A preliminary population viability analysis of the critically endangered blue‐eyed black lemur (Eulemur flavifrons)

Population viability analysis is an important tool to assess the extinction risk in small populations of highly specialized primates. The blue‐eyed black lemur (Eulemur flavifrons) is critically endangered with a restricted range in the north‐western dry deciduous forest of Madagascar, where habitat fragmentation and loss of forest connectivity threaten its survival. We performed a population viability analysis (PVA) of this lemur in Ankarafa Forest in the Sahamalaza Peninsula National Park, north‐western Madagascar, to determine the demographic parameters most influential for population persistence and to assess extinction probabilities. We conducted PVA analyses using different demographic parameters which characterize the species including reproduction, lifespan and population size using the software VORTEX for six scenarios with 100 iterations and simulated over 100 years. The simulations suggested the first extinction within 13 years when the percentage of habitat destruction increased up to 12%. Severe habitat destruction such as fire and logging was the major cause which led to the risk of population extinction. Conservation strategies, in particular measures to reduce habitat destruction, are proposed to ensure the survival of this critically endangered lemur.     

Communal nesting under climate change: fitness consequences of higher incubation temperatures for a nocturnal lizard

Communal nesting lizards may be vulnerable to climate warming, particularly if air temperatures regulate nest temperatures. In southeastern Australia, velvet geckos Oedura lesueurii lay eggs communally inside rock crevices. We investigated whether increases in air temperatures could elevate nest temperatures, and if so, how this could influence hatching phenotypes, survival, and population dynamics. In natural nests, maximum daily air temperature influenced mean and maximum daily nest temperatures, implying that nest temperatures will increase under climate warming. To determine whether hotter nests influence hatchling phenotypes, we incubated eggs under two fluctuating temperature regimes to mimic current ‘cold’ nests (mean = 23.2 °C, range 10–33 °C) and future ‘hot’ nests (27.0 °C, 14–37 °C). ‘Hot’ incubation temperatures produced smaller hatchlings than did cold temperature incubation. We released individually marked hatchlings into the wild in 2014 and 2015, and monitored their survival over 10 months. In 2014 and 2015, hot‐incubated hatchlings had higher annual mortality (99%, 97%) than cold‐incubated (11%, 58%) or wild‐born hatchlings (78%, 22%). To determine future trajectories of velvet gecko populations under climate warming, we ran population viability analyses in Vortex and varied annual rates of hatchling mortality within the range 78– 96%. Hatchling mortality strongly influenced the probability of extinction and the mean time to extinction. When hatchling mortality was >86%, populations had a higher probability of extinction (PE: range 0.52– 1.0) with mean times to extinction of 18–44 years. Whether future changes in hatchling survival translate into reduced population viability will depend on the ability of females to modify their nest‐site choices. Over the period 1992–2015, females used the same communal nests annually, suggesting that there may be little plasticity in maternal nest‐site selection. The impacts of climate change may therefore be especially severe on communal nesting species, particularly if such species occupy thermally challenging environments.     

Colonization and extinction dynamics of a declining migratory bird are influenced by climate and habitat degradation

Uncovering the mechanisms involved in the decline of long‐distance migrants remains one of the most pressing issues in European conservation. Since the 1980s, the British breeding population of Garden Warbler Sylvia borin has declined by more than 25%. Here we use data from repeated bird surveys of woodland sites in the 1980s and in 2003–2004 to show that, although the overall population declined between the two periods, the probability of occupancy for this species increased at high latitudes and decreased at low latitudes. Range shifts such as this arise from a change in the ratio of colonizations to extinctions at the range margins, and we therefore related colonization and local extinction at the patch level to concurrent changes in temperature and habitat. The probability of patch colonization by this species was significantly lower where the percentage cover of vegetation in the understorey had declined, reducing habitat quality for this species. The probability of local extinction was significantly correlated with increasing mean May temperature, which may reflect a change in phenology, making breeding conditions less suitable. Changed regimes of grazing and woodland management could be used to increase habitat suitability and thereby increase colonization probability at the local scale, which may in turn increase the probability of patch occupancy despite future climatic unsuitability.     

Quantitative evaluation of hybridization and the impact on biodiversity conservation

Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near‐threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species‐wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two‐thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q‐value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.     

