Population viability analysis of European bison populations in Polish and Belarusian parts of Bia?owie?a Forest with and without gene exchange

European bison (Bison bonasus) became extinct in the wild at the beginning of the 20th century. The contemporary Lowland line of bison was founded by seven individuals that survived in captivity. The largest population of Lowland bison live in the Bia?owie?a Forest, but the forest and the population are divided by a border fence between Poland and Belarus. This fence is a barrier to the movement of ungulates. In this study, we used population genetic models to predict the future viability of the Polish and Belarusian bison populations. We determined the founder contribution, founder equivalent, mean inbreeding coefficient, mean kinship, and the proportion of genetic diversity retained in the Belarusian bison population. Although the founding group of the Belarusian population was larger than that of the Polish population, the latter had more favourable genetic parameters. We assessed inbreeding depression for fecundity in free-ranging European bison compared to captive individuals. Using population viability analysis (PVA) we modelled both bison populations with or without gene exchange, and with or without incorporating the kinship of the founders. When founder kinship was included, in both populations the mean number of alleles and the gene diversity retained within extant populations decreased substantially compared to PVA models in which founders were not related. The worst genetic parameters were obtained for the Belarusian population under a scenario in which the founders are related and gene exchange is lacking, which is the closest to the real situation. Creation of passages for animals by partial removal of the border fence would have a favourable effect on the genetic variation and viability of both bison populations, especially the Belarusian.     

Factors influencing survival and long-term population viability of New Zealand long-tailed bats (Chalinolobus tuberculatus): Implications for conservation

A population viability analysis is important for the management of endangered populations and requires the estimation of survival parameters. The long-tailed bat (Chalinolobus tuberculatus) is one of only two native terrestrial mammals currently found in New Zealand and is classed as vulnerable. Its viability in temperate beech (Nothofagus) forest, Eglinton Valley, Fiordland, New Zealand was estimated using mark-recapture data collected between 1993 and 2003 using the Program MARK. Survival was estimated based on a total of 5286 captures representing 1026 individuals. Overall annual survival varied between 0.34 and 0.83 but varied significantly among three sub-populations and with sex and age. Females generally had a higher survival rate compared to males; and adults had higher survival relative to juveniles. Survival of all bats was lower in years when the number of introduced mammalian predators was high and when the winter temperature was warmer than average. High numbers of introduced predators occurred during three of the 10 years in the study. Climate change may mean that the conditions that promote high predator numbers may occur more frequently. A preliminary population viability analysis using a projection matrix on the overall adult female population showed an average 5% decline per year (λ = 0.95). Increased predator control targeting a range of predators is required in years when their numbers are high in order to halt the decline of this population of long-tailed bats. Population estimates using minimum number alive estimates supported the population estimates derived from Program MARK and a population viability analysis using matrices.     

Phenotypic differentiation in fitness related traits between populations of an extremely rare sunflower: Conservation management of isolated populations

Knowledge of the genetic and demographic consequences of rarity is crucial when evaluating the effects of habitat loss and fragmentation on population viability, and for creating management plans in rare plant species. Reduction in population size and in the number of populations can lead to decreased genetic diversity and increased inbreeding. Genetic diversity is often correlated with fitness and is frequently used to identify populations of greatest conservation concern, or those that may be good candidates for ex situ conservation programs. However, an association between these factors is not always clear, and crossing studies evaluating whether there is phenotypic differentiation among populations in fitness related traits can inform managers of suffering populations or good sources for ex situ materials. Crossing studies can also evaluate the potential for genetic rescue to boost fitness in suffering populations. To address these questions, we conducted two generations of controlled crosses between populations of the extremely rare and fragmented sunflower, Helianthus verticillatus. We measured achene viability, germination, survival, and pollen viability (F₁ only) in 176 F₁ and 159 F₂ families. The populations were differentiated with respect to phenotypic fitness measures with one population having significantly lower achene viability and germination. Also, the potential for genetic rescue was observed as gene flow into the less fit population resulted in higher fitness measures in both the F₁ and F₂. Results are discussed with respect to the importance of combining genetic marker data with crosses and the implications for conservation in disjunct populations of rare species.     

