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1,288 results for “threatened”
Data from: Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii)
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red-legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east-west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the 'abundant-center' model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire-flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.
Data from: Seagrass on the brink: decline of threatened seagrass Posidonia australis continues following protection
Seagrasses are in decline globally due to sustained pressure from coastal development, water quality declines and the ongoing threat from climate change. The result of this decline has been a loss of coastal productivity, a reduction in critical fisheries habitat and increased erosion. Attempts to slow this decline have included legislative protection of habitat and direct restoration efforts. Monitoring the success of these approaches requires tracking changes in the abundance of seagrasses, but such monitoring is frequently conducted on large scales that lack the sensitivity to detect changes in time. Here, we used high resolution aerial imagery to quantify the change in meadows dominated by Posidonia australis over five years at 14 sites in five estuaries in south-eastern Australia. Australia has some of the world's most diverse and extensive seagrass meadows, but the widely distributed P. australis has a slow growth rate, recovers poorly after disturbance, and suffers runaway attrition if the conditions for recovery are not met. In 2010, after declines of 12-57% between the 1940s and 1980s, P. australis was listed as a threatened ecological community in New South Wales. We quantified changes in area at fine scales and, where loss was observed, describe the general patterns of temporal decline within each meadow. Our results demonstrate that seagrass meadows dominated by P. australis underwent declines of ~ 2-40% total area at our study sites between 2009 and 2014. In the iconic Sydney Harbour, our analyses suggest that P. australis meadows are declining at an average rate greater than 10% yr-1, exceeding the global rate of seagrass decline. Highlighting these alarming declines across the study region should serve as means to prioritise management action and review the effectiveness of legislative listing as a method to limit impacts at an ecosystem level.
Data from: Plant – herbivorous beetle networks: molecular characterization of trophic ecology within a threatened steppic environment
DNA barcoding facilitates many evolutionary and ecological studies, including the examination of the dietary diversity of herbivores. In this study, we present a survey of ecological associations between herbivorous beetles and host plants from seriously threatened European steppic grasslands. We determined host plants for the majority (65%) of steppic leaf beetles (55 species) and weevils (59) known from central Europe using two barcodes (trnL and rbcL) and two sequencing strategies (Sanger for mono/oligophagous species and Illumina for polyphagous taxa). To better understand the ecological associations between steppic beetles and their host plants, we tested the hypothesis that leaf beetles and weevils differ in food selection as a result of their phylogenetic relations (within genera and between families) and interactions with host plants. We found 224 links between the beetles and the plants. Beetles belonging to seven genera feed on the same or related plants. Their preferences were probably inherited from common ancestors and/or resulted from the host plant's chemistry. Beetles from four genera feed on different plants, possibly reducing intrageneric competition and possibly due to an adaptation to different plant chemical defences. We found significant correlations between the numbers of leaf beetle and weevil species feeding on particular plants for polyphagous taxa, but not for nonpolyphagous beetles. Finally, we found that the previous identifications of host plants based on direct observations are generally concordant with host plant barcoding from insect gut. Our results expand basic knowledge about the trophic relations of steppic beetles and plants and are immediately useful for conservation purposes.
Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
Data from: Using local ecological knowledge to monitor threatened Mekong megafauna in Lao PDR
Pressures on freshwater biodiversity in Southeast Asia are accelerating yet the status and conservation needs of many of the region's threatened fish species are unclear. This impacts the ability to implement conservation activities and to understand the effects of infrastructure developments and other hydrological changes. We used Local Ecological Knowledge from fishing communities on the Mekong River in the Siphandone waterscape, Lao PDR to estimate mean and mode last capture dates of eight rare or culturally significant fish species in order to provide conservation monitoring baselines. One hundred and twenty fishermen, from six villages, were interviewed. All eight species had been captured, by at least one of the interviewees, within the waterscape within the past year. However the mean and mode last capture dates varied between the species. Larger species, and those with higher Red List threat status, were caught less recently than smaller species of less conservation concern. The status of the Critically Endangered Pangasius sanitwongsei (mean last capture date 116.4 months) is particularly worrying suggesting severe population decline although cultural issues may have caused this species to have been under-reported. This highlights that studies making use of Local Ecological Knowledge need to understand the cultural background and context from which data is collected. Nevertheless we recommend our approach, of stratified random interviews to establish mean last capture dates, may be an effective methodology for monitoring freshwater fish species of conservation concern within artisanal fisheries. If fishing effort remains relatively constant, or if changes in fishing effort are accounted for, differences over time in mean last capture dates are likely to represent changes in the status of species. We plan to repeat our interview surveys within the waterscape as part of a long-term fish-monitoring program.
