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.
1,213
datasets available to search
ShareScore release 0.9.0
Dataset results
1,213 results for “biodiversity hotspots”
Data from: The great rift valley is a greater biogeographic barrier than the blue Nile Valley for six Ethiopian highland passerines in the Eastern Afromontane biodiversity hotspot
Open the record for dataset details and reuse information.
Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America
<p><strong>Aim</strong>: We investigate the biogeographic history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity-dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate on processes governing the species assembly and evolution of the Cerrado savanna.</p> <p><strong>Location</strong>: South American ecoregions south of the Amazon (e.g. Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern Andes).</p> <p><strong>Taxon</strong>: Boana pulchella group.</p> <p><strong>Methods</strong>: We built the most complete time-calibrated phylogeny for the group to date. We then reconstructed ancestral ranges using the dispersal-extinction-cladogenesis (DEC) model comparing different dispersal scenarios considering distance, adjacency and ecological similarity among regions. A center-of-origin hypothesis in forest versus open ecoregions was also tested. Using biogeographical stochastic mapping, we additionally estimated the contribution of range shifts across different biomes. Lastly, we evaluated several diversification models, including the effect of time, diversity-dependence and temperature-dependence on speciation and extinction rates.</p> <p><strong>Results</strong>: The Boana pulchella group originated during the Early Miocene (~17.5 MYA) and underwent high speciation rates during the Middle Miocene Climatic Optimum, with a decreasing trend following the Miocene Climatic Transition. We found no support for a single ecoregion acting as a center of origin and diversification; instead, we inferred recurrent range shifts with dispersal among dissimilar adjacent ecoregions. Speciation linearly dependent on paleotemperatures, with either no or very low constant extinction rates, best explained the slowdown diversification pattern.</p> <p><strong>Main Conclusions</strong>: Our results support a species assembly of Cerrado savanna in South America during the Miocene with intermittent interchange with rainforest habitats. Past climate changes impacted the rate new species originated with apparently no impact on extinction. Finally, the repeated habitat shifts among open/dry and forested/humid ecoregions, rather than long-term in-situ diversification in single areas, highlights the very dynamic historical interchange between contrasting habitats in South America, possibly contributing to its high species diversity.</p>
Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
Supplementary material from: Alpine extremophytes in evolutionary turmoil: Complex diversification patterns and demographic responses of a Halophilic grass in a Central Asian biodiversity hotspot
<p>Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass <em>Puccinellia pamirica</em> and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of <em>P. pamirica</em> alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.</p>
Diversifying in the mountains: spatio-temporal diversification of frogs in the Western Ghats biodiversity hotspot
<p>Mountain ranges are hotspots of biodiversity. However, the mechanisms that generate biodiversity patterns in different mountainous regions and taxa are not apparent. The Western Ghats (WG) escarpment in India is a globally recognised biodiversity hotspot with high species richness and endemism. Most studies have either invoked paleoclimatic conditions or climatic stability in the southern WG refugium to explain this high diversity and endemism. However, the factors driving macroevolutionary change remain unexplored for most taxa. Here, we generated the most comprehensive dated phylogeny to date for ranoid frogs in the WG and tested the role of paleoclimatic events or climatic stability in influencing frog diversification. We found that the diversity of different ranoid frog clades in the WG either accumulated at a constant rate through time or underwent a decrease in speciation rates around 3–2.5 Ma during the Pleistocene glaciation cycles. We also find no significant difference in diversification rate estimates across elevational gradients and the three broad biogeographic zones in the WG (northern, central, and southern WG). However, time-for-speciation explained regional species richness within clades, wherein older lineages have more extant species diversity. Overall, we find that global paleoclimatic events have had little impact on WG frog diversification throughout most of its early history until the Quaternary and that the WG may have been climatically stable allowing lineages to accumulate and persist over evolutionary time.</p>
