Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management.
Ontology highlight
ABSTRACT:
SUBMITTER: Giglio RM
PROVIDER: S-EPMC8061279 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated "recovery units," found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (H e = 0.109-0.357; H o = 0.106- 0.313), (2) high levels of genetic differentiation among colonies (global F ST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long-term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential.
| S-EPMC4729250 | biostudies-other
Project description:BackgroundThe Aotearoa New Zealand takahē (Porphyrio hochstetteri), once thought to be extinct, is a nationally threatened flightless rail under intensive conservation management. While there has been previous research into disease-related microbes in takahē, little is known about the microbes present in the gastrointestinal tract. Given the importance of gut-associated microbes to herbivore nutrition and immunity, knowledge of these communities is likely to be of considerable conservation value. Here we examined the gut microbiotas of 57 takahē at eight separate locations across Aotearoa New Zealand.ResultsFaecal samples, taken as a proxy for the hindgut bacterial community, were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq. Phylogenetic analysis of > 2200 amplicon sequence variants (ASVs) revealed nine main bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Campilobacterota, Firmicutes, Fusobacteriota, Planctomycetota, Proteobacteria, and Verrucomicrobiota) that accounted for the majority of sequence reads. Location was a significant effect (p value < 0.001, 9999 permutations) that accounted for 32% of the observed microbiota variation. One ASV, classified as Lactobacillus aviarius, was present in all samples at an average relative abundance of 17% (SD = 23.20). There was strong evidence (p = 0.002) for a difference in the abundance of the genus Lactobacillus between locations. A common commensal bacterium previously described in takahē, Campylobacter spp., was also detected in most faecal samples.ConclusionsLocation plays a pivotal role in the observed variation among takahē gut bacterial communities and is potentially due to factors such as supplemental feeding and medical treatment experienced by birds housed in captivity at one of the eight sampled sites. These data present a first glimpse of the previously unexplored takahē gut microbiota and provide a baseline for future microbiological studies and conservation efforts.
| S-EPMC8790836 | biostudies-literature
Project description:The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.
| S-EPMC4578892 | biostudies-literature
Project description:Grasslands are among the most threatened and least protected terrestrial biome. Grassland forbs: (1) account for most of the floral diversity; (2) are not well studied because they have been overshadowed by grass-centered research; and (3) have been a major source for biodiversity loss. The Pacific Northwest Bunchgrass Prairie (PNB) of North America is one of the most endangered grasslands on earth. Knowledge of vegetation community dynamics in the PNB is based primarily on bunchgrasses. There is a paucity of information related to the PNB's diverse native perennial forbs (hereafter "forbs"). Consequently, PNB forb community patterns and dynamics are largely unknown. We describe forb community structure and its relationship to environmental factors and phenology. We sampled 29 plots in the Starkey Experimental Forest and Range, northeastern Oregon, at three different times during 2016 (April; May; July). Nonmetric multidimensional scaling (NMS) indicated that the dominant gradient in forb composition was related (R 2 = 0.66) to slope and soil P and K, contrasting flat, poorly drained soils (scabflats) at one end with steep, well-drained soils at the other end. The secondary gradient (R 2 = 0.16) contrasted deeper, finer textured soils at one end with shallow, rocky soils at the other. Forb richness decreased by ~40% from April to July. NMS and Indicator Species Analysis (ISA) showed that most forbs had affinities toward spring. Ubiquitous forbs (e.g., Triteleia grandiflora, Camassia quamash) were sparse to absent by July. Contradictory to general descriptions of the PNB, forb cover and richness in drought-prone sites were comparable to mesic sites when spring data were considered. Our findings suggest that PNB grasslands contain diverse forb communities that are structured primarily by water drainage and soil depth. Conventional sampling concomitant with peak grass biomass is insufficient to characterize PNB forb communities, particularly for scabflats and the most drought-prone soils.
