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opennotspecifiedOct 2020View details →

FIGURE 2 in A description of the tadpole of the Critically Endangered Botsford's leaf-litter frog (Leptobrachella botsfordi) with comments on the distribution and conservation status of the species

FIGURE 2. Tadpoles of Leptobrachella botsfordi in life. A and B, lateral views of VNMN 010898 and VNMN 010899 (Stage 25 and 26 respectively); C and D, body dorsal and ventral view of VNMN 010898; E and F, body dorsal and ventral view of VNMN 010899; G, unvouchered specimen at Stage 44 (total length 32.4 mm) in life. Scale bar in A–F is 0.5 cm.

opennotspecifiedOct 2020View details →

FIGURE 1 in A description of the tadpole of the Critically Endangered Botsford's leaf-litter frog (Leptobrachella botsfordi) with comments on the distribution and conservation status of the species

FIGURE 1. Tadpole of Leptobrachella botsfordi in preservative (VNMN 010899, Stage 26): A–C, lateral, dorsal, and ventral views; and D, oral disc. Scale bar is 0.5 cm in A–C and 0.5 mm in D.

opennotspecifiedOct 2020View details →

FIGURE 3. A in A description of the tadpole of the Critically Endangered Botsford's leaf-litter frog (Leptobrachella botsfordi) with comments on the distribution and conservation status of the species

FIGURE 3. A, The updated distribution range of Leptobrachella botsfordi in the Hoang Lien Range, northwest Vietnam. Solid blue area represents presumed range and cross-hatched blue area denotes areas where this species may be possibly extant. Blue outline denotes species' Extent of Occurrence. B, gravel mining at the type locality of L. botsfordi in September 2017.

opennotspecifiedAug 2020View details →

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).

opencc-zeroJan 2021View details →

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.

opencc-zeroJan 2021View details →

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.

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.

Data from: Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole

Glacial refugia protected and promoted biodiversity during the Pleistocene, not only at a broader scale, but also for many endemics that contracted and expanded their ranges within refugial areas. Understanding the evolutionary history of refugial endemics is especially important in the case of endangered species to recognise the origins of their genetic structure and thus produce better informed conservation practices. The Iberian Peninsula is an important European glacial refugium, rich in endemics of conservation concern, including small mammals, such as the Cabrera vole (Microtus cabrerae). This near-threatened rodent is characterised by an unusual suite of genetic, life history and ecological traits, being restricted to isolated geographic nuclei in fast-disappearing Mediterranean sub-humid herbaceous habitats. To reconstruct the evolutionary history of the Cabrera vole, we studied sequence variation at mitochondrial, autosomal and sex-linked loci, using invasive and noninvasive samples. Despite low overall mitochondrial and nuclear nucleotide diversities, we observed two main well-supported mitochondrial lineages, west and east. Phylogeographic modelling in the context of the Cabrera vole's detailed fossil record, supports a demographic scenario of isolation of two populations during the Last Glacial Maximum (LGM) from a single focus in the southern part of the Iberian Peninsula. In addition, our data suggests subsequent divergence within the east, and secondary contact and introgression of the expanding western population, during the late Holocene. This work emphasises that refugial endemics may have a phylogeographic history as rich as that of more widespread species, and conservation of such endemics includes the preservation of that genetic legacy.

opencc-zeroDec 2014View details →

Data from: Estimating effects of species interactions on populations of endangered species

Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

opencc-zeroDec 2016View details →

Data from: AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest

The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean HE=0.125), and negatively correlated with latitude. Overall population differentiation was moderate (ΦST=0.109, P<0.001), and Bayesian analysis of population structure revealed two major latitudinal clusters (I: 'Pacific North'+'Central Highland'; II: 'Pacific South'), along with a genetic cline between I and II. Population-based cluster analyses indicated a strong pattern of 'isolation by distance' as confirmed by Mantel's test. Our results suggest that (1) the low genetic diversity of these populations reflects biogeographic/population history (colonisation from South America, Pleistocene range contractions) rather than recent human impact; whereas (2) the underlying process of their isolation by distance pattern, which is best explained by 'isolation by dispersal limitation', implies contemporary gene flow between neighbouring populations as likely facilitated by the species' efficient seed dispersal capacity. Overall, these results underscore that even tree species from highly decimated forest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.

