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FIGURE 2 in Establishment of the Hohenbergia capitata complex (Bromeliaceae) with notes on leaf anatomy and description of a new endangered species
FIGURE 2. Holotypes of the species of the Hohenbergia capitata complex. A. H. belemii Smith & Read (US00091435); B. H. capitata Schult. & Schult. f. (M0120820); C. H. nidularioides B.P. Cavalcante, E.H. Souza, A.P. Martinelli & Versieux (HURB18862).
Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape
<p>The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (<em>Ambystoma bishopi</em>) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel. </p>
FIGURE 2. A–I in Adesmia subtropicalis (Leguminosae, Papilionoideae, Dalbergieae), a new endangered species from the Brazilian Pampas
FIGURE 2. A–I: Adesmia subtropicalis Cobra; A: prostrate to ascendant habit. B: densiflorous inflorescence. C: long glandular ochraceous trichomes abundant at the inflorescence. D: stipule narrow-triangular, slightly united at the base. E: paripinnate leaf, with 10 pairs of elliptic leaflets. F–I: fruit; F: calyx, with pilose lobes. G: fruit indumentum, adpressed white tector hairs and long ochraceous glandular hairs. H: fruit 5-articulated, with persistent calyx. I: short arilated seed. Voucher: M. L. Abruzzi 1641 (HAS [barcode] 24431; BOTU [bc] 34586), drawn by Klei Souza.
FIGURE 1. A–C in Adesmia subtropicalis (Leguminosae, Papilionoideae, Dalbergieae), a new endangered species from the Brazilian Pampas
FIGURE 1. A–C: Adesmia subtropicalis Cobra; A: glandular trichomes at the stem B: flower; calyx lobes longer than the corolla; glandular trichomes abundant at the lobe margins. C: racemose inflorescence; leaf pseudoimparipinnate (with an aborted leaflet at the last pair of leaflets); glandular trichomes abundant at the leaf and at the stem. Photos by Thiago Cobra e Monteiro.
FIGURE 5. A in Campanula oreodoxa (Campanulaceae), a new critically endangered species from the Aladagh Mountains, NE Iran
FIGURE 5. A. Geographical position of the study area in northeastern Iran. B. Distribution map of the Campanula oreodoxa in the western Aladagh Mountains. C. Location of the populations of C. oreodoxa and the estimation of EOO and AOO in geoCAT based on IUCN Red List criteria.
FIGURE 2 in Campanula oreodoxa (Campanulaceae), a new critically endangered species from the Aladagh Mountains, NE Iran
FIGURE 2. Campanula oreodoxa in its natural habitat. A. habitats dominated by Cousina edmondsonii and other cushion plants; B. plant in the flowering stage; C–D. close-up view of the flowers, E. plant in the fruiting stage with Cousina edmondsonii in background; F. the fruiting stage showing the dehiscence of the capsule by basal pores.
