Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,399
datasets available to search
ShareScore release 0.9.0
Dataset results
2,399 results for “fragmenter”
Data from: Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird
The Eastern Afromontane cloud forests occur as geographically distinct mountain exclaves. The conditions of these forests range from large to small and from fairly intact to strongly degraded. For this study, we sampled individuals of the forest bird species, the Montane White-eye Zosterops poliogaster from 16 sites and four mountain archipelagos. We analysed 12 polymorphic microsatellites and three phenotypic traits, and calculated Species Distribution Models (SDMs) to project past distributions and predict potential future range shifts under a scenario of climate warming. We found well-supported genetic and morphologic clusters corresponding to the mountain ranges where populations were sampled, with 43% of all alleles being restricted to single mountains. Our data suggest that large-scale and long-term geographic isolation on mountain islands caused genetically and morphologically distinct population clusters in Z. poliogaster. However, major genetic and biometric splits were not correlated to the geographic distances among populations. This heterogeneous pattern can be explained by past climatic shifts, as highlighted by our SDM projections. Anthropogenically fragmented populations showed lower genetic diversity and a lower mean body mass, possibly in response to suboptimal habitat conditions. On the basis of these findings and the results from our SDM analysis we predict further loss of genotypic and phenotypic uniqueness in the wake of climate change, due to the contraction of the species' climatic niche and subsequent decline in population size.
Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)
Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compare interspecific variation between ptSSRs and nucleotide sequences of ycf1 then test intraspecific variation for ptSSRs using 911 samples in the P. ponderosa species complex. Results: The ptSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The ptSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for ptSSR loci in a plastome alignment for the target group.
Data from: Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China
Understanding population history and genetic structure are key drivers of ecological research. Here we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 fecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K=2). We estimate that a major divergence took place between these populations 26 000 YBP, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise FS on mtDNA and nuclear DNA) so that in effect, four smaller sub-populations now exist. Promisingly, we identified two possible first generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.
Data from: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland–island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.
Data from: Genetic co-structure in a meta-community under threat of habitat fragmentation
Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the eco-evolutionary processes underlying fragmentation-compromised communities in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community module experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community module comprises a parasitic butterfly of conservation concern, and its two obligatory host species, a plant and an ant. We show that both historical dispersal and ongoing habitat fragmentation shape population genetic diversity of the butterfly Phengaris alcon and its most limited host species (the plant Gentiana pneumonanthe). Genetic structure of the individual species was strongly driven by geographical structure, altitude and landscape connectivity. Strikingly, however, was the strong degree of genetic co-structure among the three species that could not be explained by the spatial variables under study. This finding suggests that factors other than spatial configuration, including co-evolutionary dynamics and shared dispersal pathways, cause parallel genetic structure among interacting species. While the exact contribution of coevolution and shared dispersal routes on the genetic variation within and among communities deserves further attention, our findings demonstrate a considerable degree of genetic parallelism in natural meta-communities. The significant effect of landscape connectivity on the genetic diversity and structure of the butterfly also suggests that habitat fragmentation may threaten the functioning of the community module on the long run.
Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.
Data from: Impact of habitat fragmentation on the spatial structure of the Eastern Arc Forests in East Africa: implications for biodiversity conservation
The Eastern Arc Mountains in Tanzania and Kenya are one of 35 global biodiversity hotspots. The Eastern Arc forests are, as are many other tropical biodiversity hotspots, highly fragmented. Understanding the impact of habitat fragmentation (i.e., habitat loss and subdivision) on the spatial structure of the Eastern Arc forests is important because forest spatial structure highly influences species richness, persistence, and extinction debt. Here we examine the impact of habitat fragmentation on the spatial structure of the Eastern Arc forests at a patch scale using very high resolution aerial imagery having a spatial resolution of 0.5–1.5 m. Forest area across the 13 Eastern Arc Mountains is 405,852 ha and is distributed into 311 fragments ≥ 10 ha in size with a median fragment size of 84 ha. The 18 largest forest fragments in the Eastern Arc Mountains contain greater than three-quarters of total forest area. Average fragment isolation, as assessed by median distance to nearest fragment and median distance to the nearest larger fragment, is 867 and 1533 m, respectively. Of total forest area, 14% is < 100 m from the forest edge and 33% is < 300 m from the forest edge. Establishing forested linkages among the largest and closest forest fragments through forest regeneration and protection of secondary regenerating forest as well as providing protected area status to the remaining non-protected forest including unprotected smaller forest fragments are important to enhancing the long-term persistence of many plant and animal species here.