Data from: Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot
<p>These datasets have the variables used in the paper "Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot" as well as the script to perform the analysis.</p>
Data from: Land-use intensity and relatedness to native plants promote exotic plant invasion in a tropical biodiversity hotspot
<p>Exotic plant invasions threaten biodiversity and are costly to farmers. Land use is a major pathway promoting the spread of exotic plant species; however, little is known about the processes underlying the success of exotic plants in tropical agricultural landscapes. Focussing on the heterogeneous smallholder landscapes of north-eastern Madagascar, we studied exotic plants of understorey communities across a land-use intensity gradient from unburned lands (old-growth forests, forest fragments, and forest-derived vanilla agroforests) to burned ones (fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows). </p> <p>We quantified the absolute species richness, abundance, and cover of exotic plants across land-use types and their proportional contribution to community richness, abundance, and cover as indicators of exotic plant invasion. We tested for the effects of land-use parameters, namely land-use history, canopy closure, and landscape-level forest cover, on exotic plants. Additionally, we tested whether the phylogenetic relatedness between exotic and native species in the same plot affected invasion success, testing Darwin's naturalization and pre-adaptation hypotheses. </p> <p>All indicators of exotic plant invasion were lowest in old-growth forests and forest fragments and highest in fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows. Absolute and proportional exotic richness was negatively affected by canopy closure, and landscapes with high forest cover had lower proportions of exotic plant richness. High phylogenetic relatedness between exotics and natives was associated with lower proportional richness but higher proportions of exotics in abundance and cover. However, individual exotic species showed contrasting responses to land-use parameters and relatedness to natives.</p> <p>Synthesis and applications: Our results indicate that maintaining unburned lands, land-use types with dense canopies, and landscapes with high forest cover prevents the spread of exotic plants within agricultural landscapes of north-eastern Madagascar. Supporting Darwin's pre-adaptation hypothesis, exotic plants phylogenetically closely related to native plants are more likely to become successful invaders in terms of abundance and cover. Nevertheless, individual species show different responses to land-use changes and phylogenetic relatedness. Therefore, land-use decisions and management choices can be tailored to limit the spread of exotic species and to preserve native plants in this global biodiversity hotspot.</p>
Open habitats in a tropical biodiversity hotspot support pollinator diversity in both protected and unprotected areas
<p class="MsoNormal">Protected areas (PAs) are vital in the global effort to preserve biodiversity, particularly for disturbance-intolerant pollinator species in the tropics. As there is little information on the potential of PAs for pollinator conservation in sensitive tropical ecosystems, we assessed here insect pollinator diversity in protected vs. unprotected areas in two vegetation zones in Nigeria, within the West African Guinea Biodiversity Hotspot. We selected two land-use types based on predominant canopy cover type (open and tree-shaded habitats) and these were sampled in both protected and unprotected areas of tropical rain forest and savanna vegetation zones. Pollinator composition varied significantly between protected vs. unprotected areas in each vegetation zone, signifying both areas support unique assemblages of insect pollinators. However, pollinator diversity varied according to land-use type (open vs. shaded habitats) rather than protected area per se, such that pollinators were more abundant and species-rich in open habitat than shaded habitat. These findings emphasize that beyond the protection of ecosystems, fine scale habitat management promoting the availability of adequate floral resources in natural areas is critical for ensuring conservation of these pollinators in tropical ecosystems. </p>
The occurrence data of wild apple in the Mountains of Central Asia Biodiversity Hotspot
