Lower Extinction Risk Research Articles

Effects of climate change and anthropogenic modification on a disturbance‐dependent species in a large riverine system

AbstractHumans have altered nearly every natural disturbance regime on the planet through climate and land‐use change, and in many instances, these processes may have interacting effects. For example, projected shifts in temperature and precipitation will likely influence disturbance regimes already affected by anthropogenic fire suppression or river impoundments. Understanding how disturbance‐dependent species respond to complex and interacting environmental changes is important for conservation efforts. Using field‐based demographic and movement rates, we conducted a metapopulation viability analysis for piping plovers (Charadrius melodus), a threatened disturbance‐dependent species, along the Missouri and Platte rivers in the Great Plains of North America. Our aim was to better understand current and projected future metapopulation dynamics given that natural disturbances (flooding or high‐flow events) have been greatly reduced by river impoundments and that climate change could further alter the disturbance regime. Although metapopulation abundance has been substantially reduced under the current suppressed disturbance regime (high‐flow return interval ~ 20 yr), it could grow if the frequency of high‐flow events increases as predicted under likely climate change scenarios. We found that a four‐year return interval would maximize metapopulation abundance, and all subpopulations in the metapopulation would act as sources at a return interval of 15 yr or less. Regardless of disturbance frequency, the presence of even a small, stable source subpopulation buffered the metapopulation and sustained a low metapopulation extinction risk. Therefore, climate change could have positive effects in ecosystems where disturbances have been anthropogenically suppressed when climatic shifts move disturbance regimes toward more historical patterns. Furthermore, stable source populations, even if unintentionally maintained through anthropogenic activities, may be critical for the persistence of metapopulations of early‐successional species under both suppressed disturbance regimes and disturbance regimes where climate change has further altered disturbance frequency or scope.

Cost-efficient strategies to preserve dead wood-dependent species in a managed forest landscape

Negative consequences of intensive forest management on biodiversity are often mitigated by setting aside old forest, but alternative strategies have been suggested. We have compared using simulations the consequences of two of these alternatives − setting aside young forests or extending rotation periods − to that of current practice in managed boreal forest. In all scenarios we applied a constant conservation budget and predicted forest development and harvesting over 200years. As a proxy for biodiversity conservation, we projected the extinction risk of a dead wood-dependent beetle, Diacanthous undulatus, in a 50km2 landscape in central Sweden, using a colonization-extinction model. During the first century, setting aside young forest stands rather than old stands increased extinction risk because young stands have lower habitat quality. However, habitat quality of young forests increased as they aged and they were much cheaper to set aside than old stands. Therefore, the strategy allowed a larger set-aside area (within the budget constraint), resulting in lower extinction risk and harvested timber volumes in the second century. Prolonging rotations also decreased the extinction risk but was in the long-term less cost-effective. The most cost-effective strategy in the long-term (200years) was to set aside a mixture of old and young forest. However, setting aside young stands rather than prolonging rotations or setting aside old stands delays both the benefits (lower extinction risk) and costs (lost harvest volumes), so the optimal strategy depends on the assumed societal values and hence discount rates.

Population Viability Analysis for Endangered Roanoke Logperch

A common strategy for recovering endangered species is ensuring that populations exceed the minimum viable population size (MVP), a demographic benchmark that theoretically ensures low long-term extinction risk. One method of establishing MVP is population viability analysis, a modeling technique that simulates population trajectories and forecasts extinction risk based on a series of biological, environmental, and management assumptions. Such models also help identify key uncertainties that have a large influence on extinction risk. We used stochastic count-based simulation models to explore extinction risk, MVP, and the possible benefits of alternative management strategies in populations of Roanoke logperch Percina rex, an endangered stream fish. Estimates of extinction risk were sensitive to the assumed population growth rate and model type, carrying capacity, and catastrophe regime (frequency and severity of anthropogenic fish kills), whereas demographic augmentation did little to reduce extinction risk. Under density-dependent growth, the estimated MVP for Roanoke logperch ranged from 200 to 4200 individuals, depending on the assumed severity of catastrophes. Thus, depending on the MVP threshold, anywhere from two to all five of the logperch populations we assessed were projected to be viable. Despite this uncertainty, these results help identify populations with the greatest relative extinction risk, as well as management strategies that might reduce this risk the most, such as increasing carrying capacity and reducing fish kills. Better estimates of population growth parameters and catastrophe regimes would facilitate the refinement of MVP and extinction-risk estimates, and they should be a high priority for future research on Roanoke logperch and other imperiled stream-fish species.