Data from: A degradation debt? large-scale shifts in community composition and loss of biomass in a tropical forest fragment after 40 years of isolation
Habitat loss and fragmentation are among the biggest threats to tropical biodiversity and associated ecosystem services. We examined forest dynamics in a mid-elevation 365-ha fragment in southern Costa Rica. The fragment was isolated in the mid-1970s and belongs to the Las Cruces Biological Station. A 2.25-ha permanent plot was established in the center of the old-growth forest (>400 m to nearest edge boundary) and all plants >5 cm DBH were censused, mapped, and identified to species in two surveys taken ~5–6 years apart (>3,000 stems/survey). Although the reserve maintains high species richness (>200 spp.), with many rare species represented by only one individual, we document a strong shift in composition with a two-fold increase in the number of soft-wooded pioneer individuals. The dominant late-successional understory tree species, Chrysochlamys glauca (Clusiaceae), and most species in the Lauraceae, declined dramatically. Turnover was high: 22.9% of stems in the first survey were lost, and 27.8% of stems in the second survey represented new recruits. Mean tree diameter decreased significantly and there was a 10% decrease in overall biomass. Such alteration has been documented previously but only in smaller fragments or within ~100 m of an edge boundary. Further penetration into this fragment was perhaps driven by a progressive invasion of disturbance-adapted species into the fragment's core over time; the loss of once-dominant late successional species could be a contributing factor. The pattern found is of particular concern given that such fragments represent a substantial portion of today's remaining tropical habitat; further studies in similar-sized fragments that have been isolated for similar prolonged periods are called for.
Data from: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape
The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain, and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful DNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season, and distance from forest) varied between the three responses. Nuclear microsatellite amplification of DNA from jaguar faeces had lower success rates (15–44%) compared with those of the mtDNA marker. Our results show that DNA identification of carnivore species from faecal samples works efficiently in the Amazon forest and can provide data on species occurrence as well as a valuable tool for genetic, ecological and conservation studies.
Figure 2 in Urban fragment of the Atlantic Rainforest as a refuge for cavity-nesting bees and wasps (Hymenoptera: Aculeata)
Figure 2. Rarefaction curves of solitary bee species nesting on campus of Universidade Federal da Bahia (UFBA) and in Parque Zoobotânico Getúlio Vargas (PZBGV) located in urban fragment of Atlantic Rainforest in city of Salvador, state of Bahia, Brazil, from May 2014 to April 2016. Grey portions represent confidence intervals (95%) of diversity (Shannon-Wiener diversity index).
Figure 5 in Urban fragment of the Atlantic Rainforest as a refuge for cavity-nesting bees and wasps (Hymenoptera: Aculeata)
Figure 5. Nesting activity of most abundant bee and wasp species: Centris (Heterocentris) analis (Fabricius, 1804), Centris (Heterocentris) terminata Smith, 1874, and Trypoxylon sp.2 at Parque Zoobotânico Getúlio Vargas located in urban fragment of Atlantic Forest in city of Salvador, state of Bahia, Brazil, from May 2014 to April 2015 (1st year) and from May 2015 to April 2016 (2nd year).
Figure 4 in Urban fragment of the Atlantic Rainforest as a refuge for cavity-nesting bees and wasps (Hymenoptera: Aculeata)
Figure 4. Nesting activity of most abundant bee and wasp species: Centris (Heterocentris) analis (Fabricius, 1804), Centris (Heterocentris) terminata Smith, 1874, Podium denticulatum (Smith, 1856) at Universidade Federal da Bahia located in urban fragment of Atlantic Forest in Salvador, Bahia, Brazil, from May 2014 to April 2015 (1st year) and from May 2015 to April 2016 (2nd year).
Figure 3 in Urban fragment of the Atlantic Rainforest as a refuge for cavity-nesting bees and wasps (Hymenoptera: Aculeata)
Figure 3. Rarefaction curves of species solitary wasps nesting on campus of Universidade Federal da Bahia (UFBA) and in Parque Zoobotânico Getúlio Vargas (PZBGV) located in urban fragment of Atlantic Rainforest in city of Salvador, state of Bahia, Brazil, from May 2014 to April 2016. Grey portions represent confidence intervals (95%) of diversity (Shannon-Wiener diversity index).
Figure 1 in Urban fragment of the Atlantic Rainforest as a refuge for cavity-nesting bees and wasps (Hymenoptera: Aculeata)
Figure 1. Urban fragment of Atlantic Rainforest in Salvador, Bahia, Brazil, preserved by Parque Zoobotânico Getúlio Vargas (PZBGV) and campus of Universidade Federal da Bahia (UFBA). A- State of Bahia, Brazil; B- City of Salvador; C- Fragment studied where UFBA and PZBGV are located. Eight sampling sites were established: four (1 to 4) at UFBA campus and four (5 to 8) at PZBGV.
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.
Data from: Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds
1. Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases, and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. 2. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and habitat generalist bird assemblages. 3. We surveyed birds from 144 point counts in 36 different forest sites across two landscapes with different amount of forest cover in the Brazilian Atlantic forest. We analysed β-diversity among points, among sites, and between landscapes with multiplicative diversity partitioning of Hill numbers. We tested whether β-diversity among points was related to within-site variations in vegetation structure, and if β-diversity among sites was related to site location and/or to differences among sites in vegetation structure and landscape composition (i.e. percent forest and pasture cover surrounding each site). 4. β-diversity between landscapes was lower than among sites and among points in both bird assemblages. In forest specialist birds, the landscape with less forest cover showed the highest β-diversity among sites (bird differentiation among sites), but generalist birds showed the opposite pattern. At the local scale, however, the less forested landscape showed the lowest β-diversity among points (bird homogenisation within sites), independently of the bird assemblage. β-diversity among points was weakly related to vegetation structure, but higher β-diversity values were recorded among sites that were more isolated from each other, and among sites with higher differences in landscape composition, particularly in the less forested landscape. 5. Our findings indicate that patterns of bird β-diversity vary across scales and are strongly related to landscape composition. Bird assemblages are shaped by both environmental filtering and dispersal limitation, particularly in less forested landscapes. Conservation and management strategies should therefore prevent deforestation in this biodiversity hotspot.
