Genetic distinctness of isolated populations of an endangered marsupial, the mountain pygmy-possum, Burramys parvus

The mountain pygmy-possum, Burramys parvus, exists in isolated and fragmented populations in the Australian alps. To examine the degree of interpopulation divergence, mitochondrial cytochrome b and NADH dehydrogenase subunit 2 (NADH2) sequences were obtained from samples representing all populations of B. parvus. Three divergent mitochondrial DNA (mtDNA) lineages were identified which exhibited strong phylogeographical structure. This indicates the presence of three maternal clades corresponding to populations in the northern, central and southern Australian alps. Molecular clock estimates suggest that the mtDNA lineages diverged from one another 420-680 thousand years ago. On this basis it is argued that B. parvus populations have probably been isolated since the mid-Pleistocene, and that management should focus on maintaining viable B. parvus populations in each of the three regional localities.     

A method for validating stochastic models of population viability: a case study of the mountain pygmy-possum (Burramys parvus)

1.  A method of validating stochastic models of population viability is proposed, based on assessing the mean and variance of the predicted population size.
2.  The method is illustrated with a model of the population dynamics of the mountain pygmy-possum ( Burramys parvus Broom 1895), based on annual census data collected from a single population in the Snowy Mountains of New South Wales, Australia between 1986 and 1997. The model incorporates density-dependence in survivorship and recruitment, and demographic and environmental stochasticity.
3.  The model appeared to make reasonable predictions for the three populations that were used for validation, provided the equilibrium population size was estimated accurately. This may require that differences in habitat quality between populations be taken into account.
4.  Following validation, the model was given new parameters using the additional data from the three populations, and the risk of population decline within the next 100 years was assessed. Although populations as small as 15 females are predicted to be relatively safe from extinction caused by stochastic processes, B. parvus appears vulnerable to loss of habitat and reductions in the population growth rate.
5.  The approach used in this paper is one of few attempts to validate a model of population viability using field data, and demonstrates that some aspects of stochastic population models can be tested.     

Isolation and characterization of microsatellite loci from the Australian endemic mountain pygmy‐possum,Burramys parvus Broom

The endemic mountain pygmy‐possum, Burramys parvus, is an endangered Australian marsupial restricted to mainland alpine regions. Population structure, breeding system and gene flow are crucial for the development of effective conservation strategies, but have not been investigated in B. parvus. Here we have isolated eight polymorphic microsatellite markers from B. parvus to investigate these parameters. We found two to 12 alleles with observed heterozygosity values ranging from 0.321 to 0.878 for these loci in initial estimates from a single population.     

Ecology of natural hibernation in the marsupial mountain pygmy-possum (Burramys parvus)

The hibernating marsupial mountain pygmy-possum (Burramys parvus, 40 g) has to raise its slow-growing offspring during a short alpine summer. Only females provide parental care, while after mating males emigrate to marginal habitats often at lower altitudes which can sustain only low possum densities. We predicted that the hibernation strategies in mountain pygmy-possums are distinct from those of similar-sized placental hibernators, because of the developmental constraints in marsupials and because hibernation differs between the sexes. Using temperature-sensitive radio transmitters, we studied the hibernation patterns of free-living male and female mountain pygmy-possums living in a north- and a south-facing boulder field (Kosciusko National Park) for two consecutive winters. Individual possums commenced hibernation several months before the snow season. As in other hibernators, torpor in the mountain pygmy-possum was interrupted by periodic arousals which occurred most often during the late afternoon. Torpor bouts initially lasted a few days when the hibernacula temperature (T _hib) ranged from 4 to 7°C. As the hibernation season progressed, torpor bouts became longer and possum body temperatures (T _b) approached 2°C. The T _bs of females were significantly lower and torpor bouts were longer in the second half of the hibernation season than in males. Between torpor bouts, both sexes were often active and left hibernacula for periods of up to 5 days. Especially during the first months of the hibernation season, possums also frequently changed hibernacula sites probably in an attempt to select a site with a more suitable microclimate. Emergence from hibernation was closely coupled with the disappearance of snow from the possum habitat (September 1995, October 1996) and the limited fat stores probably dictate an opportunistic spring emergence. However, in 1995, spring was early and males emerged significantly earlier than females. In 1996, when snow melt was delayed, this difference vanished. Testes are regressed in males during hibernation and the time needed for testes growth and spermatogenesis favours an earlier emergence for males which was probably achieved by their preference for the more sun exposed north-facing boulder field. A sexual dimorphism in hibernation strategies and spring emergence therefore enables mountain pygmy-possums to cope with their harsh alpine environment. Received: 22 May 1997 / Accepted: 21 August 1997     

Occupancy of spoil dumps by the Mountain Pygmy‐possum Burramys parvus in Kosciuszko National Park

