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212 results for “Conserved regions”
Data from: Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards
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Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region
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Data from: The Origin Recognition Complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man
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Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence
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Long-term changes in Wolf Lake (Sudbury region, Ontario) situated in Mi’iangan Zaagagan Preserve: a proposed Indigenous conservation area
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Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers
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Empowering regional conservation: Genetic diversity assessments as a tool for eelgrass management
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Data from: Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance
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FIG. 1 in Bats of the Sangkulirang limestone karst formations, East Kalimantan - a priority region for Bornean bat conservation
FIG. 1. Map of the Sangkulirang peninsula, East Kalimantan, Indonesia, showing settlements and major rivers as well as the major karst formations (dark grey shading) and forest cover (light grey shading). Base camps used at the formations are marked by circles. Map produced by Paul Banks using a forest coverage (including plantations and burnt areas) from the Berau Forest Management Project, and karst and geographic information from Regional Development Agency (BAPPEDA) in Berau, and Anon (1973)
Microsatellite Dataset for: Weaving et al. Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England
<p class="CxSpFirst">The peregrine falcon (<i>Falco peregrinus</i>) has been affected by persecution, pollution, trade, and habitat degradation, but it is considered a flagship conservation success story because of successful reintroductions and population recoveries across broad ranges. However, in the UK there were never formal reintroduction programmes for peregrine falcons, and it appears that UK populations—and specifically the Sussex peregrines of the English south coast—recently recovered from a population crash unassisted. To study this, we obtained samples from contemporary populations in southern England, Ireland, continental Europe, domestic-bred peregrine falcons, and from England pre-population crash. Using microsatellite and mtDNA control region data, the genetic diversity and structure, signatures of genetic bottlenecks, and potential origin of the Sussex peregrines was investigated. We found low levels of genetic diversity across all peregrine falcon groups, low but significant genetic differentiation, and a few private alleles, indicating some level of genetic structure among European peregrines. Although we could not pinpoint the origin of the Sussex peregrines, the data suggests that it is not likely to have originated from escaped domestic birds or from adjacent European populations. The results obtained here parallel other studies on peregrines elsewhere showing low genetic diversity but genetic structure. We conclude that not enough time elapsed for genetic erosion to occur due to the population bottleneck, and that at least for the Sussex peregrines there is no need for genetic conservation by wild-take and subsequent captive breeding programmes as long as current protection measures remain in place.</p>
Data from: Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea
Maintaining and enabling evolutionary processes within meta-populations is critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here we estimate connectivity of Z. marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multi-generation models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale and extant genetic connectivity strongly reflects the "ghost of dispersal past" sensu Benzie 1999. The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.
Optimising nature conservation outcomes for a given region-wide level of food production
<ol> <li>The land sharing-sparing framework aims to quantify the trade-off between food production and biodiversity conservation, but it has been criticised for offering, for reasons of simplicity, an unrealistically limited set of different land uses.</li> <li>Here, we develop the framework to evaluate a much larger suite of land-use strategies in which the areas and yields of three land-use compartments, natural habitat, high-yield farmland, and lower-yield farmland, are varied simultaneously. For two regions of England, we use functions that relate the local population density of breeding bird species to farm yield to simulate species-specific region-wide population sizes under each strategy.</li> <li>We find that geometric mean population size, averaged across all species, is maximised when farmland yields are higher than the current average yield, and when spared land combines both natural habitat and low-yield farmland. This conclusion is relatively insensitive to the maximum yield considered feasible under extreme land sparing, and holds across a range of region-wide food production targets. </li> <li>To some extent, our conclusion depends on which species groups were included in the assessment. Considered alone, farmland birds preferred a strategy with little or no natural habitat. Nonetheless, the optimal strategy was broadly consistent across all widely-recognised listings of species of conservation concern.</li> <li>Synthesis and applications. Our study looks at landscapes with a long history of agricultural use, and which have little remaining natural habitat, such as those found in lowland England. In these landscapes, conservation outcomes are likely to be maximised by mixed strategies in which high-yield production enables an increase in area of both natural habitat and low-yield farmland elsewhere in the region. </li> </ol>
Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases the matching Genbank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
Data from: Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)
Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, has become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multi-locus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure molded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ("refugia within refugia"), and emphasize the importance of the Balkans as a major European biodiversity center. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.
Data from: Analysing biodiversity and conservation knowledge products to support regional environmental assessments
Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.
FIGURE 9 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status
FIGURE 9. Currently known distribution of Ameerega shihuemoy (orange circles). The main natural protected areas in the Madre de Dios region are shown in green. Amarakaeri Communal Reserve covers an area of 402.335,62 ha; A. shihuemoy has been found at six localities inside this reserve.
FIGURE 10. A in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status
FIGURE 10. A, dorsal, and B, ventral view of the body; C, lateral view of head; and D, ventral view of the hand, of the adult holotype CBF 3900 of Ameerega yungicola. Scale on every picture. Photos by Daniela Rössler.
FIGURE 6 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status
FIGURE 6. Tadpole of Ameerega shihuemoy at Gosner stage 25: (A) dorsal, (B) ventral, (C) lateral, (D) Oral disc at Gosner stage 41, (E) Free-living tadpole at Gosner stage 25. Photos by S. J. Serrano.
FIGURE 5 in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status
FIGURE 5. Spectrograms of advertisement calls of morphologically similar species of Ameerega. A) A. shihuemoy, recorded at Manu Learning Centre, Madre de Dios, Peru 12 June 2014 (temperature not noted). B) A. boliviana, recorded from Correo- Apolo, La Paz, Bolivia. C) A. simulans recorded from Marcapata, Cusco, Peru. D) A. picta recorded from Madidi National Park, Bolivia. E) A. yungicola recorded from Caranavi, Yungas, Bolivia. F) A. hahneli, recorded from Shintuya, Madre de Dios, Peru. G) A. macero, recorded at Manu Learning Centre, Madre de Dios, Peru.
FIGURE 2. A in A new species of poison-dart frog (Anura: Dendrobatidae) from Manu province, Amazon region of southeastern Peru, with notes on its natural history, bioacoustics, phylogenetics, and recommended conservation status
FIGURE 2. A, dorsal; B, and ventral views of the body of the subadult female paratype MHNC 14561 (SVL = 20.7 mm); C, dorsal; D, and ventral views of the body of the subadult male paratype MHNC 4779 (SVL = 17.4 mm); E, adult male carrying tadpoles; F, adult male paratype MHNC 15863. Photos by J.C. Chaparro (A-D), R. Coronel (E), R. Santa Cruz (F).
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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.