The evolution of microendemism in a reef fish (Hypoplectrus maya)

Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50‐km segment of the Mesoamerican Barrier Reef System (MBRS). We use whole‐genome analysis to infer the demographic history of the Maya hamlet and contrast it with the sympatric and pan‐Caribbean black (H. nigricans), barred (H. puella) and butter (H. unicolor) hamlets, as well as the allopatric but phenotypically similar blue hamlet (H. gemma). We show that H. maya is indeed a distinct evolutionary lineage, with genomic signatures of inbreeding and a unique demographic history of continuous decrease in effective population size since it diverged from congeners just ~3,000 generations ago. We suggest that this case of microendemism may be driven by the combination of a narrow ecological niche and restrictive oceanographic conditions in the southern MBRS, which is consistent with the occurrence of an unusually high number of marine microendemics in this region. The restricted distribution of the Maya hamlet, its decline in both census and effective population sizes, and the degradation of its habitat place it at risk of extinction. We conclude that the evolution of marine microendemism can be a fast and dynamic process, with extinction possibly occurring before speciation is complete.     

An ecological genetic delineation of local seed‐source provenance for ecological restoration

An increasingly important practical application of the analysis of spatial genetic structure within plant species is to help define the extent of local provenance seed collection zones that minimize negative impacts in ecological restoration programs. Here, we derive seed sourcing guidelines from a novel range‐wide assessment of spatial genetic structure of 24 populations of Banksia menziesii (Proteaceae), a widely distributed Western Australian tree of significance in local ecological restoration programs. An analysis of molecular variance (AMOVA) of 100 amplified fragment length polymorphism (AFLP) markers revealed significant genetic differentiation among populations (Φ_PT = 0.18). Pairwise population genetic dissimilarity was correlated with geographic distance, but not environmental distance derived from 15 climate variables, suggesting overall neutrality of these markers with regard to these climate variables. Nevertheless, Bayesian outlier analysis identified four markers potentially under selection, although these were not correlated with the climate variables. We calculated a global R‐statistic using analysis of similarities (ANOSIM) to test the statistical significance of population differentiation and to infer a threshold seed collection zone distance of ~60 km (all markers) and 100 km (outlier markers) when genetic distance was regressed against geographic distance. Population pairs separated by >60 km were, on average, twice as likely to be significantly genetically differentiated than population pairs separated by <60 km, suggesting that habitat‐matched sites within a 30‐km radius around a restoration site genetically defines a local provenance seed collection zone for B. menziesii. Our approach is a novel probability‐based practical solution for the delineation of a local seed collection zone to minimize negative genetic impacts in ecological restoration.     

Temporal patterns in natality and mortality of three threatened antelope species in North Africa: Oryx dammah,Addax nasomaculatus and Nanger dama

Long‐term population studies on large mammals are rare. Here, we have examined the threatened scimitar‐horned oryx, addax and dama gazelle's populations over the last 20 years in Bou Hedma National Park. Using monthly count data of the three studied species collected since 1995, we examined their population trends. Using autocorrelation analyses, we discovered endogenous natural cyclical fluctuations in the numbers of each species, with a periodicity of approximately 3 years. For all three studied species which seem to be opportunistic breeders, births and deaths occurred throughout the year, although with notable seasonality. By means of cross‐correlation, we discovered that during the first 7 years for which data were available, addax numbers were positively correlated with those of dama and inversely correlated with numbers of oryx. This pattern reversed during the following 4‐year period. The number of oryx was negatively correlated with dama during the first 4 years and then became positively correlated during the subsequent 7‐year period. Thus, we draw attention to difference in response to environmental and anthropogenic factors. Incorporating fundamental long‐term population data into developing management approaches, especially for potentially competitive species, is vital for their future long‐term survival and the success of conservation actions.     

