Genetic Variation and the Immune Response in Natural Populations of Pocket Gophers

It is thought that genetic variation can affect the persistence of a population through its influence on disease susceptibility. We assessed genome-wide genetic variation, variation at a locus involved in the immune system, and acceptance or rejection of skin grafts in three natural populations of the pocket gopher ( Thomomys bottae ). Multilocus DNA fingerprints confirmed previous allozyme data, revealing high levels of variation among Hastings Reserve pocket gophers and almost complete within-population identity for individuals from the two Patricks Point populations (Patricks J and Patricks F), although Patricks J animals were dissimilar to animals from Patricks F despite their proximity. Individuals from the high-variation population consistently rejected within-population reciprocal skin grafts, whereas Patricks J and Patricks F individuals accepted within-population grafts. Patricks J and Patricks F individuals were found to be immunocompetent, however, as revealed by the ability of all individuals to reject between-population grafts, including those that previously accepted within-population grafts. A DNA heteroduplex analysis was then used to directly characterize variability at DQα, a locus of the immune system's major histocompatability complex. Both populations low in genetic variation were fixed for unique DQα alleles, whereas observed heterozygosity in the Hastings population was 0.43, ascribable to at least three unique alleles. These data are in accord with previous cheetah skin-graft results and confirm that skin grafts can be used to assess genetic similarity. We suggest that although many animal populations can persist with extremely low levels of genetic variation in the wild, such populations may be at a greater risk of extinction from particular pathogens because of their genetic uniformity.     

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.     

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.     

Experimental Tests of Captive Breeding for Endangered Species

Abstract: Several captive breeding regimes were compared for their ability to maintain fitness ( larval viability) and genetic variation in small populations of the housefly ( Musca domestica L.). Populations were either maintained at constant sizes of 40, 200, or 2000 individuals or initiated with two pairs of flies and allowed to grow to 40 individuals ( low-founder-number populations). Low-founder-number populations without migration exhibited low larval viability (22%) after 24 generations, compared to larger populations maintained at either 200 (49%) or 2000 (69%) individuals, and suffered high extinction, with only 44% of the lines surviving 24 generations. Low-founder-number populations subjected to two additional founder ( bottleneck) episodes, reducing them to two pairs of flies, suffered little additional loss in fitness or extinction compared to the single-founder treatments. Migration as low as one individual per generation (2.5% migration) significantly offset both reduced fitness and rate of extinction. Conversely, fitness was not significantly increased for low-founder-number populations when founders were selected from the top performing 20% of pairs under full-sib mating. Populations maintained at 40 individuals were not sustainable, exhibiting low larval viability (35%) and a high extinction rate (40%) over 24 generations, similar to the extinction rates for populations initiated with only four founders. Although none of the populations maintained at 200 individuals went extinct, their fitness was reduced by 20% compared to a large control population maintained at 2000 individuals. Electrophoretic variation was significantly correlated with fitness across treatments, but the correlation of fitness to narrow-sense heritability of two morphometric traits was not significant.     

Conservation Genetics of the Endangered Isle Royale Gray Wolf

Abstract. The small group of wolves on Isle Royale has been studied for over three decades as a model of the relationship between large carnivores and their prey. During the last ten years the population declined from 50 individuals to as few as 12 individuals. The causes of this decline may be food shortages, disease, or reduced genetic variability. We address the issues of genetic variability and relationships of Isle Royale wolves using allozyme electrophoresis, mtDNA restriction-site analysis, and multilocus hypervariable minisatellite DNA analysis (genetic fingerprinting). Our results indicate that approximately 50% of the allozyme heterozygosity has been lost in the island population, a decline similar to that expected if no immigration had occurred from the mainland. The genetic fingerprinting data indicate that the seven sampled Isle Royale wolves are as similar as captive populations of siblings. Surprisingly, the Isle Royale wolves have an mDNA genotype that is very rare on the mainland, being found in only one of 144 mainland wolves ThFF suggests that the remaining Isle Royale wolves areprobably derived from a single female founder     

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.     

