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.
1,133
datasets available to search
ShareScore release 0.9.0
Dataset results
1,133 results for “phylogeography”
F I G U R E 4 in Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections
F I G U R E 4 (a) Phylogenetic tree of Tribe Melonycterini blossom bats produced using the quartet-based method implemented in SVDǪUARTETS, and (b) phylogenetic network of Nesonycteris blossom bats created using SPLITSTREE.
F I G U R E 2 in Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections
F I G U R E 2 Phylogeographic relationships among Melonycterini blossom bats (a) the Solomon Islands archipelago with bathymetric depths less than 120 m (ETOPO1, Amante & Eakins, 2009) shaded in dark grey to indicate possible land bridge connections during the Last Glacial Maximum. Islands shaded in colour represent those sampled for this study, samples were unavailable for islands shaded in light grey (EPSG: 4326–WGS 84). (b) Phylogenetic tree made using maximum likelihood methods in RAXML depicting relationships among all Nesonycteris and Melonycteris samples. Values indicate maximum likelihood bootstrap support and black circles on nodes denote values = 100. (c) Representation of the taxonomic treatment of Nesonycteris prior to this study comprising two species; (d) Alternate taxonomic treatment of Nesonycteris from the results of this study comprising four species (N. far = N. fardoulisi, N. mac = N. maccoyi); The results of STRUCTURE analyses for various datasets are presented as (e) Dataset 1, a single run, k = 4; (f) Dataset 2, a single run, k = 2; (g) Dataset 3, a single run, k = 3; and (h) Dataset 4 (five runs R1–R5, k = 4). In STRUCTURE results (e–h), each bar indicates the probability of assignment to different genetic clusters.
F I G U R E 3 in Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections
F I G U R E 3 Pairwise Nei's genetic distances for Melonycteris and Nesonycteris blossom bats from the Solomon Islands and Bismarck archipelagos. Nei's genetic distance was calculated using the R package StAMPP. Values surrounded by a yellow or green rectangle are pairwise distances between samples from New Georgia group islands, and Greater Bukida islands, respectively.
Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses
<p>Billions of genomic sequences are stored in public repositories (NCBI) as well as records of species occurrence (GBIF). By implementing analytical tools from different scientific disciplines, data mining on these databases can be a source of information to aid in the global surveillance of zoonotic pathogens that circulate among wildlife. We illustrate this by investigating the hantavirus-rodent system in the Americas, i.e. New World Hantaviruses (NWH). First we draw the circulation of pathogenic NWH among rodents; by inferring the phylogenetic links among 278 genomic samples of the S segment (N protein) of NWH found in 55 species of Cricetidae rodents. Second, machine learning was used to assess the impact of land use on the probability of presence of the rodent species linked with reservoirs of pathogenic hantaviruses. Our results show that hosts are widely present across the Americas. Some hosts are present in the primary forest and agricultural land, but not in the secondary forest; whereas other hosts are present in secondary forest and agricultural land. The diversity of host species allows Hantavirus to circulate on a wide spectrum of habitats, in particular rural rather than urban. We highlight that Public repositories of genomic data and species occurrence are very useful resources for monitoring potential enzootic transmission and spillover of zoonotic viruses in relation with the changes that humans produce in the Biosphere.</p>
Fig. 2 in Phylogeography Of The Western Populations Of Stylodipus Telum (Rodentia, Dipodidae) Based On Mitochondrial Dna
Fig. 2. Phylogeographic reconstruction of S. telum based on cytb. BI posterior probability / ML bootstrap support per 1000 replications is indicated at the nodes (only values over 70 % are shown). Photo: S. telum falzfeini from Sagi (Oleshki District) by M. Rusin, 2017-05-17.
Fig. 1 in Phylogeography Of The Western Populations Of Stylodipus Telum (Rodentia, Dipodidae) Based On Mitochondrial Dna
Fig. 1. Sampling localities of S. telum used in the study. White — range of S. telum falzfeini (original unpublished data) and green — range of S. telum turovi (Shenbrot et al., 1995).
Fig. 4 in New Data On Phylogeography Of The Boreal Owl, Aegolius Funereus (Strigiformes, Strigidae), In Eurasia
Fig. 4. Boreal Owl mtDNA CR1 haplotype distribution across it's Eurasian range. Colored dots indicate approximate regions of sampling for individuals possessing the corresponding haplotype. White dots with numbers reflect the total number of unique haplotypes for this region.
Fig. 2 in New Data On Phylogeography Of The Boreal Owl, Aegolius Funereus (Strigiformes, Strigidae), In Eurasia
Fig. 2. Mismatch distribution graph for the pairwise comparison of mtDNA CR1 sequences of Eurasian Boreal Owl population. X axis reflects pairwise difference, Y axis reflects frequency of the difference across sequences; Freq. Obs. is the studied sample's observed mismatch frequency graph, Freq. Exp. is the expected frequency for the sudden expansion model.