Causes and consequences of crayfish extinction: Stream connectivity,habitat changes,alien species and ecosystem services

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Contemporary breeding biology of critically endangered Regent Honeyeaters: implications for conservation

Identifying factors influencing the demographics of threatened species is essential for conservation, but a lack of comprehensive demographic data often impedes the effective conservation of rare and mobile species. We monitored breeding of critically endangered and semi‐nomadic Regent Honeyeaters Anthochaera phrygia (global population c. 100 pairs) over 3 years throughout their range. Overall nest success probability (0.317) was highly spatially variable and considerably lower than previous estimates for this (and many other honeyeater) species, as was productivity of successful nests (mean 1.58 juveniles fledged). Nest surveillance revealed high predation rates by a range of birds and arboreal mammals as the primary cause of nest failure. An estimated 12% of pairs either failed to establish a territory or their nests did not reach the egg stage. We also found a male bias to the adult sex ratio, with an estimated 1.18 males per female. Juvenile survival for the first 2 weeks after fledging was high (86%). Management interventions that aim to increase nest success in areas of low nest survival must be investigated to address an apparent decline in reproductive output and avoid extinction of the Regent Honeyeater. We show that temporal and spatial variation in the breeding success of rare and highly mobile species can be quantified with robust population monitoring using sampling regimens that account for their life histories. Understanding the causes of spatio‐temporal variation in breeding success can enhance conservation outcomes for such species through spatially and temporally targeted recovery actions.     

Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well‐studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θ_S), the rate of gene flow among patches (4Nm), the founding population size (N₀) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat‐specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750 000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150 000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography.     

The role of age of first breeding in modeling raptor reintroductions

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Large‐scale predator control increases population viability of a rare New Zealand riverine duck

The introduction of mammalian predators to oceanic islands has led to dramatic declines in the abundance of many native species. Conservation management of these species often relies on low‐cost predator control techniques that can be implemented over large scales. Assessing the effectiveness of such management techniques is difficult, but using population viability analyses (PVA), which identify the population growth rate (λ) and extinction risk of threatened species, may offer a solution. PVA provide the opportunity to compare the relative effectiveness of various management options and can identify knowledge gaps to prioritize research efforts. We used PVA to assess the population viability of whio (Hymenolaimus malacorhynchos), a rare riverine duck endemic to New Zealand. Current populations are threatened by introduced mammalian predators and are rapidly declining in both distribution and abundance. Whio conservation management is dominated by large‐scale, low‐intensity predator control, targeting introduced stoats (Mustela erminea). There is evidence that such control increases whio productivity but it is unknown if this increase is sufficient for long‐term population persistence. We undertook a stochastic PVA to assess the viability of whio populations under different management scenarios using data obtained from a 6‐year study of whio demographic responses to predator control. Populations with no predator control and low productivity will rapidly decline to extinction. Increasing productivity through predator control increased population viability but populations still showed a declining trajectory. A perturbation analysis showed that the growth rate of whio populations was largely driven by adult survival. Therefore, future research should target obtaining more robust estimates of adult survival, particularly how it is affected by predator control. Overall, our analysis indicated that large‐scale predator control increases the short‐term viability of whio populations but is insufficient for long‐term population persistence.     

Considering threats to population viability of the endangered Korean long-tailed goral (Naemorhedus caudatus) using VORTEX

Population viability analysis (PVA) has frequently been used in conservation biology to predict extinction rates for threatened or endangered species. In this study, we used VORTEX to model Korean long-tailed goral (Naemorhedus caudatus) using previously collected ecological data. We focused on modelling population extinction, mean population size and heterozygosity. The minimum viable population size was found to be at least 50 gorals for 100 years, regardless of carrying capacity. However, populations with fewer than 50 gorals could not remain successful in the model. Inbreeding depression, catastrophes and supplementation also affected patterns of population extinction, mean population size and heterozygosity. Supplementation with new individuals had the strongest effect on extinction, mean population size and heterozygosity, followed by initial population size, inbreeding, catastrophes and carrying capacity. These results suggest that a supplementation by extra goral individuals from goral proliferation facilities would be the most helpful means for the restoration programme. More Korean goral-specific information regarding demographic and habitat parameters is needed for further PVA of the species.     