Genetic structure of crown-of-thorns starfish (Acanthaster planci ) on the Great Barrier Reef, Australia: comparison of two sets of outbreak populations occurring ten years apart

Six populations of the crown-of-thorns starfish, Acanthaster planci, showing large increases in population size in 1994 to 1995, were examined by allozyme electrophoresis of 100 to 300 individuals collected from each population in November 1995 to February 1996. Analysis of nine loci, used to determine the structure of outbreak populations in the early-mid-1980s, demonstrated no significant differentiation among the 1996 outbreak populations in any age class (2 to 6 yr old). No significant variation was detected between age classes in any of the six populations. These data are consistent with the recent outbreak populations having been derived from one genetic source, and suggest no change in the source of recruits to these reefs between 1989/1990 to 1994/1995. In a multi-dimensional scaling analysis, the 1996 samples clustered with the eight 1986 outbreak populations in a small part of the genetic space spanned by the 1986 non-outbreak populations, suggesting that the outbreak populations were derived from the same genetic source in both 1986 and 1996. Statistically significant, but small, differences in gene frequencies detected between the 1986 and 1996 outbreak populations are thought to result from genetic drift, but are unlikely to provide a means of distinguishing sets of outbreak populations because of the large sample sizes required to detect the small shifts in gene frequency. Received: 21 March 1997 / Accepted: 2 April 1997     

利用RAPD标记分析卧龙自然保护区不同海拔沙棘种群的遗传变异

从1800m到3400m五个海拔连续取样,用RAPD分子标记研究了卧龙自然保护区中国沙棘种群的遗传结构和遗传变异.用11条寡核苷酸引物,扩增得到151个重复性好的位点,其中143个多态位点,多态率达94.7%.在5个沙棘种群中,总遗传多样性值(HT)为0.289,B种群内的遗传多样性值为0.315,这完全符合沙棘这种多年生、远交的木本植物高遗传变异的特性.5个种群内遗传多样性随海拔升高呈低—高—低变异趋势,在2200m海拔处的B种群遗传多样性达最大值0.315,3400m海拔处的E种群则表现最小,仅0.098.5个种群间的遗传分化值GST=0.406,也即是说有40.6%的遗传变异存在于种群间,59.4%存在种群内.1800m海拔处的A种群与其他种群的明显分离是造成种群间遗传分化大的原因.UPGMA聚类图和PCoA散点图分别进一步确证了5个种群间关系和所有个体间的关系.最后,经过Mantel检测,遗传距离与海拔表现了明显的相关性(r=0.646,P=0.011).     

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations.     

Genetic consequences of long larval life in the starfish Linckia laevigata (Echinodermata: Asteroidea) on the Great Barrier Reef

Gene flow between populations of the asteroid Linckia laevigata (Linnaeus) was investigated by examining over 1000 individuals collected from ten reefs throughout the Great Barrier Reef (GBR), Australia, for genetic variation at seven polymorphic enzyme loci. Despite geographic separations in excess of 1000 km, Nei's unbiased genetic distance (0 to 0.003) and standardised genetic variation between populations (F _ST) values (mean 0.0011) were small and not significant. Genetic homogeneity among L. laevigata populations is consistent with the long-distance dispersal capability of its 28 d planktonic larval phase, and is greater than that observed for other asteroid species, including another high-dispersal species, Acanthaster planci, which has a 14 d larval phase. Variation within populations was also higher than previously recorded for asteroids (mean heterozygosity=0.384; number of alleles per locus ranged from 5.1 to 6.0 in each population). Among asteroids, dispersal ability is positively correlated with gene flow and levels of variation, and negatively correlated with levels of differentiation.     