opencc-zeroDec 2014View details →

Data from: Past climate change drives current genetic structure of an endangered freshwater mussel species

Historical-to-recent climate change and anthropogenic disturbance affect species distributions and genetic structure. The Rio Grande watershed of the United States and Mexico encompasses ecosystems that are intensively exploited, resulting in substantial degradation of aquatic habitats. While significant anthropogenic disturbances in the Rio Grande are recent, inhospitable conditions for freshwater organisms likely existed prior to such disturbances. A combination of anthropogenic and past climate factors may contribute to current distributions of aquatic fauna in the Rio Grande basin. We used mitochondrial DNA and 18 microsatellite loci to infer evolutionary history and genetic structure of an endangered freshwater mussel, Popenaias popeii, throughout the Rio Grande drainage. We estimated spatial connectivity and gene flow across extant populations of P. popeii and used ecological niche models (ENMs) and approximate Bayesian computation (ABC) to infer its evolutionary history during the Pleistocene. structure results recovered regional and local population clusters in the Rio Grande. ENMs predicted drastic reductions in suitable habitat during the last glacial maximum. ABC analyses suggested that regional population structure likely arose in this species during the mid-to-late Pleistocene and was followed by a late Pleistocene population bottleneck in New Mexico populations. The local population structure arose relatively recently, perhaps due to anthropogenic factors. Popenaias popeii, one of the few freshwater mussel species native to the Rio Grande basin, is a case study for understanding how both geological and anthropogenic factors shape current population genetic structure. Conservation strategies for this species should account for the fragmented nature of contemporary populations.

opencc-zeroDec 2017View details →

Data from: Paying for conservation: a bioeconomic analysis of the effects of land management options on the viability of an endangered species, Eryngium alpinum

1. Land management is critical for biodiversity conservation in mountain grasslands. It should be both ecologically effective and economically efficient. We provide an economic analysis of different options (spring and autumn grazing, mowing and abandonment) and their effects on population viability of a rare plant species, Eryngium alpinum (Apiaceae), in two French mountain grassland sites (Fournel and Pralognan). 2. Using data collected in a ten-year, individual-based demographic study, we estimated the effects of land management options on the population growth rate and simulated the effect of combinations of options. Income earned through each option was estimated using data on associated costs (price of consumables, working time, wages) and benefits (forage production, quality and price), and we assessed the economic effects of agri-enviro nment subsidies (AESs). We also simulated the effects of increased frequencies of extreme climatic events (such as the 2003 heatwave). 3. Spring grazing was the worst option for E. alpinum demography but the best in economic terms, as it provided net positive incomes. Autumn grazing was the best option, resulting in positive growth rates and incomes, even if the latter were lower than for spring grazing. Mowing was the second best option for demography but resulted in economic losses for farmers. Abandonment provided zero income and was not favourable to population growth. 4. In Fournel, AESs allowed for economically and ecologically near-optimal combinations of management options. In Pralognan, alternating years of grazing with mowing resulted in an acceptable compromise, with positive growth rates and incomes, but AESs were not sufficient to cover the opportunity cost of spring and autumn grazing. Mowing was also unattractive because of the inaccessibility of the site and impossibility to recover the hay to make forage. 5. Simulations with increased frequency of extreme climatic events resulted in negative growth rates in Pralognan, questioning the continuation of AESs in extinction-prone populations. 6. Synthesis and applications. The conservation effectiveness and economic efficiency of grassland management could be improved by alternating practices over several years. However, existing agri-environment subsidies would barely be sufficient to increase uptake of the most favourable land management options for biodiversity.