Consistent concentrations of critically endangered Balearic shearwaters in UK waters revealed by at-sea surveys
<p><u>Aim</u>: Europe's only globally critically endangered seabird, the Balearic shearwater (<i>Puffinus mauretanicus</i>), is thought to have expanded its post-breeding range northwards into UK waters, though its distribution there is not yet well understood. This study aims to identify environmental factors associated with the species' presence, and map the probability of presence of the species across the western English Channel and southern Celtic Sea, and estimate the number of individuals in this area.</p> <p><u>Location</u>:<em><span> The </span></em>western English Channel and southern Celtic Sea</p> <p><u>Methods</u>: <em><span>This study analyses strip transect data collected from vessel-based surveys in the </span></em>western English Channel and southern Celtic Sea during the shearwater's post-breeding period between 2013 and 2017. Using environmental data collected directly and from remote sensors both Generalized Additive Models (GAMs) and the Random Forest (RF) machine learning model were used to determine shearwater presence at different locations.</p> <p><u>Results</u>: Both models indicated that oceanographic features were better predictors of shearwater presence than fish abundance. Seafloor aspect, sea surface temperature, depth, salinity, and maximum current speed were the most important predictors. Based on the timing of the surveys (mainly in October) it is probable that most of the sighted shearwaters were immatures.</p> <p><u>Main conclusions</u>: Areas with consistently high probabilities of shearwater presence were identified at the Celtic Sea front. Our estimates suggest that the study area in southwest Britain supports between 2% and 23% of the global population of Balearic shearwaters. This study provides the most complete understanding of Balearic shearwater distribution in UK waters available to date, information that will help inform any future UK conservation actions concerning this endangered species.</p>
Dog in the matrix: Envisioning countrywide connectivity conservation for an endangered carnivore
<ol> <li><span>Elevated rates of anthropogenic impacts on land-use regimes have pushed terrestrial megafauna to the brink of extinction. Consequently, it is critical to adopt conservation approaches that safeguard individual populations, while retaining connectivity among these populations. Conserving spatially structured populations of imperiled species at large scales is often complex; the past decades have therefore seen a rise in spatial conservation prioritization exercises aimed at shaping landscape-scale conservation programmes.</span></li> <li><span>We present a framework for informing nationwide connectivity conservation, linking ecological and administrative scales, to maximise relevance for management. We assessed connectivity of the endangered dhole <i>Cuon alpinus</i> among 155 potential source populations across India using a data-driven approach combined with graph and circuit theory. We used clustering algorithms to identify ecologically meaningful conservation landscapes; within each landscape, we identified priority source populations based on their connectedness, and quantified pixel-specific habitat <i>accessibility</i>. We superimposed administrative boundaries on our findings to provide conservation recommendations at this management-relevant scale.</span></li> <li><span>We first mapped potential dhole movement across India. Dhole populations fell within three primary clusters—Western and Eastern Ghats (WEG), Central Indian Landscape (CIL), and North-East India (NEI)—of which NEI had the highest forest cover, most diffuse connectivity, and lowest human density, while WEG had the highest protected area coverage, and overall connectedness. Within each conservation landscape we evaluated the relative importance of Protected Areas and accessibility<i> </i>to high-quality patches. Parts of the Eastern Ghats had low habitat accessibility, yet high potential for dhole landscape connectivity. In 114 identified administrative units of priority for habitat restoration, we highlight those with low accessibility, i.e., areas where restoration needs to be spatially targeted for maximum benefits.</span></li> <li> <i>Synthesis and applications</i>. We make recommendations for spatially-informed habitat restoration to enhance dhole connectivity in India, highlighting the importance of improving matrix permeability where dhole movement is currently restricted. More broadly, the framework we present is useful across species and management contexts, as it combines spatial and administrative scales to make ecologically-informed assessments of high relevance to management. Synergistically integrating species ecology, threats, and administrative considerations in connectivity conservation plans can enhance success of species conservation programmes.</li> </ol>
FIGURE 5 in Description of a new and critically endangered species of Atheris (Serpentes: Viperidae) from the Southern Highlands of Tanzania, with an overview of the country's tree viper fauna
FIGURE 5. Map of the Atheris species occurring in Tanzania (the occurrence of A. nitschei within Tanzania borders still need confirmation).
FIGURE 1 in Description of a new and critically endangered species of Atheris (Serpentes: Viperidae) from the Southern Highlands of Tanzania, with an overview of the country's tree viper fauna
FIGURE 1. Comparison of general shape, size and body proportion between A. matildae holotype (left) and a fully grown specimen of A. ceratophora from Udzungwa (MTSN 7506, SVL=54.2) (right) and an illustration of lateral head scalation.
Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding
<p>The salt marsh harvest mouse (<em>Reithrodontomys raviventris</em>; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (<em>Salicornia pacifica</em>), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (<em>Atriplex</em> spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitats than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (<em>Microtis californicus</em>). In contrast, RERA diet overlapped substantially with the native western harvest mouse (<em>R. megalotis</em>) and non-native house mouse (<em>Mus musculus</em>), suggesting potential for competition if these species become sufficiently abundant.</p>
Conservation genomics in an endangered citrus relative
<p>Related paper: Conservation genomics insights into the spontaneous integration of multiple reproductive strategies in an endangered citrus relative</p> <p>Related source: https://github.com/wangnan9394/conservation_genomics</p> <p>#admixture.zip</p> <p>This file including population ancestry of <em>Fortunella</em>. The estimated admixture proportions ranged from K=2 to K=5.</p> <p>#apomixis_locus_200kb_vcf.zip</p> <p>This file including VCF file of the WILDAPO group. The proportion of introgressions from cultivars and the number of heterozygous introgressed variations in samples from WILDAPO was calculated based on this file.</p> <p>#deleterious_mutations.zip</p> <p>This file including the summary of deleterious mutations in <em>Fortunella.</em> The BED file annotated the types of each variation based on the ancestry state.</p> <p>#fd_and_D_statistics.zip</p> <p>There are population level D statistic (ABBA-BABA statistic) and genome-wide fd statistic, using the Dsuite, ANGSD and genomic_general programs.</p> <p>#genome-wide_haplotype_results.zip</p> <p>We calculated the genome-wide haplontic divergence in each sample from the WILDAPO group, and the summary was zipped in this file.</p> <p>#PCA_TajimaD_value.zip</p> <p>The PCA and Tajima’D value were calculated based on the variation map using PLINK. We have included the results of genome-wide Tajima’s D from five groups.</p> <p>#ROH_500kb.zip</p> <p>This file including ROH analysis of <em>Fortunella</em>.</p> <p>#S-locus_analysis.zip</p> <p>This file including VCF file of the S-locus (Chr. 1). The phylogeny of S-locus were constructed based on this VCF file.</p> <p>#SMC_files.zip</p> <p>This file including smc.gz files of five groups (CULAPO, CULSEX, WILDAPO, WILDSEX1, WILDSEX2). The approximate lookup table of each group in this zipped file.</p> <p>#SSMs.zip</p> <p>We calculated the introgression based on the genome-wide species-specific variations (this VCF format file).</p> <p>#Subtrees_TWISST.zip</p> <p>The combination of subtrees, which were calculated based on 25 kb non-overlapped windows. The input subtrees and the output files by TWISST in this file.</p> <p>#treemix.zip</p> <p>we estimated that the potential migration events ranged from 1 to 3 with five repeats for each test.</p> <p>#variation_map_kumquats.vcf.gz</p> <p>we filtered nuclear genomic variations based on depth of coverage and missing rates using VCFtools with the following criteria: variant quality (QD) > 2.0, quality score (QUAL) > 40.0, mapping quality (MQ) > 30.0, genotype calls with a depth > 2 or <100 and with < 20% of genotypes missing across all samples.</p>
FIGURE 1 in First records of the endemic and endangered yellow land crab, Johngarthia lagostoma (Milne Edwards, 1837) (Decapoda: Gecarcinidae), in the Southwestern Atlantic continental area
FIGURE 1. Location of the record of Johngarthia lagostoma on the mainland coast (purple triangles) and in its previous and natural distribution area (white triangles): A–B, locations of specimens of the Johngarthia lagostoma were recorded in Recife (A) and São José da Coroa Grande (B), Pernambuco state; C–D, specimens of Johngarthia lagostoma recorded on the Southwestern Atlantic mainland in the cities of (C) Recife and (D) São José da Coroa Grande, Pernambuco state. RA= Rocas Atoll, FN=Fernando de Noronha Archipelago, AS=Ascension Island, TR= Trindade and Martin Vaz Islands.
Data used to generate results for Meireles et al. 2023. The future of suitable habitats of an endangered Neotropical grassland bird: a path to extinction? Ecology and Evolution.