Genetics, Taxonomy, and Conservation of the Threatened California Gnatcatcher

Abstract: The California Gnatcatcher (   Polioptila californica ) has become a flagship species in the dispute over development of southern California's unique coastal sage scrub habitat, a fragile, geographically restricted ecosystem with high endemism. One aspect of the controversy concerns the status of the subspecies of this bird in southern California coastal sage scrub that is currently listed as threatened under the U.S. Endangered Species Act. To investigate the recent population history of this species and the genetic distinctiveness of subspecies and to inform conservation planning, we used direct sequencing of mitochondrial DNA (mtDNA) for 64 individuals from 13 samples taken throughout the species' range. We found that coastal sage scrub populations of California Gnatcatchers are not genetically distinct from populations in Baja California, which are dense and continuously distributed throughout the peninsula. Rather, mtDNA sequences from this species contain the signatures of population growth and support a hypothesis of recent expansion of populations from a southern Baja California refugium northward into the southern coastal regions of California. During this expansion, stochastic events led to a reduction in genetic variation in the newly occupied range. Thus, preservation of coastal sage scrub cannot be linked to maintaining the genetic diversity of northern gnatcatcher populations, despite previous recognition of subspecies. Our study suggests that not all currently recognized subspecies are equivalent to evolutionarily significant units and illustrates the danger of focusing conservation efforts for threatened habitats on a single species.     

Post-Perturbation Genetic Changes in Populations of Endangered Virgin River Chubs

A 34-kilometer reach of the Virgin River, Utah-Arizona-Nevada, was poisoned with rotenone in an attempt to eradicate non-native red shiners ( Cyprinella lutrensis ), a species implicated in the decline of native fish populations in the American West. An error in detoxification resulted in lethal concentrations of piscicide passing through an additional 50 kilometers of stream. We used allozyme electrophoresis to analyze genetic variation among pre- and post-poison samples of endangered Virgin River chubs ( Gila seminuda ). Pre-poison samples indicated a single panmictic population in the river. In contrast, fish subsequently produced through natural recruitment in poisoned reaches exhibited deviations from the original pattern of genetic variation. A genetic bottleneck caused by severe reduction in the number of spawning adults was indicated. The altered pattern persisted 2.5 years post-poisoning, indicating unexpectedly slow recolonization from the unpoisoned reach upstream. Genetic variation among hatchery-produced young was similarly unrepresentative of the original pattern because of the small number of brood fish used in propagation. Because of their small numbers and/or restricted distribution, endangered species are particularly vulnerable to natural or anthropogenic catastrophes. Assessment of the genetic impact of such events is essential but requires that baseline data are available.     

Conservation Genetics of the Black Rhinoceros (Diceros bicornis), I: Evidence from the Mitochondrial DNA of Three Populations

Abstract: A drastic decline in the number of black rhinoceroses ( Diceros bicornis ), primarily as a result of poaching places this species in imminent danger of extinction. The remaining black rhinos are divided into small, isolated populations that are vulnerable to demographic extinction, disease epidemics, genetic drift and inbreeding. Some conservationists have suggested minimizing these threats by moving as many animals as possible from different isolated populations to a few safe "rhino sanctuaries." To examine the possible long-term genetic consequences of such a strategy, we focused our efforts on determining the level of genetic differences among the remaining black rhino populations by examining restriction fragment length polymorphisms of the rapidly evolving mitochondrial DNA molecule. The 23 black rhinos in our survey, including animals from three geographic regions and two named subspecies, showed very little mitochondrial DNA differentiation. Only 4 out of 18 restriction enzymes revealed any mtDNA polymorphism, and the average estimated percent sequence divergence between the four mtDNA genotypes observed as 0.17%. Mitochondrial DNA divergence between the two named subspecies, D. b. minor and D. b. michaeli , was estimated to be only 0.29%. These results indicate a very close genetic relationship among the black rhinos in our survey. Thus, the mitochondrial DNA data suggest that within national boundaries, the black rhino populations we sampled may be considered single populations for breeding purposes, which might increase the species' probability of survival.     