Cryptic genetic bottlenecks during restoration of an endangered tropical conifer

Forest restoration programmes aim to use material for re-planting that is genetically diverse and not inbred. However, restricted seed sampling, high variance in reproductive output, and the production of inbred seeds that survive in the nursery but not in the wild can lead to forest restoration stock being genetically compromised. The aim of this study was to evaluate whether the reproductive biology of the New Caledonian endemic conifer Araucaria nemorosa makes it susceptible to these genetic problems and to assess whether there is evidence for genetic bottlenecks and elevated inbreeding in nursery stock compared to seedlings and adults from wild source populations. Reproductive output was low with high variance among trees (only 14% of adult trees surveyed produced mature cones, >50% of examined cones had <10 viable seeds). Evidence for an extreme genetic bottleneck was detected in a nursery population established from cones collected from adult trees. A second nursery population established with seed collected from the forest floor showed no evidence of a genetic bottleneck, but was inbred compared to its wild source population. In light of these results, we do not recommend collecting cones directly from A. nemorosa as an efficient means of establishing genetically diverse stock for restoration programmes. Collecting seed from the forest floor is likely to be more effective, but the planting stock may contain a high proportion of inbred individuals. Collecting established wild seedlings already subjected to natural selection is suggested as an alternative method of maximising the diversity captured, whilst minimising sampling effort and proportion of inbred individuals.     

Relationship between population size and genetic diversity in endangered populations of the European bullhead (Cottus gobio): implications for conservation

This study investigated the relationship between the current size of endangered bullhead (Cottus gobio) populations and microsatellite genetic variability. Additionally, the microsatellite data were used to evaluate whether a genetic test for population bottlenecks was able to provide evidence of recent severe population declines. Finally, our results were used to develop conservation priorities and measures. Population size appears to be a crucial parameter in determining the amount of genetic diversity that can be preserved in bullheads, since a significant positive correlation was observed between both variables. Furthermore, in some populations we were able to detect genetic signatures of the documented decline in population size. We suggest that the most immediate goal for bullhead conservation should be to increase the size and the range of the populations, and in doing so minimise or even reverse further genetic erosion. Potential management actions like habitat quality improvement, reduction of river fragmentation and supplementation programmes (translocation, supportive breeding) are discussed.     

Genetic variation in the threatened South American conifer Pilgerodendron uviferum (Cupressaceae), detected using RAPD markers

Pilgerodendron uviferum (Cipres de las Guiatecas, Cupressaceae) is a long-lived conifer, endemic to southern Chile and Argentina, reaching a southern limit in Tierra del Fuego. Remnant populations are generally fragmented and highly disturbed because of exploitation for timber, grazing and fire. The extent of genetic variation within and between 16 populations of this species, distributed throughout its range, was assessed using random amplified polymorphic DNA (RAPD) markers. Eight 10-mer primers produced a total of 84 scorable markers, 30 of which (35.7%) were polymorphic. AMOVA indicated that 18.6% of the variation recorded was attributable to differences between populations, a relatively high value compared with other conifers from the region. Pair-wise Phi_st comparisons between populations were all significant at P<0.05, with one exception, highlighting a high degree of population differentiation. Values of Shannon's diversity index (S) differed significantly among populations (P=0.002, ANOVA), values ranging from 0.337 to 0.716, suggesting that some populations are currently characterised by very low genetic variability. Current patterns of genetic variation were related to biogeographic history and human impact. The high degree of population differentiation recorded here highlights the need for additional conservation measures for this species, both in terms of incorporating further populations into the protected areas, and the restoration of severely degraded populations, to ensure their continued viability.     

