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21 results for “range fragmentation”
METADATA for results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137–198 MeV and Linear Energy Transfer (LET) range 1–9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM)
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UniSpec: Deep Learning for Predicting the Full Range of Peptide Fragment Ion Series to Enhance the Proteomics Data Analysis Workflow
<p>UniSpec is a comprehensive DL spectrum predictor that can predict the intensity of the entire HCD MS/MS fragment ion series, going beyond existing tools limited to b/y ion series. </p> <p>All datasets developed for UniSpec model are shared on Zenodo as part of the UniSpec publication, "UniSpec: Deep Learning for Predicting Comprehensive Peptide Fragment Ion Series to Improve Peptide-Spectrum Matches from Shotgun Proteomics Experiments".</p> <p>This includes UniSpec datasets, downstream evaluation and analysis, and application case studies.</p> <p>1. pre-processed training, evaluation and testing data for machine learning;</p> <p> UniSpec-Datasets.7z, Readme_UniSpecDatasets.txt</p> <p>2. Streamlined input datasets based on the fragmentation dictionary;</p> <p> Streamlined_inputdatasets.7z, Readme_Streamlined_inputdatasets.txt</p> <p>3. Predictions on the validation and test sets;</p> <p> UniSpecPred_Validation-Test.7z, Readme_Predictons_ValidationTest.txt</p> <p>4. Evaluation by comparison with Prosit;</p> <p> a. Predictions: prosit_and_unispec_predictions.7z, Readme_prosit_and_unispec_predictions.txt</p> <p> b. Cosine similarity scores: prosit_vs_unispec_CS.7z, Readme_prosit_vs_unispec_CS.txt</p> <p>5. CSS for Different HCD Fragment Ion Series;</p> <p> CS_for_ion_splits.tsv</p> <p>6. Application 1: PSM rescoring;</p> <p> PSM rescoring_zipfiles.7z, PSM rescoring_readme.txt</p> <p>7. Application 2: In-silico spectral library search </p> <p> in-silico_librarysearch.7z, in-silico_librarysearch_readme.txt</p> <p> </p>
Data from: Eastern Whip-poor-wills have larger nonbreeding home ranges in areas with more agriculture and forest fragmentation
<p>Migratory bird populations can be limited by events in disparate parts of the world. Birds in tropical regions are facing rapid habitat loss, climate change, and intensive agricultural regimes, potentially contributing to population declines. However, an understanding of basic non-breeding ecology of species, such as habitat and space use, is critical for determining if this is the case. Populations of the nocturnal/crepuscular Eastern Whip-poor-will (<em>Antrostomus</em> <em>vociferus</em>) have declined by 70% since the 1960's, yet data on the species are sparse outside of the breeding season. We extracted data from 41 archival GPS tags deployed on whip-poor-wills and estimated non-breeding home ranges and land covers used. We used satellite imagery and stable carbon and nitrogen isotope values from claws grown during the non-breeding season to analyze how land cover and habitat moisture impacted home range size and relative trophic level. Forest was by far the most prevalent land cover used by whip-poor-wills, occurring in all home ranges and accounting for >80% of diurnal roosting points. We found that less forest, the presence of agriculture, and more edge (irrespective of land cover) were associated with larger home ranges. Stable isotope values differed by broadscale ecoregion but not local land cover characteristics in our study, indicating that regional idiosyncrasies or broadscale processes can be more important in determining stable isotope ratios. Our findings suggest that the loss, fragmentation, and replacement of forest by agriculture in the core of the whip-poor-will's non-breeding range may represent a threat to the species, as they rely heavily upon forest, and appear to alter space use in response to changes in forest cover.</p>
Data from: Eastern Whip-poor-wills have larger nonbreeding home ranges in areas with more agriculture and forest fragmentation
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Data from: Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range
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Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to exploit the resources offered by new matrix habitats and thus to persist in fragmented habitats. In this study, we were interested in the dietary plasticity of the golden-crowned sifaka (Propithecus tattersalli), an endangered species of lemur, found only in the Daraina region in north-eastern Madagascar. We used a DNA-based approach combining the barcoding concept and Illumina next-generation sequencing to (i) describe the species diet across its entire range and (ii) evaluate the influence of landscape heterogeneity on diet diversity and composition. Faeces from 96 individuals were sampled across the entire species range and their contents were analyzed using the trnL metabarcoding approach. In parallel, we built a large DNA reference database based on a checklist of the plant species of the Daraina region. Our results suggest that golden-crowned sifakas exhibit remarkable dietary diversity with at least 130 plant species belonging to 80 genera and 49 different families. We highlighted an influence of both habitat type and openness on diet composition suggesting a high flexibility of foraging strategies. Moreover, we observed the presence of numerous cultivated and naturalized plants in the faeces of groups living in forest edge areas. Overall, our findings support our initial expectation that P. tattersalli is able to cope with the current level of alteration of the landscape and confirm our previous results on the distribution and the dispersal ability of this species.
Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys. The two types of estimate were highly correlated. Overall we found genetic diversity to be only slightly lower in Britain than across a comparable area in Scandinavia where populations are large and continuous. Whilst the ensemble of British fragments maintain diversity levels close to Scandinavian populations, individually they have drifted apart and lost diversity; particularly the smaller populations. An ABC analysis, based on coalescent models, favours demographic scenarios in which Britain maintained high levels of genetic diversity through post-glacial recolonisation. This diversity has subsequently been partitioned into population fragments that have recently lost diversity at a rate corresponding to the current population-size estimates. We conclude that the British population fragments retain sufficient genetic resources to be the basis of conservation and re-planting programmes. Use of markers with different mutation rates gives us greater confidence and insight than one marker set could have alone, and we suggest that RAD-SSRs are particularly useful as high mutation rate marker set with a well-specified ascertainment bias, which are widely available yet often neglected in existing RAD datasets.
Fig. 2 in Cordulegaster bidentata Selys, 1843 in fragmented landscape of the Wielickie Foothills: reassesement of the northern limit of species range in the Western Carpathians
Fig. 2. Distribution of Cordulegaster bidentata in Poland. 1 – known range, 2 – potential range (according to Bernard et al. 2009, Smolis et al. 2012), 3 – disjuntive site in the Wiśnickie Foothills (Kłonowska-Olejnik & Buczyński 2014), 4 – past record of single imago from Kraków (Prüffer 1920), 5 – northern border of the Carpathians, 6 – state border, 7 – main rivers, 8 – study area.
Fig. 3 in Cordulegaster bidentata Selys, 1843 in fragmented landscape of the Wielickie Foothills: reassesement of the northern limit of species range in the Western Carpathians
Fig. 3. Map of the study area and discovered sites of Cordulegaster bidentata. 1 – study area, 2 – forests, 3 – cities, 4 – watercourses, 5 – searched stream sections, 6 – localities of C. bidentata larvae.
Distribution. NW Madagascar, from the Anjiamangirana region and forest fragments near Anjajavy and between Antsohihy and Analalava, N of the Sofia River and S of the Maevarano River; the range also includes the Bongolava Massif. in Lepilemuridae
Distribution. NW Madagascar, from the Anjiamangirana region and forest fragments near Anjajavy and between Antsohihy and Analalava, N of the Sofia River and S of the Maevarano River; the range also includes the Bongolava Massif.
Distribution. CE Madagascar, known only from its type locality, the Sahafina Forest (29-230 m above sea level), a lowland rainforest fragment of 15-6 km2, and its surrounding "savoka" (fallow farmland with cultivated trees), about 58 km E of Andasibe-Mantadia National Park and 18 km W of the Indian Ocean. The geographic range is presumably limited to the lowland areas (below 700 m) between the Mangoro River to the S and the Rianila River to the N, an area of about 7600 km?2. in Cheirogaleidae
Distribution. CE Madagascar, known only from its type locality, the Sahafina Forest (29-230 m above sea level), a lowland rainforest fragment of 15-6 km2, and its surrounding "savoka" (fallow farmland with cultivated trees), about 58 km E of Andasibe-Mantadia National Park and 18 km W of the Indian Ocean. The geographic range is presumably limited to the lowland areas (below 700 m) between the Mangoro River to the S and the Rianila River to the N, an area of about 7600 km?2.
Distribution. Notably disjunct distribution in Madagascar with separate populations in the N (moister forests of the Sambirano region and in scattered forest fragments on the slopes of the Tsaratanana Massif), the NW (two areas, one ranging from the Manongarivo Special Reserve to the Mahavavy du Nord River, and a more S extension from the Betsiboka River and Ankarafantsika National Park N to the Maevarano River), and the CE (NE of Antananarivo, N of the Mangoro River as far as the Ambatovaky Special Reserve); the distribution in the N part of its range and its relation to the White-fronted Brown Lemur (FE. albifrons) remain unclear; generally speaking, it occurs inland of the range of the White-fronted Brown Lemur, but additional surveys are needed. Introduced on the Comoros Is. in Lemuridae
Distribution. Notably disjunct distribution in Madagascar with separate populations in the N (moister forests of the Sambirano region and in scattered forest fragments on the slopes of the Tsaratanana Massif), the NW (two areas, one ranging from the Manongarivo Special Reserve to the Mahavavy du Nord River, and a more S extension from the Betsiboka River and Ankarafantsika National Park N to the Maevarano River), and the CE (NE of Antananarivo, N of the Mangoro River as far as the Ambatovaky Special Reserve); the distribution in the N part of its range and its relation to the White-fronted Brown Lemur (FE. albifrons) remain unclear; generally speaking, it occurs inland of the range of the White-fronted Brown Lemur, but additional surveys are needed. Introduced on the Comoros Is.