Gene Flow and Genetic Restoration: The Florida Panther as a Case Study

Populations of some endangered species have become so small that they have lost genetic variation and appear to have become fixed for deleterious genetic variants. To avoid extinction from this genetic deterioration individuals from related subspecies or populations may have to be introduced for genetic restoration i.e., elimination of deleterious variants and recovery to a normal level of genetic variation. I construct a general population genetics framework from which to evaluate the potential for genetic restoration, and I discuss its specific application to the Florida panther. The translocation of Texas cougars into the free-ranging Florida panther population has been recommended to genetically restore the Florida panther, a subspecies of Felis concolor that appears to have both a low level of genetic variation and low fitness. Specific recommendations recently given by a scientific panel are to introduce enough animals so that there is approximately 20% gene flow in the first generation of translocation and approximately 2–4% in the generations thereafter. I evaluated these recommendations in a theoretical population genetics framework and found that they should result in the removal of most detrimental genetic variation and an increase in the standing genetic variation without a high probability of loss of any adaptive Florida panther alleles. Unless the population of the free-ranging Florida panthers is very small, the planned translocation should result in genetic restoration of the Florida panther.     

Measurement of Genetic Variation in Endangered Populations: Bandicoots (Marsupialia: Peramelidae) as an Example

Abstract. Attempts to monitor the genetic variation of endangered populations by the use of blood protein electrophoresis often suffer from three drawbacks: a small sample of loci, lack of control populations with "normal" variation, and, sometimes, difficulty in confirming inheritance of electromorphs.
An endangered isolate (Hamilton, Victoria) of the eastern barred bandicoot, Perameles gunnii, was compared with a widespread, dense, conspecific population in Tasmania. A previous study of the effective size of the siolate suggested that the loss of variation should be detectable by protein electrophoresis if average heterozygosity () was approximately 0.057 in widespread, dense populations and 20 to 50 individuals from each population were analysed for 25 or more loci. However, no genetic variation was detected within or between samples.
Similar studies proposed as a baseline for monitioring genetic variation could be equally powerless to detect changes in variation, even with quite high values. The analysis of variation in DNA is expected to avoid many of the problems associated with blood protein studies.
This study highlights the importance of a control population. Analysis of the Hamilton population alone might have led us to concludce that the recent population crash has been responsible for the low variation; however, this conclusion is not warranted, because = 0 in the much larger Tasmania population.     

DNA Fingerprinting Reveals a Lack of Genetic Variation in Northern Populations of the Western Pond Turtle (Clemmys marmorata)

I used DNA fingerprinting to provide the first analysis of the genetic composition of western pond turtle ( Clemmys marmorata ) populations in Washington, Oregon, and California. Populations of the western pond turtle in Washington and northern Oregon are rapidly approaching extinction. Genetic similarity within the largest northern populations, which are located inland, is high. An analysis of population substructure (F_st) revealed significant genetic divergence between inland populations, indicating a lack of dispersal and gene flow between sites. In contrast, northern coastal sites are not genetically distinct, but there are few if any viable populations remaining in this region. Genetic variability within southern California populations is a great deal higher than in northern inland sites. Similarly, a low F_st value indicated a lack of genetic differentiation between southern sites. An inter-regional analysis of population substructure (F_st = 0.24) revealed a significant degree of genetic divergence between geographical regions throughout the range. In addition, an estimate of western pond turtle phylogeny showed a genetic break in the species between northern and southern populations. Both population subdivision and phylogenetic analyses suggest a lack of appreciable gene flow between geographical regions for a considerable period of time. Genetic analyses support traditional subdivision based solely on the morphological variation of Clemmys marmorata into two subspecies: northern Clemmys marmorata marmorata and southern Clemmys marmorata pallida . Recovery of dwindling northern populations must combine demographic and genetic considerations. A first step should be to preserve local gene pools while augmenting population numbers, with the goal of preventing the extinction of this genetically and morphologically distinct subspecies.     