High genetic diversity and heterogeneous parasite load in the earthworm Lumbricus terrestris on a German meadow

In parasite-host dynamics, parasites exert frequency-dependent selection on their hosts by favouring rare alleles that may confer resistance against infection. Therefore host populations that suffer strong parasite stress should maintain higher levels of genetic variability. We studied the Lumbricus terrestris-Monocystis sp. host-parasite system at a microgeographical scale. Using three polymorphic microsatellite loci on one large earthworm population sampled at 26 different sites (281 genotypes), we tested the relationship between parasite load and genetic variation in natural samples of the common earthworm L. terrestris. Our analysis yielded the following: (1) parasite load varied significantly across sites in this population; (2) there was no consistent evidence for heterozygote deficiency (observed heterozygosities ranged between 0.74 and 0.87), indicating a low level of inbreeding; (3) there was no significant genetic structuring among sample sites; (4) we could not identify a significant association between parasite load and population genetic diversity; (5) there was considerable population differentiation (15.17%) between our German samples and a Canadian L. terrestris reference population. Our study provides insight into the population genetics of one of the most economically important soil organisms on a microgeographic scale.     

Minimum viable population and conservation status of the Atlantic Forest spiny rat Trinomys eliasi

A population viability analysis (PVA) was conducted to assess the minimum viable population (MVP) of the Atlantic Forest spiny rat Trinomys eliasi, a species threatened by habitat loss and restricted geographical distribution. Objectives were to suggest quasi-extinction thresholds, estimate minimum areas of suitable habitat (MASH) and MVPs, and compare results with the species’ current status. The computer package VORTEX was used. The model predicted sizes of 200 animals to achieve demographic stability, but buffering declines in genetic variability required populations of 2000 animals. Estimated MASHs were approximately 250 and 2500 ha for demographic and genetic stability, respectively. Mortality rate and mean litter size were the most sensitive parameters to changes in model assumptions. The protection of known populations and the search for extant populations are the first steps in conservation. T. eliasi's issue could help protecting the coastal shrubland ecosystem of Rio de Janeiro state. Observing IUCN's criteria for listing threatened species, it is suggested that T. eliasi should be ranked as vulnerable in red lists.     

Low levels of genetic variation among southern peripheral populations of the threatened herb, Leontice microrhyncha (Berberidaceae) in Korea

Levels of genetic variation and intrapopulation genetic structures of Leontice microrhyncha S. Moore (Berberidaceae) were assessed for six populations in South Korea, representing the southern most range of a species found in Northeast China and the Korean peninsula. Detected genetic diversity (H_es) was very low (0.024) and F_IS values showed large heterozygote deficiencies. The small percentage of polymorphic loci and numbers of alleles per locus suggest that L. microrhyncha has a history of severe or long-lasting population bottlenecks that have eroded genetic diversity. This study suggests that the Korean population appears to consist of two historically isolated and independently evolving populations. It seems likely that these groups have been isolated and unstable for a significant period of time. However, the effects of recent habitat fragmentation on the historically disjunct and fragmented population system found in L. microrhyncha were not those predicted from the lack of significant relationships between population-level patterns of genetic variation and population sizes. Most non-unique genotypes were shared by most individuals and the lower level of diversity, high levels of inbreeding and population differentiation as well as high rate of seed production indicated that this species is autogamous and self-compatible and probably largely selfing. Therefore, to preserve extant genetic variation, all populations must be protected across the small geographic range of the species to retain both allelic and genotypic diversity.     

Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation

The endangered fish species Anaecypris hispanica is restricted to eight disjunct populations in the Portuguese Guadiana drainage. The genetic structure of these populations was studied in order to determine levels of genetic variation within and among populations and suggest implications for conservation of the species. Based on five microsatellite loci, the null hypothesis of population homogeneity was tested. Tests for genetic differentiation revealed highly significant differences for pairwise comparisons between all populations, and substantial overall population subdivision (F_ST=0.112). All sampled populations contained unique alleles. Our findings indicate marked genetic structuring and emphasise limited dispersal ability. The high levels of genetic diversity detected within and among A. hispanica populations suggest, however, that the observed fragmentation and reduction in population size of some populations during the last two decades, has impacted little on levels of genetic variability. Data imply that most A. hispanica populations should be managed as distinct units and that each has a high conservation value containing unique genetic variation. It is argued that geographic patterns of genetic structuring indicate the existence of eight management units.     