<p><span>To obtain high-quality occurrence records for wild apple across its whole distribution range, we compiled data from field surveys, herbariums and the literature. The field surveys were conducted in all of the countries with wild apple distribution in Central Asia. Precisely, we had several exhaustive investigations of wild apple populations in Xinjiang, China from 2008 to 2021, including distribution range and abundance of wild apple across its whole elevational ranges in six counties. For herbarium data, we combined the records from Global Biodiversity Information Facility </span><span>and Chinese Virtual Herbarium</span><span>. Finally, we obtained 8344 occurrence records for wild apple. </span></p>
New insights into the formation of biodiversity hotspots of the Kenyan flora
<p>Aim: Kenya intersects with the biodiversity hotspots Eastern Afromontane, Coastal Forests of Eastern Africa, and Horn of Africa. This study aims to investigate the distribution pattern of plant diversity in the low latitude arid area influenced by climatic fluctuation and orogeny at long historical period, and explore the formation of beta diversity pattern in Kenya.</p> <p>Location: Kenya, East Africa.</p> <p>Taxon: Angiosperms.</p> <p>Methods: We quantified patterns of turnover and nestedness components of phylogenetic beta diversity among neighbouring sites for angiosperm species by using a well-resolved phylogenetic tree and extensive distribution records from public database and a set of books. We applied clustering methods to do biota delineation based on the pairwise similarities among multiple sites, and used a random assembly null model to assess the effects of species abundance distribution on phylogenetic beta diversity.</p> <p>Results: Phylogenetic turnover for the Kenyan flora showed a non-monotonic pattern along the latitudinal gradient, which is strongly structured in volcanic and coastal areas. Whereas other areas were mainly dominated by phylogenetic nestedness, even in the eastern part of equatorial region which is parallel with volcanic area. Phylogenetic diversity and phylogenetic structure analyses elaborate the mechanism under the phylogenetic turnover or nestedness patterns we observed. We identified five phytogeographical regions in Kenya: the Mandera, Turkana, Volcanic, Pan Coastal and West Highland Regions.</p> <p>Conclusions: The variation extent of turnover gradient and the coexistence situation are highly dependent on the regional biogeographical history, that is, the process of climatic fluctuations and long-lasting orogeny jointly shaped the biodiversity pattern. The nestedness component dominated climatically unstable regions are presumed to be caused by heavy local species extinction and recolonization from the Volcanic Region. The high turnover component in climatically stable regions may preserve old lineages and the prevalence of endemic species within narrow ranges.</p>
Whole genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot
<p>1. Biodiversity hotspots<span>, such as the Caucasus mountains,</span> provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. <span>Therefore, w</span>e investigate<span>d</span> the evolution of <em>Primula</em> sect. <em>Primula</em>, a clade with a high degree of endemism in the Caucasus.</p> <p>2. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic versus cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene <span>that includes</span> all species of <em>Primula</em> sect. <em>Primula</em>.</p> <p>3. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in <em>Primula</em>. Biogeographic analyses support the "out-of-the-Caucasus" hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity.</p> <p>4. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.</p>
Data from: Three new Gesneria species (Gesneriaceae) support Parc National Pic Macaya (Haiti) as an important biodiversity hotspot
<p><span>The Caribbean Islands are a biodiversity hotspot characterized by a high taxonomic diversity and endemicity, suggesting that many species have yet to be discovered. Unfortunately, many of these undescribed species may go extinct before they are described because of the drastic habitat loss in these oceanic islands. In this study, we describe three new plant species of <em>Gesneria</em> (Gesneriaceae) that are endemic to the Massif de la Hotte in southwest Haiti, a region recently affected by extensive deforestation. Elliptical Fourier analyses of leaf shapes and DNA sequencing of five nuclear genes were used to support the species delimitations. <em>Gesneria</em> <em>flava</em> is a tall shrub with large yellow flowers, leafy sepals, and rugose leaves. <em>Gesneria</em> × <em>cornuta</em> is a hybrid between <em>Gesneria</em> <em>bicolor</em> and the newly described <em>Gesneria</em> <em>flava</em> and is morphologically intermediate between its parents. Its hybrid origin is further supported by the presence of alleles from both parents for all five nuclear genes sequenced. Finally, <em>Gesneria</em> <em>radiata</em> is a saxicolous herb with radially symmetrical corollas. The three new species described here are limited to a single mountain range in the Caribbean, the Massif de la Hotte. These recent discoveries reflect the high endemicity of this region and exemplify the urgency to conserve the remaining primary forest of Haiti in order to protect its biodiversity.</span></p>