Data from: Predator exposure improves anti-predator responses in a threatened mammal
Incorporating an understanding of animal behaviour into conservation programmes can influence conservation outcomes. Exotic predators can have devastating impacts on native prey species and thwart reintroduction efforts, in part due to prey naïveté caused by an absence of co-evolution between predators and prey. Attempts have been made to improve the anti-predator behaviours of reintroduced native prey by conducting laboratory-based predator recognition training but results have been varied and have rarely led to improved survival in reintroduction programmes. We investigated whether in situ predator exposure could improve anti-predator responses of a predator-naïve mammal by exposing prey populations to low densities of introduced predators under controlled conditions. We reintroduced 352 burrowing bettongs to a 26-km2 fenced exclosure at the Arid Recovery Reserve in South Australia and exposed them to feral cats (density 0.03–0.15 cats/km2) over an 18-month period. At the same time, we translocated a different group of bettongs into an exclosure free of introduced predators, as a control. We compared three behaviours (flight initiation distances, trap docility and behaviour at feeding trays) of cat-exposed and control bettongs before the translocations, then at 6, 12 and 18 months post-translocation. Cat-exposed bettongs displayed changes in behaviour that suggested increased wariness, relative to control bettongs. At 18 months post-reintroduction, cat-exposed bettongs had greater flight initiation distances and approached feed trays more slowly than control bettongs. Cat-exposed bettongs also increased their trap docility over time. Synthesis and applications. Translocation is recommended as a conservation tool for many threatened species yet success rates are generally low. We demonstrate that controlled levels of in situ predator exposure can increase wariness in the behaviour of naïve prey. Our findings provide support for the hypothesis that in situ predator exposure could be used as a method to improve the anti-predator responses of predator-naïve threatened species populations.
Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation challenges are large Australasian reptiles with obligate habitat requirements for lowland, coastal and mangrove forests. Plagued by habitat destruction due to high human densities along coastlines, sprawling rural development, and rapidly developing estuarine fisheries industry, coastal forest reptiles are experiencing rapid declines. And yet studies of population biology, genetics, and habitat requirements of species depending on these environments are few. We undertook the present study in order to take a multifaceted approach to understanding a poignant conservation problem. We identify significant evolutionary units for conservation in large-bodied Sailfin Lizards (genus Hydrosaurus), model suitable habitat in the Philippines from extensive occurrence data and evaluate the efficacy of the current protected area network, and identify the source of hydrosaurs in the illegal pet trade. We determine that the extent of the species' habitat coincident with protected areas is low. Our forensic evaluation of the illegal pet trade in the Philippines determines the existence of a natural population that is at risk of systematic exploitation by traders. Together, this integrative study characterizes a conservation urgency of particular significance: the genetically distinct Sailfin lizards of the Bicol faunal region, with suitable habitat virtually unprotected, and clear evidence of heavy exploitation for illegal trade. To the best of our knowledge, our study is the first conservation genetic study to evaluate the potential effectiveness of the protected landscape coverage in the Philippines, a Megadiverse nation and Biodiversity Hotspot.