Impact of introduced honey bees on native pollination interactions of the endemic Echium wildpretii (Boraginaceae) on Tenerife, Canary Islands

The aim of this study was to investigate effects of introduced honey bees (Apis mellifera) on native pollination interactions of Echium wildpretii ssp. wildpretii in the sub-alpine desert of Tenerife. We selected two study populations, one dominated by honey bees, while the other was visited by many native insects. During peak activity period of insects, nectar was nearly completely depleted in flowers of the first, but not the latter population. Thus, a high abundance of honey bees may have suppressed visitation by native animals due to exploitative competition. Honey bees stayed longer and visited more flowers on the same inflorescence than native bees, thus potentially promoting self-pollination of the plants. Level of seed set and viability was similar in the two study populations. However, we cannot rule out long-term changes in genetic population structure due to changes in gene-flow patterns caused by foraging behaviour of honey bees vs. native flower-visitors.     

Inbreeding in red-cockaded woodpeckers: Effects of natal dispersal distance and territory location

Inbreeding depression constitutes a significant threat to the viability of small populations. In addition to small size and isolation of populations, short distance dispersal may elevate risk of inbreeding, but empirical evidence is scarce. Inbreeding depression has been demonstrated in the highly endangered red-cockaded woodpecker Picoides borealis. It has been suggested that conservation efforts to support extant populations should aim at spatially aggregating territories to enhance dispersal success. This however may aggravate inbreeding risk because distance between territories and hence dispersal distances become short. We analysed empirical data from a long-term study of the demography of the red-cockaded woodpecker and found that inbreeding risk varied inversely with natal dispersal distance of the mother. Using an individual-based, spatially explicit population model that incorporates simulations of environmental and demographic stochasticity and an empirically derived, species-specific estimate of inbreeding costs, we demonstrated that inbreeding depression significantly elevated extinction risk in this species. On the other hand, even though dispersal distances in populations with spatially aggregated territories were shorter and the proportion of inbred individuals was higher than in other populations of the same size, such populations were still more persistent. Despite the overall adverse effect of inbreeding depression on viability of red-cockaded woodpecker populations, lowering interterritorial distances can be viewed as a valuable conservation tool. Given the small size and isolated location of most extant red-cockaded woodpecker populations however, our findings suggest that inbreeding depression represents a significant threat to the survival of this species.     

Congenital bone deformities and the inbred wolves (Canis lupus) of Isle Royale

The wolf (Canis lupus) population on Isle Royale, a remote island in Lake Superior, North America, is extremely inbred. Nevertheless, the consequences of genetic deterioration have not been detected for this intensively studied population, until now. We found that 58% (n = 36) of Isle Royale wolves exhibited some kind of congenital malformation in the lumbosacral region of the vertebral column and 33% exhibited a specific malformity, lumbosacral transitional vertebrae. By contrast, only 1% (1 of 99) of wolves sampled from two outbred, wolf populations exhibited this malformity. Moreover, in domestic dogs (Canis lupus familiaris) lumbosacral transitional vertebrae are associated with cauda equina syndrome, which can cause paresis, paralysis, locomotor difficulties in the rear legs and tail, and back pain. Whereas many studies illustrate how genetic deterioration affects population-level phenomena, such as survival and reproduction, these results are distinctive for demonstrating how genetic deterioration has compromised the morphology of individuals in a free-ranging population. The results are also significant because many policy makers and stakeholders and some conservation professionals use examples like Isle Royale wolves to downplay the consequences of genetic deterioration.     