Conservation and Distribution of Genetic Variation in a Polytypic Species, the Cutthroat Trout

Abstract: The cutthroat trout (Salmo clarki) presents a series of unusual and difficult problems in conservation biology. As many as 16 subspecies have been recognized in the recent literature. The genetic distance between subspecies based upon 46 enzyme loci ranges from that usually seen between congeneric species to virtual genetic identity. Subspecies from the western portion of the range of the cutthroat trout are genetically more similar to rainbow trout (Salmo gairdneri) than they are to the other subspecies of cutthroat trout. In addition, much of the genetic variation within the west-slope cutthroat trout (S. c. lewisi) results from alleles found in only one or two local populations, but they often occur at high frequencies in those populations. Thus, preserving the genetic variation in westslope cutthroat trout entails preserving as many local populations as possible.
Captive populations of cutthroat trout present a series of opportunities and genetic problems. A number of management agencies are using captive populations to supplement and reestablish natural populations. Basic genetic principles must be understood and followed in establishing and maintaining captive populations. We describe examples of unsuccessful and successful efforts by management agencies to develop captive populations.
The greatest danger to the conservation of the cutthroat trout is introgressive hybridization among subspecies and with rainbow trout. Several factors make salmonid fishes especially susceptible to problems associated with introgressive hybridization. We conclude that biochemical analysis provides a more reliable and informative means of detecting interbreeding than morphological characters. Interbreeding between westslope and Yellowstone cutthroat trout and nonnative Salmo appears to be common and widespread throughout the natural range of these subspecies.     

Genetic Diversity of Lepilemur mustelinus ruficaudatus, a Nocturnal Lemur of Madagascar

The genetic polymorphism of natural populations of Lepilemur mustelinus ruficaudatus was studied by protein electrophoresis. We sampled blood from 72 individuals from four populations separated by geographic or anthropogenic barriers from southwestern Madagascar. Six out of 22 enzyme loci showed genetic variation with a degree of polymorphism of 0.273. The expected and observed degree of genetic heterozygosity over all loci is similar to that of other primates (H_e = 0.058, H_o = 0.036). The F-statistics revealed that the four subpopulations were similar with respect to gene structure (F_ST = 0.065, p = 0.016), but the genotypic structures within subpopulations were inconsistent with random mating. For the total of the four subpopulations the proportion of heterozygous individuals was significantly smaller than expected under random mating (F_IS = 0.373, F_IT = 0.414, p < 0.01). These results correspond closely to what is expected considering the low migration ability of individuals of L. m ruficaudatus leading to small and rather isolated inbred populations.     

Genomic erosion in a demographically recovered bird species during conservation rescue

The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive-bred individuals were released into free-living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site-associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free-living population. However, further genetic rescue with captive-bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.     

Temporal Changes in Allele Frequencies and a Population's History of Severe Bottlenecks

Monitoring temporal changes in genetic variation has been suggested as a means of determining if a population has experienced a demographic bottleneck. Simulations have shown that the variance in allele frequencies over time ( F ) can provide reasonable estimates of effective population size ( N_e ). This relationship between F and N_e suggests that changes in allele frequencies may provide a way to determine the severity of recent demographic bottlenecks experienced by a population. We examined allozyme variation in experimental populations of the eastern mosquitofish ( Gambusia holbrooki ) to evaluate the relationship between the severity of demographic bottlenecks and temporal variation in allele frequencies. Estimates of F from both the fish populations and computer simulations were compared to expected rates of drift. We found that different methods for estimating F had little effect on the analysis. The variance in estimates of F was large among both experimental and simulated populations experiencing similar demographic bottlenecks. Temporal changes in allele frequencies suggested that the experimental populations had experienced bottlenecks, but there was no relationship between observed and expected values of F . Furthermore, genetic drift was likely to be underestimated in populations experiencing the most severe bottlenecks. The weak relationship between F and bottleneck severity is probably due to both sampling error associated with the number of polymorphic loci examined and the loss of alleles during the bottlenecks. For populations that may have experienced severe bottlenecks, caution should be used in making evolutionary interpretations or management recommendations based on temporal changes in allele frequencies.