Population Viability Analysis for Endangered Roanoke Logperch

Abstract A common strategy for recovering endangered species is ensuring that populations exceed the minimum viable population size (MVP), a demographic benchmark that theoretically ensures low long-term extinction risk. One method of establishing MVP is population viability analysis, a modeling technique that simulates population trajectories and forecasts extinction risk based on a series of biological, environmental, and management assumptions. Such models also help identify key uncertainties that have a large influence on extinction risk. We used stochastic count-based simulation models to explore extinction risk, MVP, and the possible benefits of alternative management strategies in populations of Roanoke logperch Percina rex, an endangered stream fish. Estimates of extinction risk were sensitive to the assumed population growth rate and model type, carrying capacity, and catastrophe regime (frequency and severity of anthropogenic fish kills), whereas demographic augmentation did little to reduce extinction risk. Under density-dependent growth, the estimated MVP for Roanoke logperch ranged from 200 to 4200 individuals, depending on the assumed severity of catastrophes. Thus, depending on the MVP threshold, anywhere from two to all five of the logperch populations we assessed were projected to be viable. Despite this uncertainty, these results help identify populations with the greatest relative extinction risk, as well as management strategies that might reduce this risk the most, such as increasing carrying capacity and reducing fish kills. Better estimates of population growth parameters and catastrophe regimes would facilitate the refinement of MVP and extinction-risk estimates, and they should be a high priority for future research on Roanoke logperch and other imperiled stream-fish species.

Priorities for management of chytridiomycosis in Australia: saving frogs from extinction

To protect Australian amphibian biodiversity, we have identified and prioritised frog species at an imminent risk of extinction from chytridiomycosis, and devised national management and research priorities for disease mitigation. Six Australian frogs have not been observed in the wild since the initial emergence of chytridiomycosis and may be extinct. Seven extant frog species were assessed as needing urgent conservation interventions because of (1) their small populations and/or ongoing declines throughout their ranges (southern corroboree frog (Pseudophryne corroboree, New South Wales), northern corroboree frog (Pseudophryne pengilleyi, Australian Capital Territory, New South Wales), Baw Baw frog (Philoria frosti, Victoria), Litoria spenceri (spotted tree frog, Victoria, New South Wales), Kroombit tinkerfrog (Taudactylus pleione, Queensland), armoured mist frog (Litoria lorica, Queensland)) or (2) predicted severe decline associated with the spread of chytridiomycosis in the case of Tasmanian tree frog (Litoria burrowsae, Tasmania). For these species, the risk of extinction is high, but can be mitigated. They require increased survey effort to define their distributional limits and to monitor and detect further population changes, as well as well-resourced management strategies that include captive assurance populations. A further 22 frog species were considered at a moderate to lower risk of extinction from chytridiomycosis. Management actions that identify and create or maintain habitat refugia from chytridiomycosis and target other threatening processes such as habitat loss and degradation may be effective in promoting their recovery. Our assessments for some of these species remain uncertain and further taxonomical clarification is needed to determine their conservation importance. Management actions are currently being developed and trialled to mitigate the threat posed by chytridiomycosis. However, proven solutions to facilitate population recovery in the wild are lacking; hence, we prioritise research topics to achieve this aim. Importantly, the effectiveness of novel management solutions will likely differ among species due to variation in disease ecology, highlighting the need for species-specific research. We call for an independent management and research fund of AU$15 million over 5 years to be allocated to recovery actions as determined by a National Chytridiomycosis Working Group of amphibian managers and scientists. Procrastination on this issue will likely result in additional extinction of Australia’s amphibians in the near future.

