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Habitat loss on seasonal migratory range imperils an endangered ungulate

<ol> <li>Endangered species policies and their associated recovery documents and management actions do not always sufficiently address the importance of migratory behavior and seasonal ranges for imperiled populations.</li> <li>Using a telemetry location dataset spanning 1981 – 2018, we tested for changes in prevalence of migratory tactics (resident, migrant) over time, switching between tactics, shifts in seasonal space-use including migration corridors, and survival consequences of migrant and resident tactics for 237 adult female endangered woodland mountain caribou in one population in western Canada.</li> <li>Over more than three decades, the proportion of individuals displaying annual migration to the low elevation forested winter range declined from nearly 100% to 38%. Correspondingly, there was a strong switch away from being migrant to being year-round residents at high elevation.</li> <li>These behavioral changes corresponded to abandonment of low elevation winter ranges in association with increasing levels of anthropogenic land uses, including forestry and oil and gas developments. Furthermore, there were no identifiable migration corridors to target for migratory route protection.</li> <li>These shifts translated to lower survival rates, particularly for caribou demonstrating resident tactics, consistent with recent declines of the caribou population. That migrants switched to residency in their largely undisturbed summer range, despite lower survival, indicates maladaptive habitat selection consistent with recent patterns of mountain caribou extirpations.</li> <li>Globally, endangered species policies and their associated recovery plans and management actions often do not explicitly consider the challenge of protecting migratory species. Effective conservation of migratory species requires protecting critical habitats needed for the entire life history of the species, including all seasonal ranges and migratory habitat.</li> </ol>

Endangered predators and endangered prey: seasonal diet of Southern Resident killer whales

Understanding diet is critical for conservation of endangered predators. The Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily in the west coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of the whales' seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite this species' rarity compared to some other salmonids. During other times of year, when ranging patterns include the U.S. and Canadian west coast and the northern and southern portions of the Salish Sea, their diet is largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and U.S. west coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the late winter/early spring, and returning to nearly 100% in the late spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions. The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on their proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although west coast samples consisted of 14 stocks, four rivers systems accounted for 90% of the samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales' winter range may be an effective conservation strategy for this population.

Using genomic information for management planning of an endangered perennial, Viola uliginosa

Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site associated DNA sequencing (ddRAD-seq). We found monophyletic populations, high levels of inbreeding (mean population FSNP = 0.407 – 0.945), low effective population sizes (Ne = 0.8 – 50.9), indications of past demographic expansion and rare long-distance dispersal. Our results are important in implementing conservation strategies for Viola uliginosa, which should include founding of seed banks, ex situ cultivations, and re-introductions with individuals of proper origin, combined with continuous population monitoring and habitat management.

opennotspecifiedAug 2020View details →

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FIGURE 1 in The advertisement call of Physalaemus caete Pombal & Madureira, 1997 (Anura Leptodactylidae: Leiuperinae), an endangered species endemic to Brazil's northern Atlantic Forest

FIGURE 1. (A–C) Spectrogram, oscillogram, and amplitude spectrum, respectively, of the advertisement call of Physalaemus caete from Igarassu (state of Pernambuco, northeastern Brazil). The dominant harmonic (H4) and adjacent harmonics (H3 and H5) are indicated. The fundamental and second harmonics are supposedly filtered out (see text). (D) Male voucher of P. caete (CHPUFRPE 5840; SVL = 23.0 mm).

A satellite-based mobile warning system to reduce interactions with an endangered species

Earth observing satellites are a major research tool for spatially explicit ecosystem nowcasting and forecasting. However, there are practical challenges when integrating satellite data into usable real-time products for stakeholders. The need of forecast immediacy and accuracy means that forecast systems must account for missing data and data latency while delivering a timely, accurate and actionable product to stakeholders. This is especially true for species that have legal protection. Acipenser oxyrinchus oxyrinchus (Atlantic Sturgeon) were listed under the United States Endangered Species Act in 2012, which triggered immediate management action to foster population recovery and increase conservation measures. Building upon an existing research occurrence model, we developed an Atlantic Sturgeon forecast system in the Delaware Bay, U.S.A. To overcome missing satellite data due to clouds and produce a three-day forecast of ocean conditions, we implemented Data Interpolating Empirical Orthogonal Functions (DINEOF) on daily observed satellite data. We applied the Atlantic Sturgeon research model to the DINEOF output and found that it correctly predicted Atlantic Sturgeon telemetry occurrences over 90% of the time within a three-day forecast. A similar framework has been utilized to forecast harmful algal blooms, but to our knowledge, this is the first time a species distribution model has been applied to DINEOF gap-filled data to produce a forecast product for fishes. To implement this product into an applied management setting, we worked with state and federal organizations to develop real-time and forecasted risk maps in the Delaware River Estuary for both state level managers and commercial fishers. An automated system creates and distributes these risk maps to subscribers' mobile devices, highlighting areas that should be avoided to reduce interactions. Additionally, an interactive web interface allows users to plot historic, current, future, and climatological risk maps as well as the underlying model output of Atlantic Sturgeon occurrence. The mobile system and web tool provide both stakeholders and managers real-time access to estimated occurrences of Atlantic Sturgeon, enabling conservation planning and informing fisher behavior to reduce interactions with this endangered species while minimizing impacts to fisheries and other projects.

