Comparisons of Genetic Diversity in the Endangered Adenophora lobophylla and Its Widespread Congener, A. potaninii

Abstract: Starch-gel electrophoresis was used to examine the levels and distribution of genetic diversity in two Adenophora species: the narrow endangered Adenophora lobophylla and its widespread congener, A. potaninii . Based on allozyme variation at 18 putative loci, we measured high levels of genetic variability both in the endangered and the widespread species, with 83.3% of the loci being polymorphic. The mean expected heterozygosity within populations (   H _ep  ) and within species (   H _es  ) were 0.234 and 0.244 for A. potaninii and were as high as 0.210 and 0.211 for A. lobophylla . There was higher differentiation among populations in A. potaninii (   F _ST = 0.155) than in A. lobophylla (   F _ST = 0.071). The high levels of genetic diversity in the present allozyme survey are consistent with the morphological variation observed in these species and may be attributed to high outcrossing rates in the Adenophora species. In addition, A. lobophylla was identified as a distinct species on the basis of Nei's genetic distances and thus should be given a high priority for protection. It is noteworthy that the endangered A. lobophylla maintains much higher genetic diversity than most endemic or narrowly distributed plant species in spite of its restricted distribution. We hypothesize that A. lobophylla has become endangered for ecological and stochastic reasons, including habitat destruction or environmental changes, mud slides, and human disturbance such as grazing and mowing. Consequently, habitat protection is of particular importance for conserving this endangered species.     

Effects of the Interaction between Genetic Diversity and UV-B Radiation on Wood Frog Fitness

Abstract:  Genetic diversity may buffer amphibian populations against environmental vicissitudes. We hypothesized that wood frogs (  Rana sylvatica ) from populations with lower genetic diversity are more susceptible to ultraviolet-B (UV-B) radiation than those from populations with higher diversity. We used RAPD markers to obtain genetic diversity estimates for 12 wood frog populations. We reared larval wood frogs from these populations and exposed experimental groups of eggs and larvae to one of three treatments: unfiltered sunlight, sunlight filtered through a UV-B-blocking filter (Mylar), and sunlight filtered through a UV-B-transmitting filter (acetate). In groups exposed to UV-B, larval mortality and deformity rates increased significantly, but egg mortality did not. We found a significant negative relationship between genetic diversity and egg mortality, larval mortality, and deformity rates. Furthermore, the interaction between UV-B treatment and genetic diversity significantly affected larval mortality. Populations with low genetic diversity experienced higher larval mortality rates when exposed to UV-B than did populations with high genetic diversity. This is the first time an interaction between genetic diversity and an environmental stressor has been documented in amphibians. Differences in genetic diversity among populations, coupled with environmental stressors, may help explain patterns of amphibian decline.     

Temporal stability of genetic population structure in the New Zealand snapper, <Emphasis Type="Italic">Pagrus auratus</Emphasis>, and relationship to coastal currents

Genetic diversity and population structure of snapper (Pagrus auratus, Bloch and Schneider), a coastal demersal sparid fish, were determined using six nuclear microsatellite loci and SSCP (single strand conformational polymorphism) analysis of themitochondrial (mt) DNA D-loop in samples collected across the range of the species in New Zealand. Microsatellite data showed similar results to allozyme data collected in the late 1970s that found differentiation between the north-east and southern populations. In addition, an isolated population of snapper in Tasman Bay was identified. The two data sets provide evidence for the temporal stability of the genetic population structure of snapper over 22 years, with differentiation over relatively small spatial scales separated by oceanographic boundaries rather than isolation by distance. In contrast to nuclear markers, mtDNA did not reveal any significant genetic heterogeneity among samples.     

