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57 results for “highly endangered”
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Predicting harvest impact and establishment success when translocating highly mobile and endangered species
<p>Harvesting individuals for translocations can negatively impact source populations, a critical challenge for species reduced to small populations. Consequently, translocation cohorts often remain small, reducing the establishment probability at the destination. Balancing the potential benefits and risks of such translocations is further complicated by philopatry and natural metapopulation dynamics if the target species is highly mobile. These challenges highlight the importance of translocation feasibility assessments, but such assessments often remain qualitative to date. The critically endangered Kuaka (Whenua Hou Diving Petrel; Pelecanoides whenuahouensis) is a philopatric, highly mobile seabird that could benefit from conservation translocations, but only one small population remains. Through expert elicitations with a user-friendly Shiny app, we developed a novel metapopulation extension to an integrated population model fitted to long-term data, allowing us to simultaneously project harvest impact on the source and establishment of destination populations under alternative translocation scenarios, while accounting for philopatry and metapopulation dynamics. Establishment of a destination population without excessive impact on the source was possible, but subject to uncertainty about philopatry and metapopulation dynamics. Accounting for juveniles returning to the source post-translocations reduced impact on the source, but also decreased establishment at the destination. Natural movements of adults and juveniles between source and destination populations were predicted to modulate effects of different harvest intensities. Synthesis and application: Using state-of-the art integrated population models and expert elicitations, we illustrate how translocation feasibility can be evaluated transparently and quantitatively, even when targeting endangered, philopatric, and highly mobile species. Our approach is a considerable improvement on current qualitative feasibility assessments. However, we also illustrate that, ultimately, the favoured translocation strategy depends on balancing biological and other fundamental objectives inherent to translocations. Therefore, the ideal strategy cannot be determined solely mathematically, and feasibility assessments should incorporate explicit value statements. Our methodology is applicable to any future translocation scenario.</p>
Fig. 1 in Topical ivermectin is a highly effective seal 'spot-on': A randomised trial of hookworm and lice treatment in the endangered Australian sea lion (Neophoca cinerea)
Fig. 1. Flow diagram of the trial course showing pup recruitment and recapture count for the three experimental groups for each of the three colony visits. P1 = time between recruitment and first recapture; P2 = time between first recapture and second recapture. Observation of deceased pups is shown relative to (i.e., before or after) the pup's sampling at that visit.
Predicting harvest impact and establishment success when translocating highly mobile and endangered species
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Restoration thinning permits stems to capitalise on high-rainfall years in a regenerating endangered forest ecosystem
<p><span>1. Passively regenerating native vegetation presents a cost-effective opportunity to sequester carbon and reinstate habitat in heavily cleared agricultural landscapes.</span></p> <p><span>2. However, in some cases a few woody species recolonise in dense, low-diversity stands that are slow to self-thin.</span></p> <p><span>3. Restoration thinning of over-dominant species has been proposed to accelerate ecosystem recovery, but its longer-term efficacy remains uncertain, and is likely to depend strongly on rainfall.</span></p> <p><span>4. This study focuses on a restoration thinning experiment established in 2007 in dense brigalow (<i>Acacia harpophylla</i>) regrowth in Queensland, Australia. Using variation in rainfall between 2007 and 2017, we examined the interactive effects of neighbourhood density and moisture availability on the growth and survival of <i>A. harpophylla. </i></span></p> <p><span>5. We also compared the strength of <i>A. harpophylla</i> density effects on itself to its effects on a sparsely distributed co-occurring tree species (<i>Casuarina cristata</i>) that was codominant in the original forest.</span></p> <p><span>6. Our results provide clear evidence that thinning permits <i>A. harpophylla</i> to grow rapidly during periods of high rainfall, and that interspecific competition between A<i>. harpophylla</i> and <i>C. cristata</i> is relatively weak. As such, thinning of dense <i>A. harpophylla</i> could be combined with seeding or planting of co-occurring tree species with complementary niches to further accelerate forest recovery in this extensive regrowth ecosystem.</span></p>
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
<p>With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality <em>de novo</em> plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus <em>Fraxinus</em> (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by <em>Syringa</em>, <em>Osmanthus</em>, <em>Olea, and Fraxinus</em>. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.</p>
The high cost of movement in an arid working landscape for an endangered amphibian
<p>Connectivity is essential for the maintenance of genetic diversity and stability of wildlife populations. Drought and changing precipitation regimes have caused natural aquatic amphibian breeding habitats to disappear or become isolated and have led to the replacement of natural surface water with artificial livestock water tanks. Terrestrial movement is the only means of responding to aquatic threats in arid landscapes and to allow population connectivity. Aridity may present an impenetrable barrier in hydrologically fragmented environments. We used a facultatively paedomorphic and federally endangered salamander to assess the challenges of movement across arid working lands. Sonoran tiger salamanders (<em>Ambystoma mavortium stebbinsi</em>) are endemic to the San Rafael Valley of southeastern Arizona, United States of America, where they depend on livestock water tanks as breeding habitat. The ecology of this species' metamorphs outside of stock tanks is virtually unknown. To assess survival on the landscape during terrestrial movement we used radio transmitters to track 78 adult metamorphosed salamanders over two years. Sonoran tiger salamanders moved up to 1 km from the tank edge, and average distances moved of over 400 m were higher than most <em>Ambystoma </em>species. However, during the study period, none reached neighboring stock tanks. We found high mortality due to predation and desiccation. Individuals that dispersed to terrestrial habitat in summer survived longer than individuals that dispersed in spring. High mortality suggests terrestrial movement is exceptionally risky and may contribute to isolated subpopulations and elevated levels of inbreeding. Conservation actions that improve and maintain artificial aquatic habitats as well as increase connectivity may improve long-term management for pond-breeding amphibians in arid regions.</p>