Distribution. Disjunct range, W fragment encompasses the Western Alps (Switzerland, NW Italy, and SE France) and the Apennine Mts of Italy as far S as Sila Massif; in the Balkans, E portion covers topographically broken landscape in SE Bosnia and Herzegovina, adjacent Dalmatia (Croatia), Montenegro, Kosovo, W Macedonia, Albania, and W Greece. in Talpidae
Distribution. Disjunct range, W fragment encompasses the Western Alps (Switzerland, NW Italy, and SE France) and the Apennine Mts of Italy as far S as Sila Massif; in the Balkans, E portion covers topographically broken landscape in SE Bosnia and Herzegovina, adjacent Dalmatia (Croatia), Montenegro, Kosovo, W Macedonia, Albania, and W Greece.
Subspecies and Distribution. S. p. priam Blyth, 1844 — S & SE India (Andhra Pradesh, Karnataka, Kerala, and Tamil Nadu states), a highly fragmented distribution ranging from the Krishna River in Andhra Pradesh S to Tirunelveli in Tamil Nadu. S. p. anchises Blyth 1844 — SC India (S Deccan Plateau), found in the districts of Kurnool, Andhra Pradesh, and in Pavagada in the district of Tumkur, Karnataka. S. p. thersites Blyth 1847 — Dry Zone of Sri Lanka, ranging from Jaffna in the N to the S coast in Cercopithecidae
Subspecies and Distribution. S. p. priam Blyth, 1844 — S & SE India (Andhra Pradesh, Karnataka, Kerala, and Tamil Nadu states), a highly fragmented distribution ranging from the Krishna River in Andhra Pradesh S to Tirunelveli in Tamil Nadu. S. p. anchises Blyth 1844 — SC India (S Deccan Plateau), found in the districts of Kurnool, Andhra Pradesh, and in Pavagada in the district of Tumkur, Karnataka. S. p. thersites Blyth 1847 — Dry Zone of Sri Lanka, ranging from Jaffna in the N to the S coast
Nesokia is sister to Bandicota and are nested in Rattus phylogenetically, making Rat- tus paraphyletic. Tarsomys, Limnomys, and Diplothrix are also phylogenetically in Rat- tus, and the clade is in need of focused re- vision at the generic level. Nesokia bunnui was originally described as a separate ge-nus, Erythronesokia, because it is morphologically very distinctive from N. indica. Type specimen was destroyed during the Iraq War, and a neotype was recently designated to replace it. Monotypic. Distribution. Tigris and Euphrates river valleys, SE Iraq. Descriptive notes. Head—body 230-260 mm, tail 205-270 mm, ear 18-21 mm, hindfoot 49-58 mm; weight 519 g. The Long-tailed Bandicoot Rat is larger than the Short-tailed Bandicoot Rat (N. indica). Pelage is soft and woolly, interspersed with harsher coarse hair and long black hairs near mid-back. Dorsum is fawn to ocherous red, washed with purple or chestnuton darker individuals. Hairs are basally slate-gray and distally rufous, occasionally with whitish or black tips. Muzzle is drab. Sides arefawn, with gray edge toward venter. Venteris whitish, extending onto cheeks where the same pattern from gray to fawn to dorsal pelage occurs. Feet are large and robust, being light brown and well-furred dorsally. Claws are amber on forefeet and dull brown on hindfeet; pollux is extremely small. Ears are moderately long and brownish, with no hair internally. Tail is ¢.82-104% of head-body length and deep brownish drab, interspersed with visible white hair. Skull is large and robust, similarly to the Short-tailed Bandicoot Rat. Habitat. Marsh and swamp land. Food and Feeding. No information. Breeding. No information. Activity patterns. The Long-tailed Bandicoot Rat is terrestrial, although it isfound in swampy and marshy areas and is probably amphibious. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Endangered on The IUCN Red List. The Longtailed Bandicoot Rat is apparently rare and is known from very few specimens. Marsh and swamp habitats in which it is found were completely destroyed during the Iraq War by draining, war damage, and agricultural expansion. In recent years, flooding from Tigris and Euphrates rivers and high snow fall and melt haveresulted in partial restoration ofits native habitat, although restoration is not a complete. Populations are now probably highly fragmented. Bibliography. Al-Ansari et al. (2012), Al-Robaae & Felten (1990), Khajuria (1981), Krystufek et al. (2017), Musser & Carleton (2005), Richardson & Hussain (2006), Stuart (2008). in Muridae