中国对虾两个不同地理种群遗传结构的RAPD分析

采用ＲＡＰＤ技术对中国对虾中国黄渤海沿岸种群（ＨＢ）和朝鲜半岛西海岸种群（ＰＫ）的遗传多样性进行检测。２０个随机引物（ＯＰＤ系列）在二个种群中都扩增出１４８条ＤＮＡ片段，其中多态性片段数分别为５４条和６５条，多态性片段的比例分别为３６．４９％和４３．９２％，种群的平均杂合度分别为０．１９８１和０．２３７５。实验表明，中国对虾朝鲜半岛西海岸种群的遗传多样性要比中国黄渤海沿岸种群高，但二个种群都处于较     

Experimental Demonstration of an Allee Effect in American Ginseng

Abstract: Harvesting of wild American ginseng (   Panax quinquefolius ) for the herbal trade has lowered natural population sizes. We tested for reproductive limitation due to small population size (a form of the Allee effect) by experimentally planting "natural" populations numbering 4, 16, and 64 using 4-year-old cultivated plants. Plant size traits and reproductive traits ( bud, flower, green fruit, and mature fruit) were recorded through the ensuing summer. Fruit production per flower and per plant increased in proportion to flowering population size (  p = 0.0063 and p = 0.0017, respectively), strongly suggesting that an Allee effect occurs in very small populations. The increase in fruit production was not explained by either plant or inflorescence size differences. Although population size-dependent pollination, through insufficient pollinator visitation rate or pollen transfer rate, seems the most likely cause of the observed effects, our limited observations of pollinators were not sufficient to demonstrate a change in pollination rates as a function of population size. Knowledge of the presence as well as the mechanism underlying this Allee effect may be especially useful for management and determination of minimum viable population size of the species in the wild.     

Acclimation of the European sea bass to freshwater: monitoring genetic changes by RAPD polymerase chain reaction to detect DNA polymorphisms

We investigated the use of the polymerase chain reaction (PCR) and the associated random amplification of polymorphic DNA (RAPD) technique to study variation in samples of the sea bass, Dicentrarchus labrax, before and after acclimation to freshwater. Acclimation trials were repeated twice, in 1989 and 1990, for two samples originating from the same broodstock (individuals from different localities along the Italian coasts), with overall mortality rates averaging 94 and 75% in the 2 yr, respectively. Analyses are based on 126 polymorphic RAPD markers, scored in at least 39 individuals for each of the starting and acclimated samples in both years. Analysis of RAPD patterns revealed high levels of DNA polymorphism in both 1989 and 1990 starting samples. The acclimated samples maintained similar polymorphism levels. Shifts in marker frequencies between starting and acclimated samples occurred in both years. A correspondence analysis carried out on multimarker individual profiles suggests that the two starting samples resulted from uneven sampling of the same heterogenous broodstock. This analysis clearly separates RAPD phenotypes from starting and acclimated samples in both years and identifies the RAPD markers responsible for such displacement. Patterns of RAPD variation are compared with previous allozymic studies carried out on the same samples. A major difference between the two studies was the number of markers available. Fewer allozyme loci were studied than were RAPD markers. The cause of repeated shifts for allozyme alleles in replicate experiments were almost certainly due to selection, while statistical chance could explain the repeated shift of only one out of more than 100 RAPD markers. We have shown that RAPD analysis, if carried out carefully, is quite reproducible and sensitive enough to reveal high levels of variation among individuals from the same broodstock. A major drawback of this approach is the still unclear inheritance patterns of RAPD polymorphisms. The use of multivariate analyses is suggested as a possible alternative to traditional population genetics techniques to analyze patterns of variation in the absence of a precise genetic interpretation.     

Developing a Sampling Strategy for Baptisia arachnifera Based on Allozyme Diversity

We analyzed the amount and distribution of genetic variation in Baptisia arachnifera Duncan to develop a sampling strategy for ex situ research. Baptisia arachnifera is an endangered plant species endemic to the coastal plain of Georgia (U.S.) where all populations are within 16 km of each other. A reduction in numbers of individuals has been observed during the last 50 years. Baptisia arachnifera was polymorphic at 24% of the 37 loci examined with an average of 1.32 alleles per locus. The genetic diversity index was relatively low ( H_e = 0.097) as expected for endemic species. Populations were in Hardy-Weinberg equilibrium, suggesting that the species is outcrossing. Consistent with this conclusion is the observation that the majority (approximately 90%) of the genetic variation present in the species is found within individual populations. Indirect evidence of gene flow between populations was detected (   Nm = 2.35). The close proximity of the populations and the recent reduction in population sizes suggest that the populations surveyed may be fragments of a once more continuous gene pool. Based on the observed distribution of genetic diversity among populations (G_ST = 0.096), sampling two populations would capture 99% of the allozyme diversity surveyed. Allozyme data were used to determine which 2 of the 10 populations surveyed should be sampled to maximize the ex situ conservation of genetic diversity. Although the paper-producing companies that own most of the land where Baptisia arachnifera occurs are modifying their harvesting techniques, the species could become extinct without more effective management and preservation efforts.     