Assessing local population vulnerability with branching process models: an application to wind energy development

Quantifying the impact of anthropogenic development on local populations is important for conservation biology and wildlife management. However, these local populations are often subject to demographic stochasticity because of their small population size. Traditional modeling efforts such as population projection matrices do not consider this source of variation whereas individual‐based models, which include demographic stochasticity, are computationally intense and lack analytical tractability. One compromise between approaches is branching process models because they accommodate demographic stochasticity and are easily calculated. These models are known within some sub‐fields of probability and mathematical ecology but are not often applied in conservation biology and applied ecology. We applied branching process models to quantitatively compare and prioritize species locally vulnerable to the development of wind energy facilities. Specifically, we examined species vulnerability using branching process models for four representative species: A cave bat (a long‐lived, low fecundity species), a tree bat (short‐lived, moderate fecundity species), a grassland songbird (a short‐lived, high fecundity species), and an eagle (a long‐lived, slow maturation species). Wind turbine‐induced mortality has been observed for all of these species types, raising conservation concerns. We simulated different mortality rates from wind farms while calculating local extinction probabilities. The longer‐lived species types (e.g., cave bats and eagles) had much more pronounced transitions from low extinction risk to high extinction risk than short‐lived species types (e.g., tree bats and grassland songbirds). High‐offspring‐producing species types had a much greater variability in baseline risk of extinction than the lower‐offspring‐producing species types. Long‐lived species types may appear stable until a critical level of incidental mortality occurs. After this threshold, the risk of extirpation for a local population may rapidly increase with only minimal increases in wind mortality. Conservation biologists and wildlife managers may need to consider this mortality pattern when issuing take permits and developing monitoring protocols for wind facilities. We also describe how our branching process models may be generalized across a wider range of species for a larger assessment project and then describe how our methods may be applied to other stressors in addition to wind.

Cost‐effective conservation of an endangered frog under uncertainty

How should managers choose among conservation options when resources are scarce and there is uncertainty regarding the effectiveness of actions? Well-developed tools exist for prioritizing areas for one-time and binary actions (e.g., protect vs. not protect), but methods for prioritizing incremental or ongoing actions (such as habitat creation and maintenance) remain uncommon. We devised an approach that combines metapopulation viability and cost-effectiveness analyses to select among alternative conservation actions while accounting for uncertainty. In our study, cost-effectiveness is the ratio between the benefit of an action and its economic cost, where benefit is the change in metapopulation viability. We applied the approach to the case of the endangered growling grass frog (Litoria raniformis), which is threatened by urban development. We extended a Bayesian model to predict metapopulation viability under 9 urbanization and management scenarios and incorporated the full probability distribution of possible outcomes for each scenario into the cost-effectiveness analysis. This allowed us to discern between cost-effective alternatives that were robust to uncertainty and those with a relatively high risk of failure. We found a relatively high risk of extinction following urbanization if the only action was reservation of core habitat; habitat creation actions performed better than enhancement actions; and cost-effectiveness ranking changed depending on the consideration of uncertainty. Our results suggest that creation and maintenance of wetlands dedicated to L.raniformis is the only cost-effective action likely to result in a sufficiently low risk of extinction. To our knowledge we are the first study to use Bayesian metapopulation viability analysis to explicitly incorporate parametric and demographic uncertainty into a cost-effective evaluation of conservation actions. The approach offers guidance to decision makers aiming to achieve cost-effective conservation under uncertainty.

Lessons from Red Data Books: Plant Vulnerability Increases with Floral Complexity

The architectural complexity of flower structures (hereafter referred to as floral complexity) may be linked to pollination by specialized pollinators that can increase the probability of successful seed set. As plant—pollinator systems become fragile, a loss of such specialized pollinators could presumably result in an increased likelihood of pollination failure. This is an issue likely to be particularly evident in plants that are currently rare. Using a novel index describing floral complexity we explored whether this aspect of the structure of flowers could be used to predict vulnerability of plant species to extinction. To do this we defined plant vulnerability using the Red Data Book of Rare and Threatened Plants of Greece, a Mediterranean biodiversity hotspot. We also tested whether other intrinsic (e.g. life form, asexual reproduction) or extrinsic (e.g. habitat, altitude, range-restrictedness) factors could affect plant vulnerability. We found that plants with high floral complexity scores were significantly more likely to be vulnerable to extinction. Among all the floral complexity components only floral symmetry was found to have a significant effect, with radial-flower plants appearing to be less vulnerable. Life form was also a predictor of vulnerability, with woody perennial plants having significantly lower risk of extinction. Among the extrinsic factors, both habitat and maximum range were significantly associated with plant vulnerability (coastal plants and narrow-ranged plants are more likely to face higher risk). Although extrinsic and in particular anthropogenic factors determine plant extinction risk, intrinsic traits can indicate a plant’s proneness to vulnerability. This raises the potential threat of declining global pollinator diversity interacting with floral complexity to increase the vulnerability of individual plant species. There is potential scope for using plant—pollinator specializations to identify plant species particularly at risk and so target conservation efforts towards them.

Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction

SummaryThe reintroduction of a species into its historic range is a critical component of conservation programmes designed to restore extirpated metapopulations. However, many reintroduction efforts fail, and the lack of rigorous monitoring programmes and statistical models have prevented a general understanding of the factors affecting metapopulation viability following reintroduction.Spatially explicit metapopulation theory provides the basis for understanding the dynamics of fragmented populations linked by dispersal, but the theory has rarely been used to guide reintroduction programmes because most spatial metapopulation models require presence–absence data from every site in the network, and they do not allow for observation error such as imperfect detection.We develop a spatial occupancy model that relaxes these restrictive assumptions and allows for inference about metapopulation extinction risk and connectivity. We demonstrate the utility of the model using six years of data on the Chiricahua leopard frogLithobates chiricahuensis, a threatened desert‐breeding amphibian that was reintroduced to a network of sites in Arizona USA in 2003.Our results indicate that the model can generate precise predictions of extinction risk and produce connectivity maps that can guide conservation efforts following reintroduction. In the case ofL. chiricahuensis, many sites were functionally isolated, and 82% of sites were characterized by intermittent water availability and high local extinction probabilities (0·84, 95% CI: 0·64–0·99). However, under the current hydrological conditions and spatial arrangement of sites, the risk of metapopulation extinction is estimated to be <3% over a 50‐year time horizon.Low metapopulation extinction risk appears to result from the high dispersal capability of the species, the high density of sites in the region and the existence of predator‐free permanent wetlands with low local extinction probabilities. Should management be required, extinction risk can be reduced by either increasing the hydroperiod of existing sites or by creating new sites to increase connectivity.Synthesis and applications. This work demonstrates how spatio‐temporal statistical models based on ecological theory can be applied to forecast the outcomes of conservation actions such as reintroduction. Our spatial occupancy model should be particularly useful when management agencies lack the funds to collect intensive individual‐level data.

A popular and potentially sustainable fishery resource under pressure–extinction risk and conservation of Brazilian Sciaenidae (Teleostei: Perciformes)

Croakers (Sciaenidae) are major fishery resource in Brazil; constituting 22% of marine and 9% of freshwater fishery landings. Croakers are subject to heavy fishing pressure throughout Brazil, but habitat alteration is also an important threat to regional populations. In this regional Sciaenidae assessment, each species was analyzed for relative risk of extinction, including the identification and quantification of the impact of major threats and existing conservation measures, based on application of the Categories and Criteria of the IUCN Red List of Threatened Species. Of the 52 species of Sciaenid fishes (34 marine and 18 freshwater) present in Brazilian waters, the majority are at low risk of extinction, with 10 species classified as Data Deficient (DD) and 36 as Least Concern (LC). However the Southern black drum (Pogonias cromis), listed as Endangered (EN) is the most threatened species in the region, while three other species are classified as Near Threatened (NT). A large portion of Brazilian croakers is landed by small-scale artisanal fisheries, which are scattered along coastal and riverine communities. However, our assessments reveal that available fishery landing statistics may have greatly underestimated the artisanal fishery production and by-catch of Sciaenids. We recommend establishing, with adequate enforcement, coastal and riverine protected areas as well as strategic fishing seasons to improve and maintain the conservation status of Sciaenids and sustainable Sciaenid fisheries.

Classifying degrees of species commonness: North Sea fish as a case study

Species commonness is often related to abundance and species conservation status. Intuitively, a “common species” is a species that is abundant in a certain area, widespread and at low risk of extinction. Analysing and classifying species commonness can help discovering indicators of ecosystem status and can prevent sudden changes in biodiversity. However, it is challenging to quantitatively define this concept. This paper presents a procedure to automatically characterize species commonness from biological surveys. Our approach uses clustering analysis techniques and is based on a number of numerical parameters extracted from an authoritative source of biodiversity data, i.e. the Ocean Biogeographic Information System. The analysis takes into account abundance, geographical and temporal aspects of species distributions. We apply our model to North Sea fish species and show that the classification agrees with independent expert opinion although sampling biases affect the data. Furthermore, we show that our approach is robust to noise in the data and is promising in classifying new species. Our method can be used in conservation biology, especially to reduce the effects of the sampling biases which affect large biodiversity collections.

