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Data from: No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)
Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.
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.
Data from: Fire does not strongly affect genetic diversity or structure of a common treefrog in the endangered Florida scrub
Fire regimes influence natural populations of organisms in diverse ways, via direct effects on population dynamics as well as indirect effects on habitat and ecosystem processes. Although many amphibian species have evolved to persist in fire-dependent ecosystems, the effects of fire on the genetic diversity of amphibian populations remain relatively unexplored. We examined how different aspects of fire history relate to population genetic diversity and structure of an abundant anuran, Hyla femoralis, in a large, intact area of Florida scrub containing hundreds of seasonally inundated ponds. Specifically, we assessed the overall population genetic structure and examined whether variation in time since fire, fire intensity, or historical fire frequency at breeding sites explained spatial variation in genetic diversity. Based on our sampling of 17 breeding aggregations within the 2,100-ha study area, neither recent nor frequent fire reduce genetic diversity or restrict connectivity among ponds for H. femoralis. Overall, mean effective population sizes were large (average range = 68–572). We detected a positive trend between effective population size (Ne) and average intensity of the most-recent fire, with this factor explaining 42% of the variation in Ne. Our results contrast with previous studies that consistently demonstrate strong relationships between fire history and population genetic structure of scrub-associated lizard species, suggesting that H. femoralis is resilient to a wide range of fire regimes. More generally, our study contributes to understanding the roles of life-history characteristics and environmental unpredictability in shaping organisms' responses to fire.
Data from: Sleeping with the 'enemy' - Hybridization of an endangered tree weta
While hybridization is an important part of the evolutionary process, for rare species mating with more common species hybridization can increase the risks of extinction. By mating with heterospecifics rare species waste valuable reproductive resources and as a result population sizes may decline. If introgression occurs, the rare species can become genetically swamped by alleles from the more common species, rendering it effectively extinct. As a consequence of these risks, hybridization with the more common species Hemideina femorata (Canterbury tree weta) may lead to the extinction of the range restricted species H. ricta (Banks Peninsula tree weta) on Banks Peninsula. The current study uses spatial interpolation to model the distribution of each species and the potential sympatric zone to guide sampling efforts. Polymorphic microsatellite markers and mitochondrial sequence data were used to determine the extent of hybridization between H. ricta and H. femorata. The results confirm that hybridization is possible between these species. However, hybrids and introgression appear to be very rare, suggesting that reproductive isolating barriers are present but incomplete. The threat of extinction to H. ricta via hybridization with H. femorata is low but extreme loss of habitat may cause changes to population densities that could increase the risks of hybridization. Therefore, landowners should be encouraged to conserve native bush.
Data from: Manipulating wetland hydroperiod to improve occupancy rates by an endangered amphibian: modelling management scenarios
Environmental managers have the difficult task of ensuring species persistence despite considerable uncertainty about their response to management. Spatially explicit population models provide one solution for simulating the dynamics of species and evaluating alternative management regimes. We used a Bayesian model to investigate wetland occupancy dynamics of the endangered growling grass frog Litoria raniformis at a wastewater treatment plant in southern Victoria, Australia. We coupled prior information from earlier research on this species with our survey data to quantify the effects of patch-scale variables and connectivity on the probabilities of occupancy, population extinction and colonization. Hydroperiods of 13 sites were experimentally enhanced to bolster occupancy rates by L. raniformis. We used simulations to assess the extent to which the enhanced hydroperiod regime improved the viability of the focal metapopulation. Occupancy rate increased by 15% among the enhanced sites in 2013–2014, whereas the rate of occupancy among unenhanced sites fell by 11% in that year. Forward simulation using the dynamic occupancy model suggested that the minimum occupancy rate across the metapopulation would be 18% higher if the enhanced hydroperiod regime was retained over the next 20 years. Mean posterior effects of patch-scale variables and connectivity on the occupancy dynamics of L. raniformis were consistent with the prior effect in all cases, with only small changes to the size of these effects. There was no clear effect of water chemistry on occupancy dynamics. Synthesis and applications. This work suggests that managing the hydroperiod of constructed wetlands can be an effective tool for the conservation of amphibians and demonstrates the utility of spatially explicit models for assessing metapopulation viability. We encourage managers to experimentally test the efficacy of manipulating patch-scale variables to improve occupancy rates within amphibian metapopulations.