Genetic tracking of the brown bear in northern Pakistan and implications for conservation

Asian bears face major threats due to the impact of human activities as well as a critical lack of knowledge about their status, distribution and needs for survival. Once abundant in northern Pakistan, the Himalayan brown bear (Ursus arctos isabellinus) has been exterminated in most of its former distribution range. It presently occurs sparsely, in small populations, the Deosai National Park supporting the largest isolate. This decline might imply a reduction in genetic diversity, compromising the survival of the population. Using a combination of fecal DNA analysis and field data, our study aimed at assessing the size and genetic status of the Deosai population and give guidelines for its conservation and management. Using fecal genetic analysis, we estimated the population to be 40-50 bears, which compares well with the field census of 38 bears. The northern Pakistani brown bear population may have undergone an approximate 200-300-fold decrease during the last thousand years, probably due to glaciations and the influence of growing human population. However, in spite of the presence of a bottleneck genetic signature, the Deosai population has a moderate level of genetic diversity and is not at immediate risk of inbreeding depression. Gene flow might exist with adjacent populations. We recommend careful monitoring of this population in the future both with field observations and genetic analyses, including sampling of adjacent populations to assess incoming gene flow. The connectivity with adjacent populations in Pakistan and India will be of prime importance for the long-term survival of Deosai bears.     

Long-term dynamics and population viability in one of the last populations of the endangered Spiranthes spiralis (Orchidaceae) in the Netherlands

During the last decades, most orchid species in much of Western Europe have suffered significant declines and the long-term survival of the remaining populations remains to a large extent uncertain. In particular, populations at range margins may be more prone to extinction than more central populations, as the former tend to be small and isolated, occur in ecologically marginal habitats and have a lower per-capita reproductive rate. In this study, we investigated the long-term dynamics and population viability of a population at the margin of its range of Spiranthes spiralis in the Netherlands. At present, only 2 out of 40 previously known populations persist. Individual plants were monitored for 24 years and their life span, flowering frequency and vegetative growth were determined. Individual plants showed large temporal variation in sexual and vegetative growth among years. The proportion of flowering plants varied from 0 (no plants were flowering) to 100 (all plants were flowering). Vegetative growth, on the other hand, increased when the number of individuals decreased. Dormancy was present, but occurred only in a few individuals. Using a non-structured population viability model, future prospects of this species were assessed. Calculation of extinction probabilities and estimated times to extinction using the diffusion approximation model showed that the species had a relatively high probability (79%) of surviving the next 20 years, whereas the median time to extinction was forty years. However, because 95% confidence intervals of the population growth included 1, we suggest that continued monitoring and additional genetic research are needed to assess the long-term viability of this species.     

Effect of stand age and management regime on genetic diversity of Thuidium cymbifolium in western China

Using random amplified polymorphic DNA (RAPD) markers, we examined genetic variability of the moss Thuidium cymbifolium (Thuidiaceae) sampled from three types of spruce (Picea asperata) stands: an intact stand, naturally regenerated stands after clearcut harvests, and planted stands after clearcut harvests in the Miyaluo area, western Sichuan of China. Stands of the latter two types were of various age since the last clearcut. Results showed that the population of T. cymbifolium from the intact stand displayed the highest level of genetic diversity, and populations from the planted stands exhibited significantly higher levels than the naturally regenerated stands. In planted stands, genetic variation within populations increased over time. These findings indicated that habitat destruction by forest harvesting led to the reduction in genetic variation within populations, but that given time, artificial reforestation after clearcut was effective in promoting the recovery of genetic diversity in the recolonized moss species. Therefore, lengthening the normal felling rotation of plantations should be favored to restore and conserve genetic diversity in recolonized species. In addition, thinning young plantations via selective logging may provide heterogenous microhabitats similar to those in the old stands, and thereby facilitate the development of bryophyte communities and the increase of genetic variation of the recolonized mosses.     

Population management of threatened taxa in captivity within their natural ranges: Lessons from Andean bears (Tremarctos ornatus) in Venezuela

Populations of threatened taxa in captivity within their natural ranges can make important contributions to conservation, but these may be compromised by the inappropriate application of population management goals developed in other contexts. We conducted demographic, genetic, and population viability analyses on the captive population of Andean bears (Tremarctos ornatus) in Venezuela to investigate the management of within-range captive populations in general, and to better integrate this population into the conservation of Andean bears in particular. We found that although the present population is very small and not internally self-sustaining, incorporation of confiscated wild individuals has resulted in a low average number of generations in captivity and low inbreeding, with moderate gene diversity and a high probability of future population persistence. However, past imports from extra-range populations have been from over-represented lineages of unknown origin, which have mixed with under-represented Venezuelan ones, reducing the future value of the Venezuelan population as a source for founder stock. Our analyses indicate that the rate of incorporation of wild recruits is a major factor influencing proxy measures of conservation value, and distinguishing within- from extra-range populations. This implies that, contrary to conventional wisdom, internal self-sustainability can be a misguided goal in within-range populations, which furthermore may not be suitable destinations for surplus animals from captive populations elsewhere.     