The efficiency of close inbreeding to reduce genetic adaptation to captivity.

Although ex situ conservation is indispensable for thousands of species, captive breeding is associated with negative genetic changes: loss of genetic variance and genetic adaptation to captivity that is deleterious in the wild. We used quantitative genetic individual-based simulations to model the effect of genetic management on the evolution of a quantitative trait and the associated fitness of wild-born individuals that are brought to captivity. We also examined the feasibility of the breeding strategies under a scenario of a large number of loci subject to deleterious mutations. We compared two breeding strategies: repeated half-sib mating and a method of minimizing mean coancestry (referred to as gc/mc). Our major finding was that half-sib mating is more effective in reducing genetic adaptation to captivity than the gc/mc method. Moreover, half-sib mating retains larger allelic and adaptive genetic variance. Relative to initial standing variation, the additive variance of the quantitative trait increased under half-sib mating during the sojourn in captivity. Although fragmentation into smaller populations improves the efficiency of the gc/mc method, half-sib mating still performs better in the scenarios tested. Half-sib mating shows two caveats that could mitigate its beneficial effects: low heterozygosity and high risk of extinction when populations are of low fecundity and size and one of the following conditions are met: (i) the strength of selection in captivity is comparable with that in the wild, (ii) deleterious mutations are numerous and only slightly deleterious. Experimental validation of half-sib mating is therefore needed for the advancement of captive breeding programs.

Unravelling the annual cycle in a migratory animal: breeding-season habitat loss drives population declines of monarch butterflies.

Threats to migratory animals can occur at multiple periods of the annual cycle that are separated by thousands of kilometres and span international borders. Populations of the iconic monarch butterfly (Danaus plexippus) of eastern North America have declined over the last 21years. Three hypotheses have been posed to explain the decline: habitat loss on the overwintering grounds in Mexico, habitat loss on the breeding grounds in the United States and Canada, and extreme weather events. Our objectives were to assess population viability, determine which life stage, season and geographical region are contributing the most to population dynamics and test the three hypotheses that explain the observed population decline. We developed a spatially structured, stochastic and density-dependent periodic projection matrix model that integrates patterns of migratory connectivity and demographic vital rates across the annual cycle. We used perturbation analysis to determine the sensitivity of population abundance to changes in vital rate among life stages, seasons and geographical regions. Next, we compared the singular effects of each threat to the full model where all factors operate concurrently. Finally, we generated predictions to assess the risk of host plant loss as a result of genetically modified crops on current and future monarch butterfly population size and extinction probability. Our year-round population model predicted population declines of 14% and a quasi-extinction probability (<1000 individuals) >5% within a century. Monarch abundance was more than four times more sensitive to perturbations of vital rates on the breeding grounds than on the wintering grounds. Simulations that considered only forest loss or climate change in Mexico predicted higher population sizes compared to milkweed declines on the breeding grounds. Our model predictions also suggest that mitigating the negative effects of genetically modified crops results in higher population size and lower extinction risk. Recent population declines stem from reduction in milkweed host plants in the United States that arise from increasing adoption of genetically modified crops and land-use change, not from climate change or degradation of forest habitats in Mexico. Therefore, reducing the negative effects of host plant loss on the breeding grounds is the top conservation priority to slow or halt future population declines of monarch butterflies in North America.

Use of Dynamic Occupancy Models to Assess the Response of Darters (Teleostei: Percidae) to Varying Hydrothermal Conditions in a Southeastern United States Tailwater