Summary The Mountain Pygmy‐possum Burramys parvus has been listed as an endangered species across its range in the alpine and subalpine areas of New South Wales and Victoria. This study reports on the occurrence of the species in an artificial habitat, spoil dumps that were created in the 1950s as a result of the construction of underground tunnels associated with the Snowy Hydro‐electric Scheme. Thirty‐four B. parvus were captured in 1065 trapnights on spoil dumps in Happy Jacks Creek valley, in northern Kosciuszko National Park in October and November 2011. In January 2012, 22 individuals were captured in 360 trapnights on a spoil dump at Guthega Adit Camp in southern Kosciuszko National Park. Seven radio‐collared individuals tracked in Happy Jacks Creek valley resulted in the location of 5 day shelters in spoil dump habitat, including individuals that were originally trapped in nearby natural habitat. This study indicates that there may be opportunity to create further artificial habitat on sites not currently used by this highly restricted species.     

Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery

Black-capped vireos ( Vireo atricapilla ), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation ( F _ST = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.     

Density,home range,seasonal movements and habitat use of the mountain pygmy‐possum Burramys parvus (Marsupialia: Burramyidae) at Mount Blue Cow,Kosciuszko National Park

A population of mountain pygmy‐possums Burramys parvus was studied at the Mount Blue Cow ski resort in Kosciuszko National Park between 1986 and 1989. Forty‐eight individuals were radiotracked during the snow‐free months and 21 individuals were tracked during winter over the 3 years of study. Trapping and radiotracking showed that the density, population structure, movements and home range sizes of B. parvus on Mount Blue Cow were strongly correlated with elevation and changed with the season. Female densities were greatest in habitats characterized by deep boulderfields, at high elevations with an abundance of Bogong moths. Males visited the areas where females were located to breed in November–December and then by February, the majority migrated to lower elevations or north and westerly aspects. Females that nested at lower elevations also visited high‐elevation habitats to access the high concentrations of Bogong moths, which were the main food source in summer. A high proportion of the juvenile males and some juvenile females dispersed to lower elevations in March and April. The resulting sexual segregation during autumn and winter may be a result of female aggression or scramble competition, but is also explainable by differences in energy requirements, seed availability and hibernation strategies between the sexes. The extraordinarily large nightly and seasonal movements between habitat patches of up to 2 km for females and 3 km for males, sexual segregation and the use of different hibernation sites have important implications for the management of this species. These include the need for movement and dispersal corridors and the conservation of boulder‐heath habitats outside the main boulderfields.     

Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas

The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations.     

景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

High levels of genetic diversity in populations of Iris aphylla L. (Iridaceae), an endangered species in Poland

We used RAPDs (Random Amplified Polymorphic DNAs) to investigate genetic diversity and its partition within and between three populations of Iris aphylla in Poland. Analysis of Molecular Variance (AMOVA) of 84 distinct RAPD multiband genotypes revealed higher variation within populations (77.2%) than genetic differentiation between them (22.8%, P  < 0.002). Values of genetic diversity indices ( H ) were similar in all three sites (0.21–0.24). The differentiation of the populations corresponded to low average gene flow ( Nm  = 0.81). Our results indicated that genetic diversity was independent of population size. We concluded that although sexual reproduction and gene flow between populations of I. aphylla were very limited, they preserved high levels of genetic diversity. Relatively large number of seeds, which migrated in the past to populations, as well as patterns of reproduction and life history of I. aphylla may explain this situation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 65–72.     

Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.     

Anthropogenic fragmentation increases risk of genetic decline in the threatened orchid Platanthera leucophaea

Protecting biodiversity requires an understanding of how anthropogenic changes impact the genetic processes associated with extinction risk. Studies of the genetic changes due to anthropogenic fragmentation have revealed conflicting results. This is likely due to the difficulty in isolating habitat loss and fragmentation, which can have opposing impacts on genetic parameters. The well‐studied orchid, Platanthera leucophaea, provides a rich dataset to address this issue, allowing us to examine range‐wide genetic changes. Midwestern and Northeastern United States. We sampled 35 populations of P. leucophaea that spanned the species’ range and varied in patch composition, degree of patch isolation, and population size. From these populations we measured genetic parameters associated with increased extinction risk. Using this combined dataset, we modeled landscape variables and population metrics against genetic parameters to determine the best predictors of increased extinction risk. All genetic parameters were strongly associated with population size, while development and patch isolation showed an association with genetic diversity and genetic structure. Genetic diversity was lowest in populations with small census sizes, greater urbanization pressures (habitat loss), and small patch area. All populations showed moderate levels of inbreeding, regardless of size. Contrary to expectation, we found that critically small populations had negative inbreeding values, indicating non‐random mating not typically observed in wild populations, which we attribute to selection for less inbred individuals. The once widespread orchid, Platanthera leucophaea, has suffered drastic declines and extant populations show changes in the genetic parameters associated with increased extinction risk, especially smaller populations. Due to the important correlation with risk and habitat loss, we advocate continued monitoring of population sizes by resource managers, while the critically small populations may need additional management to reverse genetic declines.     