Data from: Assessing the effect of predator control on an endangered goose population subjected to predator-mediated food web dynamics
1. Assessing the effectiveness of conservation actions to halt population declines is challenging when confounded by other factors. We assessed whether culling of red fox, a predator currently increasing in the sub-Arctic, contributed to recent recovery of the critically endangered Fennoscandian population of Lesser White-fronted Goose Anser erythropus, while controlling for potentially confounding food web dynamics. 2. Using 19 years of data, 10 before and 9 after the implementation of annual red fox culling, we estimated the effect of this action on annual performance of the goose population. We corrected for the potentially confounding effects of cyclic rodent dynamics and semi-domestic reindeer carrion abundance, both of which are expected to trigger predator functional and numerical responses, as well as for annual variation in spring phenology. 3. Goose reproductive success fluctuated in synchrony with the rodent cycle and was negatively related to abundant carrion. When accounting for these aspects of food web dynamics, there was no evidence for an effect of red fox culling on reproductive success. There was, however, a tendency for fox culling to increase adult survival. 4. Our analysis suggests that goose performance in their breeding area is influenced by fluctuating offspring predation, mediated by mainly natural (rodents) and partly anthropogenic (semi-domestic reindeer) dynamic components of the food web. 5. Synthesis and applications. The effect of a decade-long red fox culling on goose reproductive success and survival is currently uncertain. This is despite the fact that predation drives reproductive success through changes in rodent and reindeer carrion abundance. New management actions may consist of regulation of reindeer herd sizes and/or removal of carcasses to reduce the subsidizing effect of reindeer carrion on mesopredators. Getting robust evidence regarding the impact of red fox culling on population recovery depends on continuing research to disentangle food web dynamics and efficiency of management actions.
Data from: Wettability of juvenile plumage as a major cause of mortality threatens endangered Barau's Petrel
Seabirds spend most of their life at sea and have to possess a waterproof plumage to be able to sit on water for extended periods. We tracked juvenile Barau's petrels for the first time, when they leave their birth colony and found that half of the transmitters stopped soon after they first landed on the water off Réunion Island. We suspected from observation at sea that birds may have problems with the waterproofness of their plumage. Therefore during the next season we set up a simple protocol to assess waterproofness of the plumage of the birds just before they fledge. This protocol is based on the calculation of a wettability index expressed as the mass of water logged in the plumage after simulating the bird sitting on the sea surface. We found that at least one third of chicks ready to fledge gained more than 4 g of water in 20 sec, indicating that plumage was not waterproof. Within a sample of birds having fledged and before reaching the sea surface, a similar proportion of birds had their plumage not waterproof. For the birds tracked, only those with an index indicating a waterproof plumage successfully dispersed after their first touch on the sea surface. We provide evidence of a possible major cause of mortality of juvenile seabirds that has not been described previously in wild seabirds, but could exist in other species. This issue may be a major cause of threat to the endangered Barau's petrel.
Data from: Genetic variation and population structure in the endangered Hermann's tortoise: the roles of geography and human-mediated processes
The Hermanni's tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing one mitochondrial locus and nine nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure, and to identify the genetic priorities for the conservation of this species. We found that i) all geographic areas are highly differentiated, mainly as a function of their distance but with a clear genetic discontinuity (Fst values larger than 0.4) between the Eastern and the Western subspecies; ii) the contact zone between subspecies is located farthest to the west than previously believed, and it probably coincides with the delta of the largest Italian river; iii) extinction events due to climatic conditions in the Upper Palaeolithic and subsequent human-mediated translocations in the Neolithic possibly explain the unexpected similarity among Spain, Sicily and Corsica. For conservation purposes, the large majority of genetic pools appears autochthonous, although hybridization among subspecies, related to extensive 20th century trade of tortoises across Europe, is observed in Spain and some Italian samples. Most populations do not seem at immediate risk of low genetic variation, except the French population, which has very low nuclear genetic diversity (heterozygosity = 0.25) and where 50 out of 51 sampled animals shared the same mitochondrial sequence. In general, restocking and reintroduction plans should carefully consider the genetic background of the individuals.
Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit
Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method's efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base pair (bp) mitochondrial DNA (mtDNA) locus and 5 nuclear DNA (nDNA) microsatellite loci (111 – 221 bp). DNA degradation was influenced by sample age, DNA type, locus length, and rabbit sex. Both mtDNA and nDNA exhibited high PCR success rates (94.4%) in samples <1 day old. Success rates for microsatellite loci declined rapidly from 80.0% to 42.7% between days 5 and 7, likely due to increased environmental temperature. Success rates for mtDNA amplification remained higher than nDNA over time, with moderate success (66.7%) at 21 days. Allelic dropout rates were relatively high (17.6% at < 1 day) and increased to 100% at 60 days. False allele rates ranged from 0 to 30.0% and increased gradually over time. We recommend collecting samples as fresh as possible for individual identification during summer field conditions. Our study suggests that this method can be useful for future monitoring efforts, including occupancy surveys, individual identification, population estimation, parentage analysis, and monitoring of genetic diversity both of a reintroduced population in central Washington and across their range.
Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and female transcriptomes of brain and gonad tissues were assembled with Trans-ABySS software and merged to produce a more comprehensive S. pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder were annotated using blastx. By means of read mapping against the reference transcriptome and CDS datasets, using Bowtie2, the accuracy of read mapping was assessed. This first endemic Iberian cyprinid transcriptome of organs involved in reproduction processes may serve as a valuable genomic resource for studying sexual mechanisms and other aspects of evolution, such as speciation and responses to environmental changes, and may be a useful tool for conservation studies since S. pyrenaicus is an endangered species.
Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation?
Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand-alone tool when field data are lacking.
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.
Data from: Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican wolf (Canis lupus baileyi)
The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in three separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from three, two, and two founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all three captive lineages and cross-lineage wolves, for more than 172,000 single nucleotide polymorphisms (SNPs). We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.
Data from: Genetic variation, multiple paternity and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata)
The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within-rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs.
Data from: Local forage fish abundance influences foraging effort and offspring condition in an Endangered marine predator
1. Understanding the functional relationship between marine predators and their prey is vital to inform ecosystem-based management. However, collecting concurrent data on predator behaviour and their prey at relevant scales is challenging. Moreover, opportunities to study these relationships in the absence of industrial fishing are extremely rare. 2. We took advantage of an experimental fisheries closure to study how local prey abundance influences foraging success and chick condition of Endangered African penguins Spheniscus demersus in the Benguela Ecosystem. 3. We tracked 75 chick-provisioning penguins with GPS-time-depth devices, measured body condition of 569 chicks, quantified the diet of 83 breeding penguins and conducted 12 forage fish hydro-acoustic surveys within a 20 km radius of Robben Island, South Africa, over three years (2011–2013). Commercial fishing for the penguins' main prey, sardine Sardinops sagax and anchovy Engraulis encrasicolus, was prohibited within this 20 km radius during the study period. 4. Local forage fish abundance explained 60% of the variation in time spent diving for 14 penguins at sea within 2 days of a hydro-acoustic survey. Penguin foraging effort (time spent diving, number of wiggles per trip, number of foraging dives and the maximum distance travelled) increased and offspring body condition decreased as forage fish abundance declined. In addition, quantile regression revealed that variation in foraging effort increased as prey abundance around the colony declined. 5. Policy implications. Our results demonstrate that local forage fish abundance influences seabird foraging and offspring fitness. They also highlight the potential for offspring condition and the mean-variance relationship in foraging behaviour to act as leading indicators of poor prey abundance. By rapidly indicating periods where forage resources are scarce, these metrics could help limit seabird-fisheries competition and aid the implementation of dynamic ocean management.
Data from: Relative risks of inbreeding and outbreeding depression in the wild in endangered salmon
Conservation biologists routinely face the dilemma of keeping small, fragmented populations isolated, wherein inbreeding depression may ensue, or mixing such populations, which may exacerbate population declines via outbreeding depression. The joint evaluation of inbreeding and outbreeding risks in the wild cannot be readily conducted in endangered species, so a suggested 'safe' strategy is to mix ecologically and genetically similar populations. To evaluate this strategy, we carried out a reciprocal transplant experiment involving three neighbouring populations of endangered Atlantic salmon (Salmo salar) now bred in captivity and maintained in captive and wild environments. Pure, inbred, and outbred (first and second generation) cross types were released and recaptured in the wild to simultaneously test for local adaptation, inbreeding depression and outbreeding depression. We found little evidence of inbreeding depression after one generation of inbreeding and little evidence of either heterosis or outbreeding depression via genetic incompatibilities after one or two generations of outbreeding. A trend for outbreeding depression via the loss of local adaptation was documented in one of three populations. The effects of inbreeding were not significantly different from the effects of outbreeding. Hence, at the geographic scale evaluated (34-50 km), inbreeding for one generation and outbreeding over two generations may have similar effects on the persistence of small populations. The results further suggested that outbreeding outcomes may be highly variable or unpredictable at small genetic distances. Our work highlights the necessity of evaluating the relative costs of inbreeding and outbreeding in the conservation and management of endangered species on a case-by-case basis.