AbstractDuring the past 100 years, most large rivers in North America have been altered for flood control, hydropower, navigation or water supply development. Although these activities clearly provide important human services, their associated environmental disturbances can profoundly affect stream‐dwelling organisms. We used dynamic multi‐species occupancy models combined with a trait‐based approach to estimate the influence of site‐level and species‐level characteristics on patch dynamic rates for 15 darter species native to the Elk River, a large, flow‐regulated Tennessee River tributary in Tennessee and Alabama. Dynamic occupancy modelling results indicated that for every 2.5 °C increase in stream temperature, darters were 3.94 times more likely to colonize previously unoccupied stream reaches. Additionally, large‐bodied darter species were 3.72 times more likely to colonize stream reaches compared with small‐bodied species, but crevice‐spawning darter species were 5.24 times less likely to colonize previously unoccupied stream reaches. In contrast, darters were 2.21 times less likely to become locally extinct for every 2.5 °C increase in stream temperature, but high stream discharge conditions elevated the risk of local extinction. Lastly, the presence of populations in neighbouring upstream study reaches contributed to a lower risk of extinction, whereas the presence of populations in neighbouring downstream study reaches contributed to higher rates of colonization. Our study demonstrates the application of a trait‐based approach combined with a metapopulation framework to assess the patch dynamics of darters in a regulated river. Results from our study will provide a baseline for evaluating the ecological consequences of alternative dam operations. Copyright © 2014 John Wiley &amp; Sons, Ltd.

Predicting Extinction Risk of Brazilian Atlantic Forest Angiosperms

Understanding how plant life history affects species vulnerability to anthropogenic disturbances and environmental change is a major ecological challenge. We examined how vegetation type, growth form, and geographic range size relate to extinction risk throughout the Brazilian Atlantic Forest domain. We used a database containing species-level information of 6,929 angiosperms within 112 families and a molecular-based working phylogeny. We used decision trees, standard regression, and phylogenetic regression to explore the relationships between species attributes and extinction risk. We found a significant phylogenetic signal in extinction risk. Vegetation type, growth form, and geographic range size were related to species extinction risk, but the effect of growth form was not evident after phylogeny was controlled for. Species restricted to either rocky outcrops or scrub vegetation on sandy coastal plains exhibited the highest extinction risk among vegetation types, a finding that supports the hypothesis that species adapted to resource-limited environments are more vulnerable to extinction. Among growth forms, epiphytes were associated with the highest extinction risk in non-phylogenetic regression models, followed by trees, whereas shrubs and climbers were associated with lower extinction risk. However, the higher extinction risk of epiphytes was not significant after correcting for phylogenetic relatedness. Our findings provide new indicators of extinction risk and insights into the mechanisms governing plant vulnerability to extinction in a highly diverse flora where human disturbances are both frequent and widespread.

Global ocean conveyor lowers extinction risk in the deep sea

General paradigms of species extinction risk are urgently needed as global habitat loss and rapid climate change threaten Earth with what could be its sixth mass extinction. Using the stony coral Lophelia pertusa as a model organism with the potential for wide larval dispersal, we investigated how the global ocean conveyor drove an unprecedented post-glacial range expansion in Earth׳s largest biome, the deep sea. We compiled a unique ocean-scale dataset of published radiocarbon and uranium-series dates of fossil corals, the sedimentary protactinium–thorium record of Atlantic meridional overturning circulation (AMOC) strength, authigenic neodymium and lead isotopic ratios of circulation pathways, and coral biogeography, and integrated new Bayesian estimates of historic gene flow. Our compilation shows how the export of Southern Ocean and Mediterranean waters after the Younger Dryas 11.6kyr ago simultaneously triggered two dispersal events in the western and eastern Atlantic respectively. Each pathway injected larvae from refugia into ocean currents powered by a re-invigorated AMOC that led to the fastest postglacial range expansion ever recorded, covering 7500km in under 400 years. In addition to its role in modulating global climate, our study illuminates how the ocean conveyor creates broad geographic ranges that lower extinction risk in the deep sea.

Population viability analysis of the Japanese rock ptarmigan Lagopus muta japonica in Japan