Data from: Combining climate, land use change and dispersal to predict the distribution of endangered species with limited vagility

Aim: Many rare species are dispersal-limited and minimal land use and climate changes can impact their colonization capacity. Most ecological niche models predict the distribution of species under future climate and land use change scenarios without incorporating specie-specific dispersal abilities. Here we investigated the effect of climate and land use change on low vagile species accounting for their dispersal capacity and defined accessible areas in the future. Location: Europe. Taxon: Saproxylic beetles. Methods: We used the current (2007-2012) occurrences of six endangered saproxylics to develop ecological niche models using current climate and land use conditions. We projected species distributions under four future climate and land use change scenarios to estimate their potential occurrences. Finally, accounting for species-specific dispersal, we limited their distributions to accessible areas in 2040-50. Results: Without accounting for dispersal abilities we found a strong and positive impact of climate change on the distribution of Cerambix cerdo, Cucujus cinnaberinus, Morimus funereus and Rosalia alpina and a positive effect of land use change on the distribution of Lucanus cervus and Osmoderma eremita. When species-specific dispersal was included, we found a strong and positive impact of land use change on the distribution of all the species. In this case climate change had a lower but positive effect on the distribution of C. cerdo, C. cinnaberinus, L. cervus and R. alpina, and a negative effect on the distribution of O. eremita. Main conclusion: We found that climate change would promote the expansion of saproxylic beetles only in the unrealistic case of unlimited dispersal. Accounting for dispersal abilities, the expansion of our species would be mainly conditioned by the effect of land use change. Thus, we encourage researchers to combine climate and land use change with dispersal when projecting species distribution under future scenarios to accurately identify areas with fundamental species-specific resources.

opencc-zeroFeb 2021View details →

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years via 337 underwater acoustic receivers stationed along the west coast of North America. These sharks and an additional six were also externally fitted with spaghetti identification tags. Our tagging site was a shallow rocky reef off La Jolla (San Diego County), California, USA, where adult females were observed to aggregate every summer. Tagged soupfin sharks were highly migratory along the west coast of North America, between Washington, USA and Baja California Sur, Mexico. However, every three years, they returned to waters off La Jolla, California, where they underwent gestation. This is the first conclusive evidence of triennial migration and philopatry ('home-loving') in any animal, which is apparently driven by this species' unusual triennial reproductive cycle. Females of other shark and ray species with triennial reproductive cycles are also likely to exhibit triennial cycles of migration and philopatry. At least six (15%) of our tagged soupfin sharks were killed in commercial gillnets in Mexico. Policy implications. Identifying multiennial migratory cycles of mature females can reveal hidden stock structure in the form of discrete breeding cohorts, which are spatially and temporally segregated as they cycle through different reproductive phases. Accounting for this complexity may improve the performance of spatially structured stock assessment models, particularly when fishery removals are spatially heterogeneous, as well as inform the spatiotemporal design of fishery-independent surveys. In the US, the soupfin shark is neither actively managed nor recognized as a Highly Migratory Species; however, given the highly migratory behavior we report, this designation should be revisited by the US Pacific Fishery Management Council. Finally, given the extensive fishery removals in Mexico, any future management must be internationally cooperative.

opencc-zeroDec 2011View details →

Data from: Cannibalism as an interacting phenotype: pre-cannibalistic aggression is influenced by social partners in the endangered Socorro isopod (Thermosphaeroma thermophilum)

Models for the evolution of cannibalism highlight the importance of asymmetries between individuals in initiating cannibalistic attacks. Studies may include measures of body size but typically group individuals into size/age classes or compare populations. Such broad comparisons may obscure the details of interactions that ultimately determine how socially contingent characteristics evolve. We propose that understanding cannibalism is facilitated by using an interacting phenotypes perspective that includes the influences of the phenotype of a social partner on the behaviour of a focal individual and focuses on variation in individual pairwise interactions. We investigated how relative body size, a composite trait between a focal individual and its social partner, and the sex of the partners influenced precannibalistic aggression in the endangered Socorro isopod, Thermosphaeroma thermophilum. We also investigated whether differences in mating interest among males and females influenced cannibalism in mixed sex pairs. We studied these questions in three populations that differ markedly in range of body size and opportunities for interactions among individuals. We found that relative body size influences the probability of and latency to attack. We observed differences in the likelihood of and latency to attack based on both an individual's sex and the sex of its partner but found no evidence of sexual conflict. The instigation of precannibalistic aggression in these isopods is therefore a property of both an individual and its social partner. Our results suggest that interacting phenotype models would be improved by incorporating a new conditional ψ, which describes the strength of a social partner's influence on focal behaviour.