opencc-zeroDec 2013View details →

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for one mitochondrial gene and five nuclear loci for species of the Gekko mindorensis-G. kikuchii species complex in Southeast Asia. We used maximum likelihood and Bayesian phylogenetic methods and coalescent-based species delimitation analyses to estimate phylogeographic relationships, construct multilocus haplotype networks and test putative species boundaries. Results: Phylogenetic and population genetic analyses suggest that Kikuchi's Gecko may represent a peripheral population of a widespread species distributed from the northern Philippines to Taiwan. However, we identify a discrepancy between inferences of species boundaries resulting from methods based on allele frequencies versus coalescent-based methods that incorporate evolutionary history. Coalescent-based analyses suggest that G. kikuchii may be a distinct evolutionary lineage. Our study underscores the need for coalescent-based methods in conjunction with population genetic approaches for conservation genetic assessments of widespread species. Main conclusions: This study joins a few recent works suggesting that Philippine-derived anomalies in the fauna of Lanyu (and possibly greater Taiwan) are worthy of careful reconsideration. Determining whether each is the result of recent human-mediated introduction or (possibly more ancient) natural dispersal should be the goal of future studies on this seldom-conceived biogeographic relationship. Isolated species endemic to islands on the outer periphery of biogeographic and political regions represent particular conservation challenges. This is especially true if a species occurs on an isolated island that is allied biogeographically with one nation, but politically administered by another.

Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse-jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species-tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species.

opencc-zeroDec 2017View details →

Data from: Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand

Unresolved taxonomy of threatened species is problematic for conservation as the field relies on species being distinct taxonomic units. Differences in breeding habitat and results from a preliminary molecular analysis indicated that the New Zealand population of the South Georgian Diving Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species. We measured 11 biometric characters and scored eight plumage characters in 143 live birds and 64 study skins originating from most populations of P. georgicus, to assess their taxonomic relationships. We analysed differences with principal component analyses (PCA), factorial ANOVAs, and Kruskal-Wallis rank sum tests. Results show that individuals from New Zealand differ significantly from P. georgicus from all other populations as following: 1) longer wings, 2) longer outer tail feathers, 3) deeper bills, 4) longer heads, 5) longer tarsi, 6) limited collar extent, 7) greater extent of contrasting scapulars, 8) larger contrasting markings on the secondaries, 9) paler ear coverts, 10) paler collars, and 11) paler flanks. Furthermore, we used a species delimitation test with quantitative phenotypic criteria; results reveal that the New Zealand population of P. georgicus indeed merits species status. We hereby name this new species Pelecanoides whenuahouensis sp. nov. Due to severe reductions in its range and the very low number of remaining birds (~150 individuals limited to a single breeding colony on Codfish Island/Whenua Hou) the species warrants listing as 'Critically Endangered'.

Data from: Isodars unveil asymmetric effects on habitat use caused by competition between two endangered species

In order for competing species to coexist, segregation on some ecological niche component is required and is often mediated by differential habitat use. When unequal competitors are involved, the dominant species tends to displace the subordinate one to its less preferred habitat. Here, we use habitat isodars, an approach which reflects evolutionary stable strategies of habitat selection, to evaluate whether interspecific competition between two competing species with distinct habitat preferences, the little bustard Tetrax tetrax and the great bustard Otis tarda, modulates their habitat use. Field data on these endangered species demonstrate that unequal competitors can coexist without completely segregating on their preferred habitats. The negatively sloped isodar of the subordinate little bustard unveils its competition with the dominant great bustard. Interference from great bustards in secondary cereal habitats reinforces use of preferred natural habitat by little bustards. Studies of density-dependent habitat selection by a single-species can thus aid in identifying the effects of competition on community composition, and guide the conservation of at-risk species. Isodars, in particular, represent a promising method to gain clear knowledge on interspecific competition for species in which experimental manipulations are not feasible.