Data from: Movement of avian predators points to biodiversity hotspots in agricultural landscape
<p>Global agricultural landscapes are witnessing a concerning decline in biodiversity, and this trend is predicted to persist. To safeguard these biodiversity-rich areas, it's crucial to pinpoint hotspots effectively. In doing so, we utilized various species of birds of prey as suitable sentinel animals due to their mobility and dependence on prey diversity and abundance. Between 2019 and 2021, we tracked 62 individuals from four predator species using GPS loggers in Estonian farmland. Dividing the study area into 50-meter grids and overlaying them with tracked individuals' locations enabled us to differentiate between hotspots of their activity and control sites. We conducted surveys on amphibians, birds, small mammals, and plant diversity to determine if avian predator activity hotspots correlated with overall biodiversity. Our findings revealed significantly higher diversity and abundance in the surveyed groups within activity hotspots compared to control sites. These hotspots continued to be frequented by raptors in the subsequent year, albeit not two years later. In conclusion, multispecies GPS telemetry of avian predators emerges as an objective, dependable, and spatially accurate biodiversity indicator. With the accumulation of movement data, we anticipate increased interest and adoption of this approach in biodiversity monitoring.</p>
Fig. 4 in Amphibian diversity of a West African biodiversity hotspot: an assessment and commented checklist of the batrachofauna of the Ivorian part of the Nimba Mountains
Fig. 4. Lower to mid-elevation dense, evergreen forest (habitat C) at 847 m asl.
Fig. 3 in Amphibian diversity of a West African biodiversity hotspot: an assessment and commented checklist of the batrachofauna of the Ivorian part of the Nimba Mountains
Fig. 3. Mid-elevation savannah (habitat B).
Fig. 2 in Amphibian diversity of a West African biodiversity hotspot: an assessment and commented checklist of the batrachofauna of the Ivorian part of the Nimba Mountains
Fig. 2. Montane grasslands (habitat A) at 1,241 m asl.
Data from: Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)
<p>The California Floristic Province (CA-FP) is the most species-rich region of North American north of Mexico. Several hypotheses have been proposed to explain why this region is exceptionally diverse, including that it harbors many recently diverged clades with weak or no barriers to reproduction.</p> <p><em>Salvia</em> subgenus <em>Audibertia</em> is a conspicuous element of the CA-FP, with multiple species often occurring in sympatry. Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of geneflow and mechanical reproductive isolation.</p> <p>Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades and species are generally not mechanically isolated.</p> <p>Rapid, recent speciation with some horizontal geneflow during the rise of Mediterranean climate is the underlying cause of extant diversity in subgenus <em>Audibertia</em>. Geneflow has largely not facilitated speciation. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different events of historical geneflow, perhaps characteristic of many lineages in the CA-FP. Mechanical reproductive isolation is likely only part of a mosaic of factors limiting geneflow.</p>
Fig. 7 in New Records and Range Extensions of Some Marine Sponges (Porifera: Demospongiae and Homoscleromorpha) from the Andaman Islands, India; Part of the Indo-Burma Biodiversity Hotspot.
Fig. 7. Geographical extension of Biemna fortis (Topsent, 1897).
Fig. 15 in New Records and Range Extensions of Some Marine Sponges (Porifera: Demospongiae and Homoscleromorpha) from the Andaman Islands, India; Part of the Indo-Burma Biodiversity Hotspot.
Fig. 15. Geographical extension of Plakortis communis Muricy, 2011.
Fig. 1 in New Records and Range Extensions of Some Marine Sponges (Porifera: Demospongiae and Homoscleromorpha) from the Andaman Islands, India; Part of the Indo-Burma Biodiversity Hotspot.
Fig. 1. Study Area.
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.