Nesokia is sister to Bandicota and are nested in Rattus phylogenetically, making Rat- tus paraphyletic. Tarsomys, Limnomys, and Diplothrix are also phylogenetically in Rat- tus, and the clade is in need of focused re- vision at the generic level. Nesokia bunnui was originally described as a separate ge-nus, Erythronesokia, because it is morphologically very distinctive from N. indica. Type specimen was destroyed during the Iraq War, and a neotype was recently designated to replace it. Monotypic. Distribution. Tigris and Euphrates river valleys, SE Iraq. Descriptive notes. Head—body 230-260 mm, tail 205-270 mm, ear 18-21 mm, hindfoot 49-58 mm; weight 519 g. The Long-tailed Bandicoot Rat is larger than the Short-tailed Bandicoot Rat (N. indica). Pelage is soft and woolly, interspersed with harsher coarse hair and long black hairs near mid-back. Dorsum is fawn to ocherous red, washed with purple or chestnuton darker individuals. Hairs are basally slate-gray and distally rufous, occasionally with whitish or black tips. Muzzle is drab. Sides arefawn, with gray edge toward venter. Venteris whitish, extending onto cheeks where the same pattern from gray to fawn to dorsal pelage occurs. Feet are large and robust, being light brown and well-furred dorsally. Claws are amber on forefeet and dull brown on hindfeet; pollux is extremely small. Ears are moderately long and brownish, with no hair internally. Tail is ¢.82-104% of head-body length and deep brownish drab, interspersed with visible white hair. Skull is large and robust, similarly to the Short-tailed Bandicoot Rat. Habitat. Marsh and swamp land. Food and Feeding. No information. Breeding. No information. Activity patterns. The Long-tailed Bandicoot Rat is terrestrial, although it isfound in swampy and marshy areas and is probably amphibious. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Endangered on The IUCN Red List. The Longtailed Bandicoot Rat is apparently rare and is known from very few specimens. Marsh and swamp habitats in which it is found were completely destroyed during the Iraq War by draining, war damage, and agricultural expansion. In recent years, flooding from Tigris and Euphrates rivers and high snow fall and melt haveresulted in partial restoration ofits native habitat, although restoration is not a complete. Populations are now probably highly fragmented. Bibliography. Al-Ansari et al. (2012), Al-Robaae & Felten (1990), Khajuria (1981), Krystufek et al. (2017), Musser & Carleton (2005), Richardson & Hussain (2006), Stuart (2008).
Distribution. Widespread but fragmented range across mainland N Australia, from the Pilbara E in Muridae
Distribution. Widespread but fragmented range across mainland N Australia, from the Pilbara E to SE Queensland, and many islands off N Australian mainland.
Subspecies and Distribution. M.f.fuscusThomas,1882—nowrestrictedtoN&WTasmania,butsubfossilevidence(owlpellets)indicatesaformerlymoreextensiverangeacrossTasmania. M. f. mordicus Thomas, 1922 — highly fragmented in mainland SE Australia, including the Otway and Dandenong ranges, coastal areas of Gippsland and SE New South Wales, and the Great Dividing Range around Barrington Tops and from near the Brindabella Range S to Warburton. in Muridae
Subspecies and Distribution. M.f.fuscusThomas,1882—nowrestrictedtoN&WTasmania,butsubfossilevidence(owlpellets)indicatesaformerlymoreextensiverangeacrossTasmania. M. f. mordicus Thomas, 1922 — highly fragmented in mainland SE Australia, including the Otway and Dandenong ranges, coastal areas of Gippsland and SE New South Wales, and the Great Dividing Range around Barrington Tops and from near the Brindabella Range S to Warburton.
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75 in Integrative taxonomy of Parasabella and Sabellomma (Sabellidae: Annelida) from Australia: description of new species, indication of cryptic diversity, and translocation of some species out of their natural distribution range
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75% shown on nodes. Scale bar, average of nucleotide substitutions per site.
Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
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Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
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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.
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DANDI Archive for NWB datasets
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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
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