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.     

Genetic structure and allozyme variation of sea bass (Dicentrarchus labrax and D. punctatus) in the Mediterranean Sea

This paper reports data on 28 allozyme loci in wild and artificially reared sea bass (Dicentrarchus labrax) samples, originating from either coastal lagoon or marine sites in the Mediterranean Sea. F _ST analysis (θ estimator) indicated strong genetic structuring among populations; around 34% of the overall genetic variation is due to interpopulation variation. Pairwise θ estimates showed that, on average, the degree of genetic structuring was much higher between marine populations than between samples from lagoons. Six polymorphic loci showed differences in allele frequencies between marine and lagoon samples. Multivariate analyses of individual allozymic profiles and of allele frequencies suggested that different arrays of genotypes prevail in lagoons compared to marine samples, particularly at those loci that, on the basis of previous acclimation experiments, had been implicated in adaptation to freshwater. On the other hand, variation at “neutral” allozyme loci reflects to a greater extent the geographic location of populations. Allozyme differentiation was also studied in a D. labrax population from the Portuguese coast. Average genetic distance between this population and the Mediterranean populations was quite high (Nei's D = 0.236) and calls into question the taxonomic status of the Portuguese population. Finally, genetic relationships between D. labrax and D. punctatus were evaluated. Average Nei's D was 0.648, revealing high genetic differentiation between the two species, even for two sympatric populations of these species in Egypt; thus gene flow was not indicated between species. Received: 24 October 1996 / Accepted: 27 November 1996     

Genetic Structure of Fragmented Populations of the Endangered Daisy Rutidosis leptorrhynchoides

Abstract: The endangered grassland daisy Rutidosis leptorrhynchoides has been subject to severe habitat destruction and fragmentation over the past century. Using allozyme markers, we examined the genetic diversity and structure of 16 fragmented populations. The species had high genetic variation compared to other plant species, and both polymorphism and allelic richness showed strong positive relationships with log reproductive population size, reflecting a loss of rare alleles (frequency of q < 0.1) in smaller populations. Fixation coefficients were positively related to size, due either to a lack of rare homozygotes in small populations or to Wahlund effects (owing to spatial genetic structure) in large ones. Neither gene diversity nor heterozygosity was related to population size, and other population parameters such as density, spatial contagion, and isolation had no apparent effect on genetic variation. Genetic divergence among populations was low , despite a large north-to-south break in the species' current distribution. To preserve maximum genetic variation, conservation strategies should aim to maintain the five populations larger than 5000 reproductive plants, all of which occur in the north of the range, as well as the largest southern population of 626 plants at Truganina. Only one of these is currently under formal protection. High heterozygosity in smaller populations suggests that they are unlikely to be suffering from inbreeding depression and so are also valuable for conservation. Erosion of allelic richness at self-incompatibility loci, however, may limit the reproductive capacity of populations numbering less than 20 flowering plants.     