Data from: Prescribed burning protects endangered tropical heathlands of the Arnhem Plateau, northern Australia
1. There are concerns that frequent intense fires are reducing biodiversity on the Arnhem Plateau within Kakadu National Park, northern Australia. Since the 1980s, prescribed burning in the early dry season has aimed to reduce the extent of late dry season wildfires. A programme of more strategic prescribed burning has been undertaken since 2007, aiming to increase intervals between fires affecting heathland and rain forest communities. 2. We assess the effectiveness of prescribed burning in Kakadu's Stone Country using a Landsat satellite-derived fire history (1980–2011), in terms of achieving 'tolerable fire intervals' for dominant plant communities. 3. Our analysis indicates that fire regimes have become substantially more favourable for biodiversity since the early 1980s. Although annual extent of burning has remained unchanged, two significant changes in fire regimes have occurred over the long term: (i) a switch from late dry season dominance to early dry season dominance and (ii) an increase in the abundance of long-unburnt vegetation, both of which are likely to benefit biodiversity. Demonstrating the statistical significance of changes associated with recent, more strategic fire management (2007–2011) is limited by the short duration of this management approach, although there is evidence of increasing abundance of long-unburnt vegetation during this time. 4. The view that the Arnhem Plateau's fire regimes are increasingly driving biodiversity loss (due to frequent late dry season wildfires) is erroneous; they are in a more benign state now than at any time over the last three decades, most likely due to extensive use of prescribed burning. 5. Synthesis and applications. In highly fire-prone landscapes, such as savannas, prescribed burning can be an effective means of: (i) bringing forward peak fire activity to the time of year when fire conditions are relatively mild and (ii) increasing abundance of long-unburnt vegetation. These changes are likely to favour persistence of a range of fire-sensitive communities. Our case study supports the strategic use of prescribed burning to protect fire-sensitive biota within highly fire-prone landscapes throughout the world.
Data from: Regional population structure of the endangered Bridle Shiner (Notropis bifrenatus)
In the last 100 years, the Bridle Shiner has declined over significant parts of its range. We used mitochondrial and nuclear microsatellite markers to investigate population structure of this species. Tissue samples were collected from populations in six drainages in PA, NJ, NY and CT. One predominant haplotype was observed in the Delaware, Housatonic, Passaic, and Raritan specimens. Specimens from the Hudson and St. Lawrence drainages had a separate unique haplotype. Microsatellite loci revealed low within-population genetic diversity and pairwise population comparisons of allelic divergence showed significant genetic differences among most drainages. Population structure analysis of microsatellite loci recover the same population clusters inferred using mtDNA. Within the Delaware drainage, there was significant differentiation among areas separated by 128 km. Several alternate scenarios of population divergence and population bottlenecks were investigated using approximate Bayesian computing. These supported a scenario with a bottleneck occurring in the ancestral population of Bridle Shiner followed by recent divergence of Northern and Southern drainages.
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: Environmental niche divergence between genetically distant lineages of an endangered water beetle
Historically, there has been considerable disagreement between researchers about the criteria used to discriminate among species. Decisions based on traditional morphological and genetic data alone can be potentially problematic, especially if the hypotheses are contradictory. Today, taxonomy is integrating new methods from different disciplines that study species' limits and evolution; this diverse range of evidence aids researchers in the recognition of species. Differences in niche characteristics could become a new and useful criterion in helping to decide the status of conflicting taxonomical entities. Ochthebius glaber (family Hydraenidae) is an endangered water beetle typical from southeast Iberian hypersaline streams that shows three clear discrete genetic units within its distribution range. However, there is no evidence to date that these lineages of O. glaber exhibit any adaptive morphological or ecological divergence. Using a modelling approach directed to generate niche representation from distributional data, we found a significant environmental niche divergence for allopatric lineages of O. glaber that followed an aridity gradient. Although we can not conclude firmly at present that the separate populations of O. glaber studied represent separate, reproductively isolated species, this study complements and supports previous phylogeographic analyses through the inclusion of measures of another form of evolutionary change; in this case, ecological diversification. Despite the existence of some methodological limitations, also discussed in this work, we emphasise the importance of recent conceptual advances that allow taxonomy to improve species delimitation practices through the integration of theory and methods from disciplines that study the origin and evolution of species.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.