survival in a natural population of the bivalve Spisula ovalis sampled on three occasions (1993, 1994, and 1995) in three different sites (2855 individuals analyzed). This species displays annual growth lines allowing identification of annual cohorts. Therefore we could avoid cohort mixing, a frequent bias in such studies, and evaluate the consistency of the observed effects across cohorts and sites. Significant viability differences were observed both among alleles and between heterozygotes and homozygotes at some loci. Multiple-locus heterozygosity was positively correlated with viability in the 1993-1994 period, but not in the 1994-1995 interval. The observed selective effects were significantly dependent on the cohort and the site considered. A bibliographic survey suggests that such variability is a common feature of studies analyzing heterozygosity-survival relationships. Two explanations are consistent with our results. First, allozyme genotypes may have direct effects on viability that interact with subtle environmental variation in a complex and unpredictable way. Second, allozyme genotypes may be transiently associated with other viability genes responsible for heterotic effects. In any case, the results militate against allozyme loci being themselves consistently overdominant for viability in natural populations.     

Demographic Genetics of Brown Trout (Salmo Trutta) and Estimation of Effective Population Size from Temporal Change of Allele Frequencies

We studied temporal allele frequency shifts over 15 years and estimated the genetically effective size of four natural populations of brown trout (Salmo trutta L.) on the basis of the variation at 14 polymorphic allozyme loci. The allele frequency differences between consecutive cohorts were significant in all four populations. There were no indications of natural selection, and we conclude that random genetic drift is the most likely cause of temporal allele frequency shifts at the loci examined. Effective population sizes were estimated from observed allele frequency shifts among cohorts, taking into consideration the demographic characteristics of each population. The estimated effective sizes of the four populations range from 52 to 480 individuals, and we conclude that the effective size of natural brown trout populations may differ considerably among lakes that are similar in size and other apparent characteristics. In spite of their different effective sizes all four populations have similar levels of genetic variation (average heterozygosity) indicating that excessive loss of genetic variability has been retarded, most likely because of gene flow among neighboring populations.     

EFFECTS OF POPULATION BOTTLENECKS ON GENETIC DIVERSITY AS MEASURED BY ALLOZYME ELECTROPHORESIS

Low levels of allozyme heterozygosity in populations are often attributed to previous population bottlenecks; however, few experiments have examined the relationship between heterozygosity and bottlenecks under natural conditions. The composition and number of founders of 55 experimental populations of the eastern mosquitofish (Gambusia holbrooki), maintained under simulated field conditions, were manipulated to examine the effects of bottlenecks on three components of allozyme diversity. Correlations between observed and expected values of allozyme heterozygosity, proportions of polymorphic loci, and numbers of alleles per locus were 0.423, 0.602, and 0.772, respectively. The numbers of polymorphic loci and of alleles per locus were more sensitive indicators of differences in genetic diversity between the pre-bottleneck and post-bottleneck populations than was multiple-locus heterozygosity. In many populations, single- and multiple-locus heterozygosity actually increased as a result of the founder event. The weak relationship between a population's heterozygosity and the number and composition of its founders resulted from an increase in the variance of heterozygosity due to drift of allele frequencies. There was little evidence that selection influenced the loss of allozyme variation. When it is not possible to estimate heterozygosity at a large number of polymorphic loci, allozyme surveys attempting to detect founder events and other types of bottlenecks should focus on levels of locus polymorphism and allelic diversity rather than on heterozygosity.