opencc-zeroDec 2016View details →

Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus

Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

Data from: Temporal patterns in the abundance of a critically endangered marsupial relates to disturbance by roads and agriculture

The aim of this study was to investigate how landscape disturbance associated with roads, agriculture and forestry influenced temporal patterns in woylie (Bettongia penicillata) abundance before, during and after periods of rapid population change. Data were collected from an area of approximately 140,000 ha of forest within the Upper Warren region in south-western Australia. Woylie abundance was measured using cage trapping at 22 grid and five transect locations with varying degrees of landscape disturbance between 1994 and 2012. We found evidence that the distribution and abundance of woylies over time appears to be related to the degree of fragmentation by roads and proximity to agriculture. Sites furthest from agriculture supported a greater abundance of woylies and had slower rates of population decline. Sites with fewer roads had a greater abundance of woylies generally and a greater rate of increase in abundance after the implementation of invasive predator control. The results of this study suggest that landscape disturbance is less important at peak population densities, but during times of environmental and population change, sites less dissected by roads and agriculture better support woylie populations. This may be due to the role these factors play in increasing the vulnerability of woylies to introduced predators, population fragmentation, weed species invasion, mortality from road collisions or a reduction in available habitat. Strategies that reduce the impact of disturbance on woylie populations could include the rationalisation of forest tracks and consolidation of contiguous habitat through the acquisition of private property. Reducing the impact of disturbance in the Upper Warren region could improve the resilience of this critically important woylie population during future environmental change.

opencc-zeroDec 2016View details →

Data from: Genetic diversity of the critically endangered lake minnow Eupallasella percnurus in Poland and its implications for conservation

The lake minnow (Eupallasella percnurus) is critically endangered. In this paper we characterize the genetic properties of this fish over its range of occurrence in Poland and propose the use of this knowledge in its active protection. Twelve populations of lake minnow from across its range in Poland were investigated. 13 microsatellite loci were investigated to evaluate genetic variation and distance among populations. The magnitude of the genetic bottleneck or founder effects was investigated. In the studied populations, the allelic diversity and heterozygosity showed that genetic variation in this species is low. At most loci, only 2–3 alleles per population were detected. The average number of alleles detected across all loci was 35, and ranged from 24 to 53. The average observed heterozygosity (Ho) across all investigated loci was 0.38 (range 0.21–0.59); the average expected heterozygosity (He) was 0.36 (range 0.18–0.55). The populations remained in Hardy-Weinberg equilibrium. The average Garza-Williamson M index value for all populations was low (0.47), suggesting a reduction in genetic variation due to a founder effect or a genetic bottleneck. Genetic distance among populations was high or very high (FST range: 0.20–0.64; δμ2 range: 1.32–16.98); this was likely a consequence of low gene flow among isolated populations, a founder effect or other genetic bottleneck, and strong genetic drift. The large genetic differences among the investigated lake minnow populations are likely to also exist among other populations of this species, and knowledge of these differences should inform active protection programs based on translocation of wild or cultivated fish of this species. The method presented here can potentially be applied to any population of lake minnows or closely related species.

opencc-zeroDec 2017View details →

Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison to the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based in Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.

opencc-zeroDec 2012View details →

Data from: Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide- ranging, but endangered, freshwater mussel

Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure range-wide. MtDNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in northern populations, however, all population have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.

Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)

Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non-invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable. We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time. The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples. We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.

Data from: Taxa, petitioning agency, and lawsuits affect time spent awaiting listing under the US Endangered Species Act