| S-EPMC9217882 | biostudies-literature
Project description:Rangelands cover 40-50% of the Earth's terrestrial surface. While often characterized by limited, yet variable resource availability, rangelands are vital for humans, providing numerous ecosystem goods and services. In the conterminous United States (CONUS), the dominant component of rangeland conservation is a network of public rangelands, concentrated in the west. Public rangelands are interspersed with private and tribal rangelands resulting in a complex mosaic of land tenure and management priorities. We quantify ownership patterns of rangeland production at multiple scales across CONUS and find that both total production and average productivity of private rangelands is more than twice that of public and tribal rangelands. At finer scales, private rangelands are consistently more productive than their public counterparts. We also demonstrate an inverse relationship between public rangeland acreage and productivity. While conserving acreage is crucial to rangeland conservation, just as critical are broad-scale ecological patterns and processes that sustain ecosystem services. Across CONUS, ownership regimes capture distinct elements of these patterns and services, demonstrated through disparate production dynamics. As ownership determines the range of feasible conservation actions, and the technical and financial resources available to implement them, understanding ownership-production dynamics is critical for effective and sustained conservation of rangeland ecosystem services.
| S-EPMC6850440 | biostudies-literature
Project description:Cypripedium tibeticum is a threatened orchid which efficient conservation requires knowledge of its extent and structure of genetic variation. Using two chloroplast DNA fragments (rps16 and trnL-F), we analyzed 157 individuals from 9 populations representing the species range in China. Seven haplotypes were identified. C. tibeticum had high total genetic diversity (H T = 0.80) with major contribution to this diversity made by among-population component (G ST = 0.64, ? ST = 0.86). However, despite high population differentiation there was no clear phylogeographic structure. The populations CY and DC made the greatest contribution to the total gene diversity as well as allelic richness. The possible mechanisms and implications of these findings for conservation of the species are discussed.
| S-EPMC6412106 | biostudies-literature
Project description:Much biodiversity lives on lands to which Indigenous people retain strong legal and management rights. However this is rarely quantified. Here we provide the first quantitative overview of the importance of Indigenous land for a critical and vulnerable part of biodiversity, threatened species, using the continent of Australia as a case study. We find that three quarters of Australia's 272 terrestrial or freshwater vertebrate species listed as threatened under national legislation have projected ranges that overlap Indigenous lands. On average this overlap represents 45% of the range of each threatened species while Indigenous land is 52% of the country. Hotspots where multiple threatened species ranges overlap occur predominantly in coastal Northern Australia. Our analysis quantifies the vast potential of Indigenous land in Australia for contributing to national level conservation goals, and identifies the main land management arrangements available to Indigenous people which may enable them to deliver those goals should they choose to do so.
| S-EPMC5349676 | biostudies-literature
Project description:BackgroundClimate change is already affecting the distributions of many species and may lead to numerous extinctions over the next century. Small-range species are likely to be a special concern, but the extent to which they are sensitive to climate is currently unclear. Species distribution modeling, if carefully implemented, can be used to assess climate sensitivity and potential climate change impacts, even for rare and cryptic species.Methodology/principal findingsWe used species distribution modeling to assess the climate sensitivity, climate change risks and conservation implications for a threatened small-range mammal species, the Iberian desman (Galemys pyrenaicus), which is a phylogenetically isolated insectivore endemic to south-western Europe. Atlas data on the distribution of G. pyrenaicus was linked to data on climate, topography and human impact using two species distribution modeling algorithms to test hypotheses on the factors that determine the range for this species. Predictive models were developed and projected onto climate scenarios for 2070-2099 to assess climate change risks and conservation possibilities. Mean summer temperature and water balance appeared to be the main factors influencing the distribution of G. pyrenaicus. Climate change was predicted to result in significant reductions of the species' range. However, the severity of these reductions was highly dependent on which predictor was the most important limiting factor. Notably, if mean summer temperature is the main range determinant, G. pyrenaicus is at risk of near total extinction in Spain under the most severe climate change scenario. The range projections for Europe indicate that assisted migration may be a possible long-term conservation strategy for G. pyrenaicus in the face of global warming.Conclusions/significanceClimate change clearly poses a severe threat to this illustrative endemic species. Our findings confirm that endemic species can be highly vulnerable to a warming climate and highlight the fact that assisted migration has potential as a conservation strategy for species threatened by climate change.