Data from: Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis)
Conflicting results from different molecular datasets have long confounded our ability to characterise species boundaries. Here we use genome-wide SNP data and an expanded allozyme dataset to resolve conflicting systematic hypotheses on an enigmatic group of fishes (Gadopsis, river blackfishes, Percichthyidae) restricted to southeastern Australia. Previous work based on three sets of molecular markers: mtDNA, nuclear intron DNA and 51 allozyme loci was unable to clearly resolve the status of a putative fifth candidate species (SWV) within Gadopsis marmoratus. Resolving the taxonomic status of candidate species SWV is particularly critical as based on IUCN criteria this taxon would be considered Critically Endangered. After all filtering steps we retained a subset of 10,862 putatively unlinked SNP loci for population genetic and phylogenomic analyses. Analyses of SNP loci based on maximum likelihood, fastSTRUCTURE and DAPC were all consistent with the previous and updated allozyme results supporting the validity of the candidate Gadopsis species SWV. Immediate conservation actions should focus on preventing take by anglers, protection of water resources to sustain perennial reaches and drought refuge pools, and aquatic and riparian habitat protection and improvement. In addition, a formal morphological taxonomic review of the genus Gadopsis is urgently required.
Data from: Mountain pine beetle host-range expansion threatens the boreal forest
The current epidemic of the mountain pine beetle (MPB), an indigenous pest of western North American pine, has resulted in significant losses of lodgepole pine. The leading edge has reached Alberta where forest composition shifts from lodgepole to jack pine through a hybrid zone. The susceptibility of jack pine to MPB is a major concern, but there has been no evidence of host-range expansion, in part due to the difficulty in distinguishing the parentals and their hybrids. We tested the utility of a panel of microsatellite loci optimized for both species to classify lodgepole pine, jack pine and their hybrids using simulated data. We were able to accurately classify simulated individuals, and hence applied these markers to identify the ancestry of attacked trees. Here we show for the first time successful MPB attack in natural jack pine stands at the leading edge of the epidemic. This once unsuitable habitat is now a novel environment for MPB to exploit, a potential risk which could be exacerbated by further climate change. The consequences of host-range expansion for the vast boreal ecosystem could be significant.
Data from: Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae)
Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well-differentiated nuclear marker frequencies should be treated separately. However a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here we re-explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long-term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re-introduction efforts for G. pusilla which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.
Data from: Expansion of industrial plantations continues to threaten Malayan tiger habitat
Southeast Asia has some of the highest deforestation rates globally, with Malaysia being identified as a deforestation hotspot. The Malayan tiger, a critically endangered subspecies of the tiger endemic to Peninsular Malaysia, is threatened by habitat loss and fragmentation. In this study, we estimate the natural forest loss and conversion to plantations in Peninsular Malaysia and specifically in its tiger habitat between 1988 and 2012 using the Landsat data archive. We estimate a total loss of 1.35 Mha of natural forest area within Peninsular Malaysia over the entire study period, with 0.83 Mha lost within the tiger habitat. Nearly half (48%) of the natural forest loss area represents conversion to tree plantations. The annual area of new plantation establishment from natural forest conversion increased from 20 thousand ha year−1 during 1988–2000 to 34 thousand ha year−1 during 2001–2012. Large-scale industrial plantations, primarily those of oil palm, as well as recently cleared land, constitute 80% of forest converted to plantations since 1988. We conclude that industrial plantation expansion has been a persistent threat to natural forests within the Malayan tiger habitat. Expanding oil palm plantations dominate forest conversions while those for rubber are an emerging threat.
Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. eDNA concentration and individual counts both gradually increased from May–July, then both decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.
Data from: Genetic diversity and population structure of Varronia curassavica: a medicinal polyploid species in a threatened ecosystem
Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44 % of the alleles occurred at low frequency in adults of all populations and 41 % in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina.