High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
<p>Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (<em>Echinophthirius horridus</em>) infesting the Saimaa ringed seal (<em>Phoca hispida saimensis</em>), which is endemic to Lake Saimaa in Finland and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.</p>
Data from: Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission. DOI: 10.1038/s41598-021-95166-5
<p>An increasing number of studies have found that the implementation of feeding sites for wildlife-related tourism can affect animal health, behaviour and reproduction. Feeding sites can favour high densities, home range overlap, greater sedentary behaviour and increased interspecific contacts, all of which might promote parasite transmission. In the Yunnan snub-nosed monkey (Rhinopithecus bieti), human interventions via provisioning monkeys at specific feeding sites have led to the sub-structuring of a group into genetically differentiated sub-groups. The fed subgroup is located near human hamlets and interacts with domesticated animals. Using high-throughput sequencing, we investigated Entamoeba species diversity in a local host assemblage strongly influenced by provisioning for wildlife-related tourism. We identified 13 Entamoeba species or lineages in faeces of Yunnan snub-nosed monkeys, humans and domesticated animals (including pigs, cattle, and domestic chicken). In Yunnan snub-nosed monkeys, Entamoeba prevalence and OTU richness were higher in the fed than in the wild subgroup. Entamoeba polecki was found in monkeys, pigs and humans, suggesting that this parasite might circulates between the wild and domestic components of this local social–ecological system. The highest proportion of faeces positive for Entamoeba in monkeys geographically coincided with the presence of livestock and humans. These elements suggest that feeding sites might indirectly play a role on parasite transmission in the Yunnan snub-nosed monkey. The implementation of such sites should carefully consider the risk of creating hotspots of disease transmission, which should be prevented by maintaining a buffer zone between monkeys and livestock/humans. Regular screenings for pathogens in fed subgroup are necessary to monitor transmission risk in order to balance the economic development of human communities dependent on wildlife-related tourism, and the conservation of the endangered Yunnan snub-nosed monkey.</p>
High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species
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High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
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Restoration thinning permits stems to capitalise on high-rainfall years in a regenerating endangered forest ecosystem
Open the record for dataset details and reuse information.
The high cost of movement in an arid working landscape for an endangered amphibian
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Supplementary material 1 from: McPartland JM, Small E (2020) A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives. PhytoKeys 144: 81-112. https://doi.org/10.3897/phytokeys.144.46700
A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives
Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii
Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison to the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based in Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.
Data from: Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide- ranging, but endangered, freshwater mussel
Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure range-wide. MtDNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in northern populations, however, all population have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.
Data from: 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'.
Figure 8 in Redescription of the highly endangered species Scutellastra mexicana (Broderip & G.B. Sowerby I, 1829) (Mollusca, Gastropoda)
Figure 8. Consensus tree of the families of Patellidae and Nacellidae with the position of S. mexicana using maximum likelihood and Bayesian methods based on the mitochondrial COI mtDNA gene. The bootstrap values/posterior probabilities (ML/BI) are indicated under the principal nodes. The taxon names are followed by their GenBank accession numbers (S. mexicana specimens were sequenced in the present study). The shaded area indicates the position of S. mexicana.
Figure 7 in Redescription of the highly endangered species Scutellastra mexicana (Broderip & G.B. Sowerby I, 1829) (Mollusca, Gastropoda)
Figure 7. Consensus tree of the families Patellidae and Nacellidae with the position of S. mexicana using maximum likelihood and Bayesian methods based on partial 16S rRNA. The bootstrap values/ posterior probabilities (ML/BI) are indicated under the principal nodes. The taxon names are followed by their GenBank accession numbers (specimen AF058235 belonging to Scutellastra mexicana was also downloaded from GenBank, whereas the other S. mexicana specimens were sequenced in the present study). The shaded area indicates the position of S. mexicana.
Figure 3 in Redescription of the highly endangered species Scutellastra mexicana (Broderip & G.B. Sowerby I, 1829) (Mollusca, Gastropoda)
Figure 3. Small specimen BR21. (a) Dorsal view of the shell of the small specimen. (b) Ventral view of the shell of the small specimen. (c) Ventral view of the soft tissue parts showing a diagnostic feature of small specimens, i.e. a 'scalloped' edge of the mantle. Scale bar: 5 cms.
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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.