Fig. 3 in New Data On Phylogeography Of The Boreal Owl, Aegolius Funereus (Strigiformes, Strigidae), In Eurasia
Fig. 3. Median joining network of mtDNA CR1 haplotypes for the studied Boreal Owl sample. Each circle reflects a mtDNA CR1 haplotype. Circle sizes reflect the number of studied individuals possessing the haplotype; circle colors reflect geographic origin of individuals possessing the haplotype. Bars connect related haplotypes, with notches on bars reflecting the number of nucleotide differences between them. Black dots indicate implied haplotypes not present in the sample.
Fig. 1 in New Data On Phylogeography Of The Boreal Owl, Aegolius Funereus (Strigiformes, Strigidae), In Eurasia
Fig. 1. The source regions of Boreal Owl mtDNA CR1 sequences used in the present study. Numbered yellow circles indicate sampling regions for utilized Boreal Owl mtDNA CR1 sequences, as well as the number of sequences per each region. Green coloration indicates boreal owl's range.
Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species' range
<p>Files required to run analyses related to the journal article:" Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species’ range."<br><br>Code which utilizes these data are found at: https://github.com/k-lamb/Campanula-range-history</p> <p>DOI code link: https://doi.org/10.5281/zenodo.12097775</p>
figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95% highest posterior density interval is shown in blue.
figure 3 Mismatch distributions within the G in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 3 Mismatch distributions within the G. subgutturosa. The expected line (green color) compared with the observed frequencies under the sudden expansion model using cytb. (A) the mmd diagram for the Asiatic population shows a recent expansion. (B) the mmd diagram for the Middle Eastern population and (C) the mmd diagram for the Central Iranian population.
figure 8 Potential distribution modeling for G. subgutturosa across different time periods, including a in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 8 Potential distribution modeling for G. subgutturosa across different time periods, including a) the Last Glacial Maximum (lgm; 21 Kya) and b) mid-Holocene (6 kya) as past scenarios, c) the present as a current scenario, and future climatic projections for 2070 are based on specific climate models (d: bcc-csm 1, rcp: 4.5; e: bcc-csm1, rcp: 6; f: ccsm 4, rcp: 4.5; g: ccsm 4, rcp: 6.0). Habitat suitability is visualized using color gradients, with blue representing the highest suitability Downloaded from Brill.com 06/21/2024 06:25:06PM and green representing the via lowestOpensuitability Access..This The is presence an openof access article distributed under the terms G. subgutturosa is denoted by a red dot. of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95% highest posterior density intervals of the estimated node ages; numbers next to the nodes are mean node ages (Mya). The red and green lines show new haplotypes from this study.
figure 1 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 1 Sampling locations of new specimens of G. subgutturosa from four locations in the present study. Parvar Protected Area, Sorkheh-Hesar National Park, Bashgol Protected Area, and Sohrein Protected Area. Hatched areas on the map indicate the provinces where each location is situated.
figure 6 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 6 Median-joining haplotype network of G. subgutturosa using the cytb gene. The blue color Haplogroup refers to the Asiatic clade, the pink color Haplogroup is assigned to the Middle Eastern clade and the yellow color Haplogroup demonstrates the Central Iranian clade.
figure 7 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 7 The biogeographic analysis of G. subgutturosa using s-diva (1) and bbm (2) based on cytb. For these analyses, three clades were considered: the Asiatic distribution (A), the Middle Eastern distribution (B), and the central Iranian distribution (C). The green and red circles around the nodes show vicariance and dispersal events, respectively.
Fig. 2 in Intraspecific Genetic Variation And Phylogeography Of The Oak Gallwasp Andricus Caputmedusae (Hymenoptera: Cynipidae): Effects Of The Anatolian Diagonal
Fig. 2. UPGMA dendrogram of A. caputmedusae populations (see Fig. 1 and Table 1) based on pair wise estimates of percentage sequence divergence. A. q. H-1, A. q. H-2 are the haplotypes of A. quercustozae and A. l. H is the haplotype of A. lucidus gall wasp species used as outgroups. Numbers above branches represent the bootstrap values obtained from 1000 replicates of the restriction fragment data between the haplotypes. Support
Fig. 4 in Intraspecific Genetic Variation And Phylogeography Of The Oak Gallwasp Andricus Caputmedusae (Hymenoptera: Cynipidae): Effects Of The Anatolian Diagonal
Fig. 4. Unrooted Dollo parsimony majority-rule consensus tree of mtDNA haplotypes. Numbers at nodes indicates bootstrap values. Support values <50% are not represented
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.