Genetic and demographic responses of fragmented Acacia dealbata (Mimosaceae) populations in southeastern Australia

Genetic and demographic studies of fragmented populations of common plant species often reveal negative impacts that are likely to constrain persistence. Examining species that are broadly representative of functional groups within fragmented landscapes is one approach to providing a better understanding of how these processes will influence vegetation persistence. Acacias are a significant component of the Australian flora, with Acacia dealbata being a common and representative species of fragmented landscapes across New South Wales. Previous reproductive assessments of fragmented A. dealbata populations indicated significant constraints for small populations through low reproductive output mediated by fertilisation success. This study examined genetic diversity, mating system, and progeny growth parameters of the seed crops produced by these populations to assess whether further constraints to persistence could be detected. Spatially explicit simulation studies were also conducted to assess the persistence likelihood of fragmented populations. Landscape parameters such as population size and plant density were useful predictors for some of the genetic and demographic responses, but a poor response signal was generally observed. Strong evidence for a self-incompatibility mechanism was observed in A. dealbata and is likely to be the major driver of population persistence. Self-incompatibility in small populations limits mate availability and eliminates inbred progeny early in the reproductive cycle leading to poor reproductive output. The simulation data provides further evidence that mate limitation in smaller populations (<200 plants and 40 S alleles) constrains reproductive output and persistence. These data indicate that introducing new germplasm to smaller populations can dramatically improve their persistence likelihood.     

Effects of fishing protection on the genetic structure of fish populations

Marine reserves have been identified as an important tool in the management of fishery resources and their number is increasing rapidly, most of them being on islands. However, knowledge on the real effect of protection from fishing on the genetic structure of populations, the spatial scales involved, or the suitability of islands as reserves in terms of connectivity, is scarce. This paper analyses the effects of fishery protection on the genetic structure of populations of Diplodus sargus, a target species, in protected and non-protected areas of the western Mediterranean. Populations studied showed high genetic variability at spatial scales from 10¹ to 10³ km. Protected areas have significantly higher allelic richness. The lower levels of heterozygosis and higher heterozygote deficit showed by islands compared with coastal areas makes clear the importance of considering the connectivity processes when designing a MPA.     

Removing erosion control projects increases bank swallow (Riparia riparia) population viability modeled along the Sacramento River, California, USA

Spatially-explicit population viability analysis (PVA) is a powerful method for modeling the extinction risk of populations that show variation over space and time. It is especially effective for comparing relative effect of different management scenarios on population dynamics. Here, I present a habitat patch-based PVA for a population of the California state-listed threatened bank swallow (Riparia riparia) nesting along the Sacramento River. This model incorporates the effects of habitat availability and location, density dependence, site fidelity, and stochasticity in survival and fecundity. River bank habitat patches suitable for this species were delineated using a geographic information systems (GIS) model of river bank height and were used in a PVA scenario analysis to assess the effects of habitat restoration—that could occur by removing bank erosion control projects (bank revetment)—on population viability. Sensitivity analysis showed that the model estimated probability of quasi-extinction (dropping below 2000 breeding pairs) ranged from 0 to 0.8 depending on the input parameters, with juvenile survival causing the greatest variability. However, comparing changes to the probability of quasi-extinction between the restored habitat scenario and current conditions showed a consistent 40-60% decrease in probability of quasi-extinction across all parameter combinations. The results of this research reaffirm the need for continued protection of the bank swallow as a listed species indicate that the removal of bank erosion control projects would increase viability of this population.