Conservation status assessment of the Sharp‐shinned Hawk,an endangered insular raptor in Puerto Rico

Sharp‐shinned Hawks (Accipiter striatus) are forest raptors that are widely distributed in the Americas. A subspecies endemic to Puerto Rico (A. s. venator) is listed as endangered and restricted to mature and old secondary montane forests and shade coffee plantations. However, recent information about the population status and distribution of Puerto Rican Sharp‐shinned Hawks is lacking. We developed a spatial geographic distribution model for Sharp‐shinned Hawks in Puerto Rico from 33 locations collected during four breeding seasons (2013–2016) using biologically relevant landscape variables (aspect, canopy closure, elevation, rainfall, slope, and terrain roughness). Elevation accounted for 89.8% of the model fit and predicted that the greatest probability of occurrence of Sharp‐shinned Hawks in Puerto Rico (> 60%) was at elevations above 900 m. Based on our model, an estimated 56.1 km² of habitat exists in Puerto Rico with a high probability of occurrence. This total represents ~0.6% of the island's area. Public lands included 43.8% of habitat with high probability of occurrence (24.6 km²), 96% of which was located within four protected areas. Our results suggest that Sharp‐shinned Hawks are rare in Puerto Rico and restricted to the higher elevations of the Cordillera Central. Additional research is needed to identify and address ecological limiting factors, and recovery actions are needed to avoid the extinction of this endemic island raptor.     

Is there genetic connectivity among the critically endangered White‐winged Flufftail (Sarothrura ayresi) populations from South Africa and Ethiopia?

The White‐winged Flufftail (Sarothrura ayresi) is known to occur in the highland marshes of Ethiopia, as well as almost 4000 km in South Africa. The White‐winged Flufftail is listed globally as Critically Endangered. In South Africa the population is estimated to be <50 birds. These birds are severely threatened by habitat destruction. Thus far, no genetic studies have been conducted on S. ayresi to confirm genetic connectivity between the South African and Ethiopian populations. In this study, analysis of mitochondrial and nuclear markers was conducted for White‐winged Flufftail samples from South African and Ethiopian birds, as well as Red‐chested Flufftail (Sarothrura rufa) for species comparison. Analyses of the DNA regions identified three variations between the two populations, supporting the hypothesis that these two populations are not different species or subspecies but are rather one migrating population with different seasonal occupied ranges. However, these results do not exclude the possibility of additional breeding and nonbreeding sites. Low genetic diversity in the populations of White‐winged Flufftails was observed, which needs to be further elucidated with fast evolving co‐dominant markers such as microsatellites, as this low diversity may ultimately contribute to the extinction of the species.     

Shifts in population size structure for a drying‐tolerant fish in response to extreme drought

For freshwater systems, climate change‐induced alterations to drought regimes are a considerable threat to already threatened species. This is particularly poignant for kōwaro (or Canterbury mudfish, Neochanna burrowsius), a critically endangered fish largely restricted to drying‐prone waterways on the Canterbury Plains, New Zealand. By comparing three catchment‐wide surveys (2007, 2010, 2015) within the Waianiwaniwa Valley, we assessed the scale and magnitude of population change induced by 2 years of consecutive drought (2014–15), when compared to surveys during wetter conditions (2007, 2010). The droughts triggered a catchment‐wide switch from adult‐dominated populations to populations comprised of juveniles indicated by a significant reduction in median size (~95 mm during the wet to ~60 mm after drought). In comparison, population abundances were highly variable, indicated by no significant change in catch‐per‐unit‐effort. The large variation in catch rates and connection of median size to reproductive potential mean median size will be useful to measure in monitoring to infer potential changes to population resilience, particularly during extreme events. Furthermore, because N. burrowsius could be regarded as extremophile fish, already restricted to harsh habitats, they are likely to become increasingly threatened by climate change. Thus, tools that allow for insightful comparisons between populations, such as a population resilience framework based on both abundance and body size distribution, will be increasingly important for pragmatic decision‐making for targeted conservation measures.     

Flood pulses drive the temporal dynamics of assemblages of aquatic insects (Heteroptera and Coleoptera) in a temperate floodplain

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Lack of genetic diversity across diverse immune genes in an endangered mammal,the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll‐like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome‐level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole‐genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29–220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long‐term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad‐scale immunogenetic diversity analysis in threatened species.     

Size‐structured vulnerability of the colonial cyanobacterium,Microcystis aeruginosa,to grazing by zebra mussels (Dreissena polymorpha)

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