<p>Here we include all occurrence records (264) found for Campo Miner, in addition to the 47 records of current distribution of the species (*) used for ecological niche modeling analyses. </p>
FIGURE 1 in Typification and threat assessment of Jasminum parkeri (Oleaceae), a point endemic and critically endangered species of Indian Western Himalaya
FIGURE 1. Lectotype (K000901337) http://specimens.kew.org/herbarium/K000901337 and Epitype (K000901336) http://specimens. kew.org/herbarium/K000901336 of Jasminum parkeri Dunn © copyright of the Board of Trustees of the Royal Botanic Gardens, Kew.
Genetic differentiation of a critically endangered population of the limpet Patella candei candei d'Orbigny, 1840, in the Canary Islands
<p>The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, <em>P. candei candei</em> d'Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, <em>P. candei candei</em> was genetically differentiated from the closely related <em>P. candei crenata</em> for the first time. Moreover, genetic differentiation was detected between <em>P. candei candei</em> samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.</p>
Data for the article: Trophic niche partitioning between two prey and their incidental predators revealed various threats for an endangered species
<p><span>Documenting trophic niche partitioning and resource use within a community is critical to evaluate underlying mechanisms of coexistence, competition or predation. Detailed knowledge about foraging is essential as it may influence the vital rates, which, in turn, can affect trophic relationships between species and population dynamics. The aims of this study were to evaluate resource and trophic niche partitioning in summer/autumn between the endangered Atlantic-Gaspésie caribou (<em>Rangifer tarandus caribou</em>) population, moose (<em>Alces americanus</em>) and their incidental predators, the black bear (<em>Ursus americanus</em>) and coyote (<em>Canis latrans</em>), and to quantify the extent to which these predators consumed caribou. Bayesian isotopic analysis showed a small overlap in trophic niche for the two sympatric ungulates suggesting a low potential for resource competition. Our result also revealed that caribou occupied a larger isotopic niche area than moose, suggesting a greater diversity of resources used by caribou. Not surprisingly, coyote consumed mainly deer (<em>Odocoileus virginianus</em>), moose, snowshoe hare (<em>Lepus americanus</em>), and occasionally caribou, while bears consumed mainly vegetation and, to a lesser extent, moose and caribou. As coyotes and bears also feed on plant species, we documented trophic niche overlap between caribou and their predators, as searching for similar resources can force them to use the same habitats and thus increase the encounter rate and, ultimately, mortality risk for caribou. Although the decline of the Gaspésie caribou population is mostly driven by habitat-mediated predation, we found evidence that the low level of resource competition with moose added to the shared resources with incidental predators, mainly bears, may contribute to jeopardize the recovery of this endangered caribou population. Highlighting the trophic interaction between species is needed to establish efficient conservation and management strategies to insure the persistence of endangered populations. The comparison of trophic niches of species sharing the same habitat or resources is fundamental to evaluate the mechanisms of coexistence or competition and eventually predict the consequences of ecosystem changes in the community.</span></p>
FIG. 3 in Using Demography to Evaluate Reintroductions for Conservation of the Endangered Frog, Rana sierrae, in Streams
FIG. 3.—Fate of captive-reared frogs released into the South Fork Rock Creek reaches in 2017 and 2018. The number of frogs released into each stream is shown below each bar.
FIG. 2 in Using Demography to Evaluate Reintroductions for Conservation of the Endangered Frog, Rana sierrae, in Streams
FIG. 2.—Maximum number of years between captures of marked Rana sierrae first captured 2009–2013 in three northern Sierra Nevada streams. First captures occurred 2009–2011 in Lone Rock Creek and South Fork (SF) Rock Creek main channel, or 2009–2011 or 2013 in Independence Creek. Last captures occurred 2009–2011 in all three streams; 2013 in Independence Creek, 2015 in Lone Rock Creek and SF Rock Creek main channel, or 2016–2018 in all three streams.
FIG. 3 in Molecular dietary analysis of the endangered Ozark big-eared bat (Corynorhinus townsendii ingens)
FIG. 3. The occurrence of each moth family recovered through molecular identification of insect DNA recovered from 33 Ozark big-eared bat fecal pellets
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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.