| S-EPMC2861593 | biostudies-literature
Project description:The biodiversity crisis we live in, marked by high extinction rates, requires well-planned conservation efforts. To overcome this issue, red lists of threatened species are recognized as the main objective approach for evaluating the conservation status of species and therefore guiding conservation priorities. This work focuses on the Myriapoda (Chilopoda and Diplopoda) species listed in the Brazilian red list of fauna to enable discussion of the practical implications of red lists for conservation. Almost all myriapods assessed are endemic to Brazil (99 %) and 73 % are known from subterranean habitats only. Despite of 33 % being recorded from protected areas (PAs), downgrading, degazettement or downsizing of PAs and intense and unregulated ecotourism represent great threats. The PAs network in Brazil tends to fail in conserving myriapod species. The number of data deficient species (42 %) states the need of investing in ecological and taxonomic studies about the group, in order to fill in important knowledge gaps in species assessments nationally and globally. In this work we show that there is a lack of communication between national and global agencies concerning red lists, which results in a significant loss for science and for conservation. Despite investing in national and state red lists, individual countries must take the final step of submitting its data to IUCN global database, as significant international funding is available for IUCN red listed species conservation. Being one of the most diverse countries in the world, and facing the biggest cuts ever on national science funding, losing these important funding opportunities is a huge loss for Brazilian biodiversity conservation and for science. This study raises awareness on subterranean habitats conservation, due to its high endemism and fragility. Since the first edition of the Brazilian Red List in 1968, centipedes are now included for the first time, and millipedes for the second time. The presence of these myriapods in the list brings attention to the group, which usually receives little or no attention in conservation programs and environmental impact assessments. Rather than a specific case for Myriapoda and for Brazil, the points discussed here can be related to arthropods and the tropics, as the most biodiverse countries are emerging economies facing similar challenges in PAs network management, species extinction risks and science funding.
| S-EPMC5904424 | biostudies-literature
Project description:The Tasmanian devil, the world's largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has established an insurance population, which currently holds over 600 devils in captive facilities across Australia. Microbes are known to play a crucial role in the health and well-being of humans and other animals, and increasing evidence suggests that changes in the microbiota can influence various aspects of host physiology and development. To improve our understanding of devils and facilitate management and conservation of the species, we characterised the microbiome of wild devils and investigated differences in the composition of microbial community between captive and wild individuals.A total of 1,223,550 bacterial 16S ribosomal RNA (rRNA) sequences were generated via Roche 454 sequencing from 56 samples, including 17 gut, 15 skin, 18 pouch and 6 oral samples. The devil's gut microbiome was dominated by Firmicutes and showed a high Firmicutes-to-Bacteroidetes ratio, which appears to be a common feature of many carnivorous mammals. Metabolisms of carbohydrates, amino acids, energy, cofactors and vitamins, nucleotides and lipids were predicted as the most prominent metabolic pathways that the devil's gut flora contributed to. The microbiota inside the female's pouch outside lactation was highly similar to that of the skin, both co-dominated by Firmicutes and Proteobacteria. The oral microbiome had similar proportions of Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria.Compositional differences were observed in all four types of microbiota between devils from captive and wild populations. Certain captive devils had significantly lower levels of gut bacterial diversity than wild individuals, and the two groups differed in the proportion of gut bacteria accounting for the metabolism of glycan, amino acids and cofactors and vitamins. Further studies are underway to investigate whether alterations in the microbiome of captive devils can have impacts on their ability to adapt and survive following re-introduction to the wild.
| S-EPMC4687321 | biostudies-literature