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1,288 results for “threatened”
Data from: Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species
Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals. Annual breeding targets are based on previous productivity, but do not account for changes in reproductive success that may occur over generations in captivity and which may impair the ability of a program to meet its goals. We utilise a large studbook from the Tasmanian devil (Sarcophilus harrisii) captive breeding program to investigate biological, genetic and environmental factors that affect variation in reproductive success among individuals and over generations of captive breeding. Reproductive success declined with increasing generations in captivity: wild-born females had a 56.5% chance of producing a litter compared to a 2.8% chance for generation 5 captive-born females (N = 182) and when they did, wild-born females produced more offspring (3.1 joeys, 95% CI: 2.76 - 3.38, compared to 2.7 joeys, 95% CI: 2.55 - 2.90, in captive-born females [N = 105]). Reproductive success also declined as dam age at first breeding increased. Our results reveal a conflict with the widely-cited conservation strategy to limit opportunity for selection by extending generation length through delaying reproduction, as captive breeding programs that delay female breeding with this goal in mind risk reduced productivity. Our data demonstrate the benefit of pedigree analysis to identify biological processes that reveal crucial trade-offs with conservation best-practice.
Data from: Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a reintroduced population of a threatened species
During population establishment, genetic drift can be the key driver of changes in genetic diversity, particularly while the population is small. However, natural selection can also play a role in shaping diversity at functionally important loci. We used a well-studied, re-introduced population of the threatened Stewart Island robin (N = 722 pedigreed individuals) to determine whether selection shaped genetic diversity at innate immunity toll-like receptor (TLR) genes, over a 9-year period of population growth following establishment with 12 genetic founders. We found no evidence for selection operating with respect to TLR diversity on first-year overwinter survival for the majority of loci, genotypes and alleles studied. However, survival of individuals with TLR4BE genotype was significantly improved: these birds were less than half as likely to die prior to maturity compared with all other TLR4 genotypes. Furthermore, the population frequency of this genotype, at a two-fold excess over Hardy–Weinberg expectation, was increased by nonrandom mating. Near-complete sampling and full pedigree and reproductive data enabled us to eliminate other potential causes of these patterns including inbreeding, year effects, density dependence, selection on animals at earlier life history stages or genome-level association of the TLR4E allele with 'good genes'. However, comparison of observed levels of gene diversity to predictions under simulated genetic drift revealed results consistent with neutral expectations for all loci, including TLR4. Although selection favoured TLR4BE heterozygotes in this population, these effects were insufficient to outweigh genetic drift. This is the first empirical study to show that genetic drift can overwhelm natural selection in a wild population immediately following establishment.
Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity
Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection, and identifying subtle signatures of polygenic adaptation. We used paired-end restriction-site associated-DNA sequencing data (6605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomics studies.
Data from: Conservation of the threatened species Pulsatilla vulgaris Mill. (pasqueflower) is aided by reproductive system and polyploidy
Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using ten nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations is not as evident as expected from demographic trends. Restored populations show genetic variation comparable to their source populations and, in general, to the wild ones. Genetic homogeneity is observed in regeneration trials, although some alleles not captured in source populations are detected. We infer that polyploidy, longevity and clonal reproduction have provided P. vulgaris with the standing genetic variation necessary to make the species resilient to the effects of demographic decline, suggesting that the use of multiple sources for reintroduction may be beneficial to mimic natural gene flow and the availability of multiple allele copies typical of polyploid species.
Data from: Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus)
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and non-threatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises). Genetic diversity at the MHC class II locus and microsatellites was greater in populations in the non-threatened portion of the gopher tortoise's range (MHC class II difference in mean A = 8.11, AR = 0.79, HO = 0.51, and HE = 0.16; microsatellite difference in mean A = 1.05 and AR = 0.47). Only MHC class II sequences showed evidence of positive selection (dN/dS > 1, Z = 1.81, P = 0.04). Historical gene flow as estimated with Migrate-N was greater than recent migration estimated with BayesAss, suggesting that populations were better connected in the past when habitat was less fragmented. MHC genetic differentiation was correlated with microsatellite differentiation (Mantel r = 0.431, P = 0.001) suggesting neutral genetic processes are influencing MHC evolution, and advantageous MHC alleles could be lost due to genetic drift.
FIGURE 6 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 6. Avian species with parasitological records cited in IUCN red list 2008
FIGURE 4 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 4. Amphibian species with parasitological records cited in IUCN red list 2008
FIGURE 7 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 7. Mammalian species with parasitological records cited in IUCN red list 2008
FIGURE 5 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 5. Reptilian species with parasitological records cited in IUCN red list 2008
FIGURE 3 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 3. Chondrichthyes species with parasitological records cited in IUCN red list 2008
FIGURE 2 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 2. Actinopterygii species with parasitological records cited in IUCN red list 2008
FIGURE 1 in Checklist of helminth parasites of threatened vertebrate species from Brazil
FIGURE 1. Vertebrate species with parasitological records cited in IUCN red list 2008
FIGURE 12. Oligosarcus platensis, MHNM 762 in A threatened new species of Oligosarcus and its phylogenetic relationships, with comments on Astyanacinus (Teleostei: Characidae)
FIGURE 12. Oligosarcus platensis, MHNM 762, holotype, 97.0 mm SL. Alcohol-preserved specimen.
FIGURE 10 in A new avocado pest in Central America (Lepidoptera: Tortricidae) with a key to Lepidoptera larvae threatening avocados in California
FIGURE 10. SEM of male coremata scales.
FIGURE 5 in A new species of karst forest Bent-toed Gecko (genus Cyrtodactylus Gray) not yet threatened by foreign cement companies and a summary of Peninsular Malaysia's endemic karst forest herpetofauna and the need for its conservation
FIGURE 5. Google Earth photograph of Hutan Lipur Gunung Senyum, Pahang, Peninsular Malaysia.
Fig. 5 in The Impact of Upgrading Roads on the Conservation of the Threatened Flightless Dung Beetle,Circellum bacchus(F.) (Coleoptera: Scarabaeidae)
Fig. 5. The relationship between time since rainfall
Supplementary material 3 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801
Plant pathogenic bacteria assessment for Zambia
Supplementary material 4 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801
Plant pathogenic protist assessment for Zambia
Supplementary material 2 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801
Guidelines for scoring species
Supplementary material 5 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801
Assessment for vector species
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.