Fine‐scale genetic structure in an eastern Alpine black grouse Tetrao tetrix metapopulation

Understanding genetic consequences of habitat fragmentation is crucial for the management and conservation of wildlife populations, especially in case of species sensitive to environmental changes and landscape alteration. In central Europe, the Alps are the core area of black grouse Tetrao tetrix distribution. There, black grouse dispersal is limited by high altitude mountain ridges and recent black grouse habitats are known to show some degree of natural fragmentation. Additionally, substantial anthropogenic fragmentation has occurred within the past ninety years. Facing losses of peripheral subpopulations and ongoing range contractions, we explored genetic variability and the fine‐scale genetic structure of the Alpine black grouse metapopulation at the easternmost fringe of the species’ Alpine range. Two hundred and fifty tissue samples and non‐invasive faecal and feather samples of eleven a priori defined subpopulations were used for genetic analysis based on nine microsatellite loci. Overall, eastern Alpine black grouse show similar amounts of genetic variation (H_O = 0.65, H_E = 0.66) to those found in more continuous populations like in Scandinavia. Despite of naturally and anthropogenically fragmented landscapes, genetic structuring was weak (global F_ST < 0.05), suggesting that the actual intensity of habitat fragmentation does not completely hamper dispersal, but probably restricts it to some extent. The most peripheral subpopulations at the edge of the species range show signs of genetic differentiation. The present study gives new insights into the population genetic structure of black grouse in the eastern Alps and provides a more fine‐scale view of genetic structure than previously available. Our findings will contribute to monitor the current and future status of the population under human pressures and to support supra‐regional land use planning as well as decision making processes in responsibilities of public administration.     

Is there genetic structure in populations of Helicoverpa armigera from Australia?

Recent studies suggest that populations of the pest moth Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) may be genetically differentiated over short distances and time periods within Queensland, Australia. To test for genetic structure in another region of Australia, we characterized population differentiation in Victorian samples of H. armigera using eight microsatellite loci. We found no evidence of genetic structure among samples from different locations or among samples collected at different times. Moreover, Victorian samples were not differentiated from other samples of H. armigera from Queensland and New Zealand. All samples showed substantial deviations from Hardy–Weinberg equilibrium, suggesting a high frequency of null alleles typically found in microsatellites of Lepidoptera. These results indicate that populations of H. armigera are not strongly structured among regions in south‐eastern Australia.     

Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi)

Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300‐ km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30‐ km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522‐base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.     

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species’ range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and significant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale ( <10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining ‘connected’8 brush-tailed rock-wallaby colonies in the northern parts of the species’8 range and the remnant endangered populations in the south.     

Anthropogenic fragmentation may not alter pre‐existing patterns of genetic diversity and differentiation in perennial shrubs

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird‐pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F′_ST = 0.615 and 0.454; S_p = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long‐term effects of inbreeding in self‐compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self‐compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.     

Microsatellite variation in natural Drosophila melanogaster populations from New South Wales (Australia) and Tasmania

Microsatellite variation was studied at 48 microsatellite loci in 10 Drosophila melanogaster populations to investigate the population structure on the Australian east coast. Low, but statistically significant population differentiation was observed among most populations. The populations on the Australian mainland did not show evidence for isolation by distance. We conclude that the population structure of D. melanogaster on the Australian mainland is probably the result of a shared history (recent colonization). The observed differences between local D. melanogaster populations probably reflect variation in effective population sizes rather than patterns of gene flow. Two populations from Tasmania were more differentiated from the Australian mainland than a population from Israel, raising the question whether they are derived from the Australian mainland or colonized from a different source population.     

High genetic variation in leopards indicates large and long-term stable effective population size

In this paper we employ recently developed statistical and molecular tools to analyse the population history of the Tanzanian leopard (Panthera pardus), a large solitary felid. Because of their solitary lifestyle little is known of their past or present population dynamics. Eighty-one individuals were scored at 18 microsatellite loci. Overall, levels of heterozygosity were high (0.77 +/- 0.03), with a small heterozygote deficiency (0.06 +/- 0.03). Effective population size (Ne) was calculated to be 38 000-48 000. A Ne:N ratio of 0.42 (average from four cat studies) gives a present population size of about 100 000 leopards in Tanzania. Four different bottleneck tests indicated that this population has been large and stable for a minimum of several thousand years. FST values were low and no significant genetic structuring of the population could be detected. This concurs well with the large migration values (Nm) obtained (>3.3 individuals/generation). Our analysis reveals that ecological factors (e.g. disease), which are known to have had major impact on other carnivore populations, are unlikely to have impacted strongly on the population dynamics of Tanzanian leopards. The explanation may be found in their solitary life-style, their often nonconfrontational behaviour toward interspecific competitors, or that any bottlenecks have been of limited size, localized, or too short to have affected genetic variation to any measurable degree. Since the genetic structuring is weak, gene flow is not restricted to within protected areas. Local loss of genetic variation is therefore not of immediate concern.