The Japanese rock ptarmigan Lagopus muta japonica breeds only in limited alpine areas at high elevations (&gt; 2,500 m a.s.l.) in Japan. The estimated population size is about 2,000 birds and their breeding distribution is subdivided into several local areas, in each of which they may be at risk of local extinction. We estimated age‐specific demographic parameters of the core population breeding on Mt. Norikura in Gifu and Nagano prefecture in Japan. We also estimated population viability using deterministic and stochastic population models. Age‐specific fertility (the number of female offspring that survived to the next breeding season per female) was 0.417 ± 0.086, 0.490 ± 0.080, 0.513 ± 0.153, 0.435 ± 0.078, 0.562 ± 0.139, 0.580 ± 0.122 (mean ± SE) for ages 1‐6+, respectively. The annual survival rate was 0.739 ± 0.047, 0.624 ± 0.064, 0.513 ± 0.087, 0.732 ± 0.151, 0.447 ± 0.220, 0.486 ± 0.089. The population growth rate, evaluated by use of a deterministic projection‐matrix model, predicted a stable population, λ = 1.105 ± 0.063, 95% CI = 0.985‐1.231 and λ = 1.114 ± 0.062, 0.996‐1.239, using two different assumptions for the final age of reproduction by ptarmigan. We evaluated the risk of extinction as the proportion of λs that was &lt; 1, and this was ≤ 4.4%. To complement the deterministic model, we developed an individual‐based stochastic population model in which each of the individuals produced a variable number of offspring and survived one year with certain probabilities that were drawn from estimated distributions of age‐specific clutch size and survival rates. Averaged population growth rate under the stochastic model was λ = 1.1, and the risk of extinction defined as the proportion of trials in which population size ≤ 1 within 30 years was ≤ 8.9%, even when the starting population was small (15 birds). These results suggest that the local population at Mt. Norikura is stable in size and suffers a relatively low risk of extinction. We suggest that this population can serve as a potential source for surrounding small local populations that may be sink populations.

Management of genetic diversity using gene dropping method based on pedigree information

Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.

Management strategy evaluation applied to the conservation of an endangered population subject to incidental take

Management strategy evaluation (MSE) is a simulation method commonly used to evaluate the expected performance of harvest strategies with respect to target populations. However, MSE is also useful for evaluating strategies designed to manage incidental take from endangered populations. We adapted MSE to the case of Sacramento River winter Chinook salmon, an endangered population that is subject to incidental take by mixed-stock ocean salmon fisheries that target more abundant stocks. Pursuant to the US Endangered Species Act, the US National Marine Fisheries Service called for a new fishery management strategy that would link the allowable fishing mortality to the population’s risk of extinction. Our objective was to evaluate extinction risk under different harvest strategies. We simulated the dynamics of the salmon population and the management process simultaneously. The management process included harvest strategies that set allowable fishing mortality rates as a function of population size. Strategies that reduced fishing mortality rates in response to low estimates of population size resulted in lower extinction risk than strategies that set fishing mortality rates at current or historical levels. The number of years of data taken into account by a strategy and the extent of reductions in fishing mortality resulted in different frequencies and durations of reduced fishing opportunity. By quantifying the trade-off between the risk of extinction of an endangered population and the opportunity for fisheries to harvest target stocks, our study illustrated the utility of MSE for applications to endangered populations.

Deep barriers, shallow divergences: reduced phylogeographical structure in the collared pika (Mammalia:Lagomorpha:Ochotona collaris)

AbstractAimPikas (Ochotonaspp.) are alpine specialists that show considerable morphological and genetic variation structured along latitudinal and elevational gradients. Recent studies ofNorthAmerican andAsian pikas have uncovered phylogeographical partitioning among separate mountain ranges and drainages, driven byQuaternary climate fluctuations. We tested the prediction that collared pikas (O. collaris) exhibit lower genetic diversity and less structure than other species of pika due to lower long‐term habitat stability.LocationEasternBeringia (Alaska and north‐westernCanada).MethodsWe examined phylogeographical variation in the collared pika (O. collaris) throughout much of its known range using the mitochondrial cytochromebgene. Population divergence and genetic diversity were compared within and between mountain ranges. Genetic diversity was contrasted with current andPleistocene habitat fragmentation inferred from ecological niche models.ResultsLow but significant differentiation was evident between most populations ofO. collaris, with little haplotype sharing among populations and a single phylogeographical break separating a genetically distinct haplogroup in the south‐eastern part of its range. Variation was mostly structured within populations (as opposed to between populations or mountain ranges). When within‐species nucleotide diversity inO. collaris,O. princepsandO. curzoniaewas compared, genetic diversity was found to decline with increasing latitude.Main conclusionsPopulations ofO. collarisare less geographically structured and exhibit less variability than populations of eitherO. princepsorO. curzoniae. This pattern is better explained by the amount of availablePleistocene habitat predicted for each species than by current predicted habitat or population discontinuity. Collared pikas are currently considered to be a common species at low risk of extinction, but their habitat specificity, population subdivision, and low genetic variation may have consequences for their continued viability in a warming world.