Data from: Sensitivity to habitat fragmentation across European landscapes in three temperate forest herbs
<p>Context. Evidence for effects of habitat loss and fragmentation on the viability of temperate forest herb populations in agricultural landscapes is so far based on population genetic studies of single species in single landscapes. However, forest herbs differ in their life histories, and landscapes have different environments, structures and histories, making generalizations difficult.</p> <p>Objectives. We compare the response of three slow-colonizing forest herbs to habitat loss and fragmentation and set this in relation to differences in life-history traits, in particular their mating system and associated pollinators.</p> <p>Methods. We analysed the herbs' landscape-scale population genetic structure based on microsatellite markers from forest fragments across seven European agricultural landscapes.</p> <p>Results. All species responded to reductions in population size with a decrease in allelic richness and an increase in genetic differentiation among populations. Genetic differentiation also increased with enhanced spatial isolation. In addition, each species showed unique responses. Heterozygosity in the self-compatible <i>Oxalis acetosella</i> was reduced in smaller populations. The genetic diversity of <i>Anemone nemorosa</i>, whose main pollinators are less mobile, decreased with increasing spatial isolation, but not that of the bumblebee-pollinated <i>Polygonatum multiflorum</i>.</p> <p>Conclusions. Our study indicates that habitat loss and fragmentation compromises the long-term viability of slow-colonizing forest herbs despite their ability to persist for many decades by clonal propagation. The distinct responses of the three species studied within the same landscapes confirm the need of multi-species approaches. The mobility of associated pollinators should be considered an important determinant of forest herbs' sensitivity to habitat loss and fragmentation.</p>
FIGURE 5. Anthoceros subtilis Steph. A. Capsule epidermis with thin walls and stomata. B. SEM micrograph showing sporophyte fragment with tetrads and pseudoelaters. C in A revision of the genus Anthoceros (Anthocerotaceae, Anthocerotophyta) in China
FIGURE 5. Anthoceros subtilis Steph. A. Capsule epidermis with thin walls and stomata. B. SEM micrograph showing sporophyte fragment with tetrads and pseudoelaters. C. Pseudoelaters with thin-walls and irregular thickenings. D. SEM micrograph showing proximal face of spore which is spinulose and has distinct trilete mark. E. SEM micrograph showing distal spore face which is papillate to spinulose with spines often united at the base. All from R.-H. Dai PX95106 (GACP). Scale bars: A, C=50 µm; B, D, E=10 µm.
Data for: The role of habitat fragmentation in Pleistocene megafauna extinction in Eurasia by Mondanaro et al.
<p>This dataset provides the complete list of data and necessary information in order to reproduce all the analyses performed in the paper:<br> "Mondanaro, A., Di Febbraro, M., Melchionna, M., Maiorano, L., Di Marco, M., Edwards, N.R., Holden, P.B., Castiglione, S., Rook, L., Raia, P. (2021)<br> The role of habitat fragmentation in Pleistocene megafauna extinction in Eurasia. Ecography, online version"</p> <p>The idea<b> </b>that than several small, rather than a single large, habitat areas, should hold the highest total species richness (the so-called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long-term dimension of extinction risk. Here, we provide the first long-term evaluation of the role of habitat fragmentation in species extinction, focusing on 22 large mammal species that lived in Eurasia during the last 200,000 years. By combining species distribution models and landscape pattern analysis, we compared temporal dynamics of habitat spatial structure between extinct and extant species, estimating size, number, and degree of geographical isolation of their suitable habitat patches. Our results evidenced that extinct mammals went through considerable habitat fragmentation during the last glacial period and started to fare worse than extant species from about 50 ka. In particular, our modelling effort constrains the fragmentation of habitats into a narrow time window, from 46 to 36 kilo years ago, surprisingly coinciding with known extinction dates of several megafauna species. Landscape spatial structure was the second most important driver affecting megafauna extinction risk (ca. 38% importance), after body mass (ca. 39%) and followed by dietary preferences (ca. 20%). Our results indicate a major role played by landscape fragmentation on extinction. Such evidence provides insights on what might likely happen in the future, with climate change, habitat loss, and fragmentation acting as the main forces exerting their negative effects on biodiversity.</p>
Figure 2 in Helminths of some tree frogs of the families Hylidae and Phyllomedusidae in an Atlantic rainforest fragment, Brazil
Figure 2. Rarefaction curve of the component community richness of tree frogs from an Atlantic Rainforest fragment, north-east Brazil, June 2015 to February 2016.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.