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1,999 results for “Endangered”
Figure 3 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 3 Hydrangea durifolia. Branch with distinct "vegetative" leaves, floral axes with leaves and inflorescence buds. Image of specimen E.P. Killip & A.C. Smith 18366 (GH).
Data from: Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds
Critically endangered breeds and populations are often crossed with more common breeds or subspecies. This results in genetic admixture that can be undesirable when it challenges the genetic integrity of wild and domestic populations, causing a loss in special characteristics or unique genetic material and ultimately extinction. Here, we present two genomic selection strategies, using genome-wide DNA markers, to recover the genomic content of the original endangered population from admixtures. Each strategy relies on the estimation of the proportion of nonintrogressed genome in individuals based on a different method: either genomic prediction or identification of breed-specific haplotypes. Then, breeding programs that remove introgressed genomic information can be designed. To test these strategies, we used empirical 50K SNP array data from two pure sheep breeds, Merino (used as target breed), Poll Dorset and an existing admixed population of both breeds. Sheep populations with varying degrees of introgression and admixture were simulated starting from these real genotypes. Both strategies were capable of identifying segment origin, and both removed up to the 100% of the Poll Dorset segments. While the selection process led to substantial inbreeding, we controlled it by imposing a minimum number of individuals contributing to the next generation.
Data from: Genetic depletion at adaptive but not neutral loci in an endangered bird species
Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.
Data from: Local genetic structure in the critically endangered, cave-associated perennial herb Primulina tabacum (Gesneriaceae)
The local spatial genetic structures of cave-associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave-associated plant, and provides valuable information for the sustainable conservation of such species.
Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (A. platyrhynchos) and Laysan duck (A. laysanensis). Whereas mtDNA clearly shows a sister-relationship between Hawaiian ducks and mallards, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan ducks and mallards. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the pre-defined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian sub-fossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically, and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin, and support the hypothesis that the Hawaiian duck may represent a young hybrid species.
Data from: Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates
High-throughput sequencing platforms are generating massive amounts of genomic data from nonmodel species, and these data sets are valuable resources that can be mined to advance a number of research areas. An example is the growing amount of transcriptome data that allow for examination of gene expression in nonmodel species. Here, we show how publicly available transcriptome data from nonmodel primates can be used to design novel research focused on immunogenomics. We mined transcriptome data from the world's most endangered group of primates, the lemurs of Madagascar, for sequences corresponding to immunoglobulins. Our results confirmed homology between strepsirrhine and haplorrhine primate immunoglobulins and allowed for high-throughput sequencing of expressed antibodies (Ig-seq) in Coquerel's sifaka (Propithecus coquereli). Using both Pacific Biosciences RS and Ion Torrent PGM sequencing, we performed Ig-seq on two individuals of Coquerel's sifaka. We generated over 150 000 sequences of expressed antibodies, allowing for molecular characterization of the antigen-binding region. Our analyses suggest that similar VDJ expression patterns exist across all primates, with sequences closely related to the human VH3 immunoglobulin family being heavily represented in sifaka antibodies. Moreover, the antigen-binding region of sifaka antibodies exhibited similar amino acid variation with respect to haplorrhine primates. Our study represents the first attempt to characterize sequence diversity of the expressed antibody repertoire in a species of lemur. We anticipate that methods similar to ours will provide the framework for investigating the adaptive immune response in wild populations of other nonmodel organisms and can be used to advance the burgeoning field of eco-immunology.
Data from: "Transcriptomic resources for the critically endangered stellate sturgeon Acipenser stellatus" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015
This article documents the public availability of transcriptomic resources of the non-model and critically endangered starlet sturgeon Acipenser stellatus.
Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
Data from: Multi-locus analyses indicate that Melastoma dendrisetosum, an endemic and endangered shrub in Hainan, is a distinct species
Melastoma dendrisetosum is an extremely narrowly distributed taxon endemic to the Diaoluo Mountain region in Hainan, China, and was recently taxonomically incorporated under a widespread species, M. sanguineum. Based on its distinct morphological traits, especially the indumentum on the hypanthium, we propose that it should represent a distinct species. In this study, we sequenced six partial nuclear genes and two chloroplast intergenic spacers of M. dendrisetosum and three other morphologically similar species, M. sanguineum, M. penicillatum, and M. normale, to clarify its taxonomic status. M. dendrisetosum exhibited an extremely low level of genetic diversity, and was well-separated from the three other species with no shared haplotypes at all six nuclear genes, supporting the hypothesis that it is a distinct species. This finding was also supported by the Bayesian clustering-based STRUCTURE analysis, phylogenetic analysis, and Bayesian species delimitation analysis. We further propose that M. dendrisetosum be categorized as 'Critically Endangered' under the IUCN criteria, due to its extremely small population and declining habitat quality. We suggest that the conservation of M. dendrisetosum be prioritized, and road construction in its range should be avoided, to protect this distinct and critically endangered species.
FIGURE 3 in The tulip Magnolia (Magnoliaceae), an endangered new shrubby species endemic to Baja Verapaz, Guatemala
FIGURE 3. Magnolia claudiae, holotype (BIGU).
FIGURE 4 in The tulip Magnolia (Magnoliaceae), an endangered new shrubby species endemic to Baja Verapaz, Guatemala
FIGURE 4. Map of Magnolia claudiae and morphologically similar and geographically nearby species.
FIGURES 9–10 in Notes on Falsocis Pic (Coleoptera: Tenebrionoidea: Ciidae), with the description of an endangered Brazilian species
FIGURES 9–10. Falsocis brasiliensis sp. nov.; male holotype. 9. Ventral view. 10. Frontal view.
FIGURES 1–2. Falsocis opacus Pic, male. 1. Dorsal view. 2 in Notes on Falsocis Pic (Coleoptera: Tenebrionoidea: Ciidae), with the description of an endangered Brazilian species
FIGURES 1–2. Falsocis opacus Pic, male. 1. Dorsal view. 2. Lateral view.
FIGURES 7–8 in Notes on Falsocis Pic (Coleoptera: Tenebrionoidea: Ciidae), with the description of an endangered Brazilian species
FIGURES 7–8. Falsocis brasiliensis sp. nov.; male holotype. 7. Dorsal view. 8. Lateral view.
FIGURE 6 in Redescription of Aetobatus flagellum (Bloch & Schneider, 1801), an endangered eagle ray (Myliobatoidea: Myliobatidae) from the Indo – West Pacific
FIGURE 6. Dorsal view of the head of Aetobatus flagellum, MNHN A-7949 (adult male 543 mm DW).
FIGURE 3 in Redescription of Aetobatus flagellum (Bloch & Schneider, 1801), an endangered eagle ray (Myliobatoidea: Myliobatidae) from the Indo – West Pacific
FIGURE 3. Ventral view of Aetobatus flagellum, CSIRO H 6134–01 (subadult male 431 mm DW).
FIGURE 1 in Systematics of the endangered toad genus Andinophryne (Anura: Bufonidae): phylogenetic position and synonymy under the genus Rhaebo
FIGURE 1. (Continued)
FIGURE 2 in Systematics of the endangered toad genus Andinophryne (Anura: Bufonidae): phylogenetic position and synonymy under the genus Rhaebo
FIGURE 2. (Continued)
FIGURE 4 in A new blind snake (Serpentes: Typhlopidae) from an endangered habitat in south-eastern Queensland, Australia
FIGURE 4. Type locality of Anilios insperatus sp. nov. in July 2014.
FIGURE 1 in Redescription of the rare and endangered Broadfin Shark Lamiopsis temminckii (Müller & Henle, 1839) (Carcharhiniformes: Carcharhinidae) from the northeastern Arabian Sea
FIGURE 1. Original illustration of Carcharias (Prionodon) temminckii by Muller & Henle (1839).
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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.