Patterns of Genetic Diversity and Its Loss in Mammalian Populations

Abstract:  Policy aimed at conserving biodiversity has focused on species diversity. Loss of genetic diversity, however, can affect population persistence, evolutionary potential, and individual fitness. Although mammals are a well-studied taxonomic group, a comprehensive assessment of mammalian genetic diversity based on modern molecular markers is lacking. We examined published microsatellite data from populations of 108 mammalian species to evaluate background patterns of genetic variability across taxa and body masses. We tested for loss of genetic diversity at the population level by asking whether populations that experienced demographic threats exhibited lower levels of genetic diversity. We also evaluated the effect of ascertainment bias (a reduction in variability when microsatellite primers are transferred across species) on our assessment of genetic diversity. Heterozygosity did not vary with body mass across species ranging in size from shrews to whales. Differences across taxonomic groupings were noted at the highest level, between populations of marsupial and placental mammals. We documented consistently lower heterozygosity, however, in populations that had experienced demographic threats across a wide range of mammalian species. We also documented a significant ( p = 0.01) reduction in heterozygosity as a result of ascertainment bias. Our results suggest that populations of both rare and common mammals are currently losing genetic diversity and that conservation efforts focused above the population level may fail to protect the breadth of persisting genetic diversity. Conservation policy makers may need to focus their efforts below the species level to stem further losses of genetic resources.     

Application of random amplified polymorphic DNA (RAPD) markers to evaluate intraspecific genetic variation in red mullet (Mullus barbatus)

The random amplified polymorphic DNA (RAPD) technique was used to evaluate genetic affinities among eight red mullet (Mullus barbatus L., 1758) samples from the Mediterranean Sea. Twenty-nine random primers were used. Despite the variability which was found within samples, no specific RAPD marker for the discrimination of the populations was detected. The data analysis revealed that the genetic diversity among populations is positively related to their geographic distances. The results of this study indicate that the estimated intraspecific variation may be more␣pronounced with RAPD markers than with allozymes when the two approaches are applied on the same populations. Received: 7 November 1997 / Accepted: 30 May 1998     

Estimating the Density of Honeybee Colonies across Their Natural Range to Fill the Gap in Pollinator Decline Censuses

Abstract: Although pollinator declines are a global biodiversity threat, the demography of the western honeybee (Apis mellifera) has not been considered by conservationists because it is biased by the activity of beekeepers. To fill this gap in pollinator decline censuses and to provide a broad picture of the current status of honeybees across their natural range, we used microsatellite genetic markers to estimate colony densities and genetic diversity at different locations in Europe, Africa, and central Asia that had different patterns of land use. Genetic diversity and colony densities were highest in South Africa and lowest in Northern Europe and were correlated with mean annual temperature. Confounding factors not related to climate, however, are also likely to influence genetic diversity and colony densities in honeybee populations. Land use showed a significantly negative influence over genetic diversity and the density of honeybee colonies over all sampling locations. In Europe honeybees sampled in nature reserves had genetic diversity and colony densities similar to those sampled in agricultural landscapes, which suggests that the former are not wild but may have come from managed hives. Other results also support this idea: putative wild bees were rare in our European samples, and the mean estimated density of honeybee colonies on the continent closely resembled the reported mean number of managed hives. Current densities of European honeybee populations are in the same range as those found in the adverse climatic conditions of the Kalahari and Saharan deserts, which suggests that beekeeping activities do not compensate for the loss of wild colonies. Our findings highlight the importance of reconsidering the conservation status of honeybees in Europe and of regarding beekeeping not only as a profitable business for producing honey, but also as an essential component of biodiversity conservation.     

Shell shape variation in populations of Mytilus chilensis (Hupe 1854) from southern Chile: a geometric morphometric approach

The pattern of shell shape variation in populations of the mussel, Mytilus chilensis (Hupe 1854) from Southern Chile was analyzed as a function of sample origin (cultivated vs. wild) and latitude, using standard tools of geometric morphometrics for landmark data. Additionally, posterior adductor muscle index (PAMI), Freeman condition index and shell thickness were measured in each sample. Highly significant differences in shell shape components were found among mussel populations. These differences are related to the origin of samples (expansion of the posterior adductor muscle scar, elongation of the lateral ligament and of the ventral umbo position in non-cultivated samples) and to latitude (more elongated shells and more extended posterior adductor muscle scar in most southern samples when compared with the northernmost ones). PAMI and shell thickness were statistically higher in wild population, and Freeman condition index was higher in cultivated shells. It is suggested that in wild populations of M. chilensis, the mussels may face higher predator pressures and other environmental stress factors. Consequently, individuals may be using higher energy fraction to reinforce shells and to promote adductor muscle growth at the expense of somatic growth. In contrast, individuals found in calm aquaculture environments are relatively protected from predators and use most of their assimilated energy in somatic growth. In turn, this growth depends on changes that covariate with shell morphology.     