Data from: Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the U.S., have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In contemplating future management actions for this species should major Snake River dams ever be removed (as many have proposed), it will be important to understand whether evolution is at least partially responsible for this life-history change. We hypothesized that if this trait is genetically based, parents who migrated to sea as subyearlings should produce faster-growing offspring that would be more likely to reach a size threshold to migrate to sea in their first year. We tested this with phenotypic data for over 2600 juvenile SRFCS that were genetically matched to parents of hatchery and natural origin. Three lines of evidence supported our hypothesis: 1) the animal model estimated substantial heritability for juvenile growth rate for three consecutive cohorts; 2) linear modeling showed an association between juvenile life history of parents and offspring growth rate; and 3) faster-growing juveniles migrated at greater speeds, as expected if they were more likely to be heading to sea. Surprisingly, we also found that parents reared a full year in a hatchery produced the fastest-growing offspring of all—apparently an example of cross-generational plasticity associated with artificial propagation. We suggest that SRFCS is an example of a potentially large class of species that can be considered to be "anthro-evolutionary"—signifying those whose evolutionary trajectories have been profoundly shaped by altered selective regimes in human-dominated landscapes.
Data from: An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert
PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. METHODS: Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively. KEY RESULTS: Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas. CONCLUSIONS: Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity.
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: Close kin mating, but not inbred parents, reduces hatching rates and offspring quality in a threatened tortoise
Inbreeding depression, the reduction of fitness due to mating of related individuals, is of particular conservation concern in species with small, isolated populations. Although inbreeding depression is widespread in natural populations, long-lived species may be buffered from its effects during population declines due to long generation times, and thus are less likely to have evolved mechanisms of inbreeding avoidance than species with shorter generation times. However, empirical evidence of the consequences of inbreeding in threatened, long-lived species is limited. In this study, we leverage a well-studied population of gopher tortoises, Gopherus polyphemus, to examine the role of inbreeding depression and the potential for behavioral inbreeding avoidance in a natural population of a long-lived species. We tested the hypothesis that increased parental inbreeding leads to reduced hatching rates and offspring quality. Additionally, we tested for evidence of inbreeding avoidance. We found that high parental relatedness results in offspring with lower quality, and that high parental relatedness is correlated with reduced hatching success. However, we found that hatching success and offspring quality increase with maternal inbreeding, likely due to highly inbred females mating with more distantly-related males. We did not find evidence for inbreeding avoidance in males and outbred females, suggesting sex-specific evolutionary tradeoffs may have driven the evolution of mating behavior. Our results demonstrate inbreeding depression in a long-lived species and that the evolution of inbreeding avoidance is shaped by multiple selective forces.
Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds
Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.
Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.
Data from: Variation across river channels in demographic dynamics of a riparian herb with threatened status: management and conservation implications
PREMISE OF THE STUDY: Gesneria pauciflora is a rare-threatened plant growing in riparian forests. Periodic disturbances, expected in this habitat, could influence demographic dynamics on plant populations, yet their impact may not be the same across watershed. We hypothesize that differences in disturbances between the main-channel and tributaries may lead to spatial dissimilarities in population growth rate (λ), structure, and fecundity. METHODS: 1277 plants were tagged and monitored over a 1.5-years period. Every 6-months we measured plant size, survival and fecundity, in addition to appearance of seedlings. These variables were applied in Integral Projection Models to assess the population status of G. pauciflora. KEY RESULTS: Plants in the main-channel were smaller but were more likely to flower and fruit than those in the tributaries. Overall mortality was greater in the main-channel and more so during the rainy season. At both sites λ ranged from 0.9114-0.9865, and survival/growth of larger plants had a greater effect on lambda (> 0.90) regardless of site. CONCLUSIONS: Lambda values suggest that G. pauciflora is declining across the watershed. Higher mortality rates in the main channel (more-perturbed sites) might driving G. pauciflora to reproduced at smaller sizes, while the tributaries (less-perturbed sites) may benefit growth and lead to larger plant sizes. Extreme climatic events are expected to increase in the Caribbean and might decrease the population if left unmanaged. Management strategies that reduce the time plants require to reach larger sizes might be necessary to increase λ, and reintroduction of cuttings might be a possible solution.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.