The United States' Endangered Species Act (ESA) is the world's foremost law for protecting species at risk of extinction; however, species must first be listed as threatened or endangered before receiving protection under the Act. We used an information theoretic approach to assess whether listing budget, policy phase (which was correlated with presidential administration), or both factors were associated with the number of species listed annually between 1983 and 2014. Annual listing rates were positively affected by larger listing budgets; policy phase also had a significant impact on annual listing rates after accounting for the effects of budget. However, the listing process for any one species spans multiple years, thus we also evaluated how taxonomic affiliation, the initiating organization, and lawsuits affected the amount of time 1338 listed species spent in review between 1973 and 2014. Species waited a median of 12.1 years to receive protection, with plants and invertebrates experiencing longer wait times than vertebrates. These process times exceed ESA deadlines, which are two years when initiated from a third party; this may perpetuate population declines and hinder recovery efforts. We observed that at the time of a lawsuit filling for either a proposed or final rule, species had waited, respectively, 4.19 and 0.70 years longer than species for which no lawsuits were filed, indicating lawsuits targeted species that experienced longer delays. We discuss how changes in ESA implementation over time interacted to produce high variability and often long wait times in the listing process. Our results indicated a positive role for both citizen petitions and budget increases to advance the listing process, thus hastening biodiversity protection.

opencc-zeroDec 2013View details →

Data from: Genetic diversity, demographical history and conservation aspects of the endangered yew tree Taxus contorta (syn. Taxus fuana) in Pakistan

Western Himalayan yew (Taxus contorta Griffith, synonym T. fuana Nan Li & R.R. Mill), one of the highly prized tree species for its anticancer properties is experiencing severe reduction in populations across its range in Pakistan. We examined a chloroplast DNA region (trnL-F) and ten nuclear microsatellite loci variations among seven populations to investigate the levels of genetic diversity and demographical history of T. contorta in Pakistan. Low haplotype diversity (HT = 0.182), moderate level of microsatellite diversity (HE = 0.526 ± 0.034), significant population differentiation (FST = 0.106) and high level of inbreeding (FIS = 0.222-0.418) was found in T. contorta compared with its congeners. Results of mismatch distribution analysis, neutrality tests and data on glacial chronologies of western Himalaya indicated that demographic expansion of T. contorta in Pakistan predates extensive glaciations that occurred during late Pleistocene (140.06 thousand years ago (kya), and the spatial expansion most likely happened very recently in the Holocene (6.71 kya). An unprecedented level of habitat disturbances since past few decades coupled with the severe historic climate may have played an important role on an extant population structure of T. contorta. We have discussed a range of sustainable management measures for the ecological restoration of remnant populations as well as to exploit high economic benefits that can be obtained from this species.

opencc-zeroDec 2012View details →

Data from: A comparison of pedigree- and genetic-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken

The primary goal of captive breeding programs for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study both pedigree- and DNA-based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie-chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction of neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree-based inbreeding coefficients (f_pedigree) was less than that obtained from DNA-based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree-based measures when controlling for additional variables such as age, breeding facility, gender, and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie-chickens. This study highlights the importance of using DNA-based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.

opencc-zeroDec 2012View details →

Data from: Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae)

The present study investigated the genetic diversity, population structure, FST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei's genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.

Data from: Resource selection and landscape change reveal mechanisms suppressing population recovery for the world's most endangered antelope

Understanding how bottom-up and top-down forces affect resource selection can inform restoration efforts. With a global population size of <500 individuals, the hirola Beatragus hunteri is the world's most endangered antelope, with a declining population since the 1970s. While the underlying mechanisms are unclear, some combination of habitat loss and predation are thought to be responsible for low abundances of contemporary populations. Efforts to conserve hirola are hindered by a lack of understanding as to why population density remains low, despite eradication of the viral disease, rinderpest. To elucidate factors underlying chronically low numbers, we examined resource selection and landscape change within the hirola's native range. Because hirola are grazers, we hypothesized that the availability of open areas would be linked both to forage and safety from predators. We quantified: (1) changes in tree cover across the hirola's historical range in eastern Kenya over the past 27 years; (2) how tree cover has influenced resource selection by hirola; and (3) interactions between tree cover and predation. Between 1985 and 2012, tree cover increased by 251% across the historical range of hirola. Tree encroachment was associated with a 98% decline of hirola and elephant Loxodonta africana populations, a 74% decline in cattle Bos indicus, an increase in browsing livestock by 327%, and a reduction in rainfall. Although hirola avoided tree cover, we found no evidence that predation on hirola increased with increasing tree cover. Synthesis and applications. Hirola may qualify as a refugee species, in which contemporary populations are restricted to suboptimal habitat and exhibit low survival, reproduction, or both. The extinction of hirola would be the first of a mammalian genus on the African continent in modern history. We conclude that contemporary low numbers of hirola are due at least partly to habitat loss via tree encroachment, triggered by some combination of elephant extirpation, overgrazing, drought, and perhaps fire suppression. We recommend a combination of rangeland restoration efforts (including conservation of elephants, manual clearing of trees, and grass seeding), increased enforcement of an existing protected area (Arawale National Reserve), and reintroductions to enhance recovery for this endangered species. These efforts will rely on enhanced support from the international conservation community and the cooperation of pastoralist communities with which the hirola coexist.