Reproductive Success of Captive-Bred Steelhead Trout in the Wild: Evaluation of Three Hatchery Programs in the Hood River

Abstract:  Population supplementation programs that release captive-bred offspring into the wild to boost the size of endangered populations are now in place for many species. The use of hatcheries for supplementing salmonid populations has become particularly popular. Nevertheless, whether such programs actually increase the size of wild populations remains unclear, and predictions that supplementation fish drag down the fitness of wild fish remain untested. To address these issues, we performed DNA-based parentage analyses on almost complete samples of anadromous steelhead ( Oncorhynchus mykiss ) in the Hood River in Oregon (U.S.A.). Steelhead from a supplementation hatchery (reared in a supplementation hatchery and then allowed to spawn naturally in the wild) had reproductive success indistinguishable from that of wild fish. In contrast, fish from a traditional hatchery (nonlocal origin, multiple generations in hatcheries) breeding in the same river showed significantly lower fitness than wild fish. In addition, crosses between wild fish and supplementation fish were as reproductively successful as those between wild parents. Thus, there was no sign that supplementation fish drag down the fitness of wild fish by breeding with them for a single generation. On the other hand, crosses between hatchery fish of either type (traditional or supplementation) were less fit than expected, suggesting a possible interaction effect. These are the first data to show that a supplementation program with native brood stock can provide a single-generation boost to the size of a natural steelhead population without obvious short-term fitness costs. The long-term effects of population supplementation remain untested.     

Hybridization between Wolves and Dogs

Concern has been expressed that European populations of gray wolves ( Canis lupus ) have extensively hybridized with domestic dogs ( C. familiaris ). We reviewed and analyzed surveys of mitochondrial and biparentally inherited genetic markers in dogs and wild populations of wolf-like canids. Although dog-wolf hybrids have been observed in the wild, significant introgression of dog markers into wild wolf populations has not yet occurred. Our investigation suggests that hybridization may not be an important conservation concern even in small, endangered wolf populations near human settlements. The behavioral and physiological differences between domestic dogs and gray wolves may be sufficiently great such that mating is unlikely and hybrid offspring rarely survive to reproduce in the wild.     

Genetic variation in Symbiodinium isolates from giant clams based on random-amplified-polymorphic DNA (RAPD) patterns

We have compared the random-amplified-polymorphic DNA (RAPD) patterns of Symbiodinium isolates from seven species of giant clams to investigate the large genetic variation that we previously reported for this group of dinoflagellate symbionts using allozyme analysis. Comparisons of 163 RAPD characters by unweighted pair-group arithmetic-average cluster analysis (UPGMA) corroborate our previous findings that giant clams associate with a large number of genetically distinguishable algal symbionts, and that the isolates from a single Tridacna gigas individual form a group of closely related algae. However, the overall topology of the UPGMA tree constructed from RAPD data differs from that of the previous allozyme data, indicating that the combined data we have collected to date are insufficient to accurately infer phylogenetic affiliations between the isolates studied. Comparisons of our data set with those published for strains of Gymnodinium catenatum, a toxic dinoflagellate with a sexual life stage, shows that our isolates are even more diverse. Algal isolates from giant clams have a level of RAPD variation comparable to organisms that are able to undergo sexual recombination. This study demonstrates the sensitivity of the RAPD technique in detecting genetic diversity in this group of algae, and highlights the need for more comparative data for the major clades of Symbiodinium. Received: 24 August 1999 / Accepted: 8 March 2000     

Nuclear and mtDNA lineage diversity in wild and cultured Pacific lion-paw scallop, Nodipecten subnodosus (Baja California Peninsula, Mexico)

Pacific lion-paw scallops were collected from natural aggregations in Laguna Ojo de Liebre (Pacific Ocean), the Gulf of California, and from aquaculture facilities for genetic diversity analyses. Mitochondrial DNA sequencing uncovered two highly supported clades separated by 2.5% divergence. Data from ten microsatellite markers suggest individuals from these mitogroups are introgressed, raising questions about the mitotype origin. Some evidence suggests gene flow between La Paz and Ojo de Liebre; otherwise the Gulf of California and Ojo de Liebre are acting as two distinct populations. It is unclear whether translocations between sites have influenced the observed genetic structure or whether gene flow has been facilitated by past geologic events. Finally, scallops spawned for aquaculture are unique from the wild and have significantly less diversity. These results warrant the attention of managers and producers who should work to monitor and conserve genetic diversity in both wild and aquaculture populations.     

Effects of habitat fragmentation on the genetic structure and connectivity of the black-lipped pearl oyster Pinctada margaritifera populations in French Polynesia

Habitat destruction leading to increased fragmentation is detrimental to species by reducing population size and genetic diversity and by restraining population connectivity. However, little is known about the effects of naturally fragmented habitats on wild populations, especially when it comes to marine benthic invertebrates with long pelagic larval duration. In this framework, we investigated the connectivity and genetic diversity variation among nine wild populations of the black-lipped pearl oyster, Pinctada margaritifera, throughout French Polynesia using ten microsatellite DNA markers. Despite the naturally fragmented habitat (South Pacific oceanic islands), we found high values of genetic diversity and population admixture, indicating connectivity at small and large spatial scales within sampled sites of the Tuamotu, and between the Society and Tuamotu Archipelagos. In the meantime, habitat geomorphology increased genetic drift in populations occurring in small, closed lagoons. Significant genetic structure not correlated to geographic distance was detected mainly between closed and open lagoons. The Marquesas Islands hosted the most divergent populations, likely a result of vicariance. Our results also highlight that migration patterns among lagoons are not symmetrical. Altogether, the general pattern of gene flow, nonsymmetrical migration rates among populations, absence of isolation by distance and absence of recent extinction events found in our study strongly suggest that P. margaritifera populations of French Polynesia follow an asymmetrical island model of dispersal.     

Use of Congeneric Assessment to Reveal the Linked Genetic Histories of Two Threatened Fishes in the Murray‐Darling Basin,Australia

Abstract: The intensely regulated Murray‐Darling Basin in southeastern Australia is the nation's most extensive and economically important river system, and it contains fragmented populations of numerous fish species. Among these is the Murray hardyhead (Craterocephalus fluviatilis), a species listed as endangered (International Union for Conservation of Nature Red List) in the mid‐1990s prior to its acute decline with the progression of a severe drought that began in 1997. We compared the genetic structure of Murray hardyhead with 4 congeneric species (Darling hardyhead[C. amniculus], Finke hardyhead[C. centralis], Lake Eyre hardyhead[C. eyresii], and unspecked hardyhead[C. stercusmuscarum]), selected on the basis of their taxonomic or biological similarity to Murray hardyhead, in order to affirm species boundaries and test for instances of introgressive hybridization, which may influence species ecology and conservation prospects. We used allozyme (52 loci) and mtDNA markers (1999 bp of ATPase and cytochrome b) to provide a comparative genetic assessment of 139 Murray hardyhead, which represented all extant and some recently extirpated populations, and 71 congeneric specimens from 12 populations. We confirmed that Murray hardyhead and Darling hardyhead are taxonomically distinct and identified a number of potential conservation units, defined with genetic criteria, in both species. We also found allozyme and mtDNA evidence of historic genetic exchange between these 2 allopatric species, apparently involving one population of each species at the geographic edge of the species’ ranges, not in the most proximate populations sampled. Our results provide information on species boundaries and offer insight into the likely causes of high genetic diversity in certain populations, results which are already being used to guide national recovery planning and local action. Given the prevalence of incorrect taxonomies and introgression in many organismal groups, we believe these data point to the need to commence genetic investigations of any threatened species from an initially broad taxonomic focus.