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10 results for “Global phylogeography”
Figure 3 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figure 3. Global Mantel's correlation test for genetic and geographic distance of the Aedes vexans populations analyzed.
Figures 4–5. Phylogenetic tree for Aedes vexans populations constructed from 395 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figures 4–5. Phylogenetic tree for Aedes vexans populations constructed from 395 haplotypes from the COI gene by using Bayesian Inference, BI (4) and Maximum Likelihood, ML (5). The evolutionary history for both analyses was inferred by using the GTR + G model, as suggested by jModelTest version 2.1.10. The BI tree was obtained by using 2-million generations, while the ML used 1,000 replicas. For BI, the support of the branches is indicated by the subsequent probability values, while for ML the bootstrap values are shown. Numbers in blue represent sequences from the A. nipponii subspecies. In both figures the colors below denote the continents and their respective countries: (z) America (Canada and USA) + Europe (Turkey); (z) Asia (China, India, Japan, Singapore and South Korea); (z) Europe (Sweden and Belgium) + Asia (China); (z) Eurasia (Romania, Sweden, Belgium, Russia, Kosovo, the Netherlands, China, Spain, Germany, Iran, Austria and Hungary); (z) Africa (South Africa); (z) America (USA) + Africa (South Africa).
Figures 1–2 in Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA
Figures 1–2. Map (1) showing the origin of COI gene sequences for Aedes vexans, and haplotype network (2) based on COI sequences showing the genetic relationship between populations. On the map (1), the circles indicate the location of the sequences used and the arrows, the genetic relationships between the populations. In the haplotypes network (2), the size of the circles is proportional to the haplotype frequency and each circle in color belongs to a haplotype that is respectively numbered; black docks represent ancestral haplotypes. On the map (1) and in the haplotype network (2), the following colors, group the cluster observed on the network and in the ML and BI trees (see Figs 4, 5 for details): (z) America (Canada and USA) + Europe (Turkey); (z) Asia (China, India, Japan, Singapore and South Korea); (z) Europe (Sweden and Belgium) + Asia (China); (z) Eurasia (Romania, Sweden, Belgium, Russia, Kosovo, the Netherlands, China, Spain, Germany, Iran, Austria and Hungary); (z) Africa (South Africa); (z) America (USA) + Africa (South Africa).
Fig. 3 in Predicting the global mammalian viral sharing network using phylogeography
Fig. 3 Taxonomic and geographic patterns of mean predicted viral sharing link numbers (degree centrality). Top row: all viral sharing links; middle row: viral sharing links with species in the same order; bottom row: viral sharing links with species in another order. a, c, e Average species-level viral sharing link numbers for mammalian orders in our dataset. Bars represent means; error bars represent standard errors. b, d, f Geographic distributions of mean viral sharing link numbers. Distributions were derived by summing the viral sharing link numbers of all species inhabiting a 25 km2 grid square and dividing them by the number of species inhabiting the grid square, giving mean degree number at the grid level.
Fig. 1 Viral sharing GAMM outputs and data distribution. a in Predicting the global mammalian viral sharing network using phylogeography
Fig. 1 Viral sharing GAMM outputs and data distribution. a Predicted viral sharing probability increases with increasing phylogenetic relatedness; the different coloured lines represent different geographic overlap values. b Predicted viral sharing probability increases with increasing geographic overlap; the different coloured lines represent different phylogenetic relatedness values. c The geographic overlap:phylogenetic similarity interaction surface, where the darker colours represent increased probability of viral sharing. White contour lines denote 10% increments of sharing probability. Labels have been removed from some contours to avoid overplotting. d Hexagonal bin chart displaying the data distribution, which was highly aggregated at low values of phylogenetic similarity and especially of geographic overlap.
Figure 2 in Global phylogeography of the genus Capreolus (Artiodactyla: Cervidae), a Palaearctic meso-mammal
Figure 2. Phylogeny of Capreolus obtained from the Bayesian analysis of 54 mtDNA haplotypes (925 nt) under the TIM3 model of sequence evolution. Branch length units are expected substitutions per site. Bayesian posterior probability and bootstrap values for NJ, MP and ML, respectively, are shown for the main haplogroups (inner nodes) shared by all trees. Only values over 50% are indicated. A mitochondrial CR sequence of Cervus elaphus was used as an outgroup.
Figure 1. Distribution ranges for C. capreolus and C in Global phylogeography of the genus Capreolus (Artiodactyla: Cervidae), a Palaearctic meso-mammal
Figure 1. Distribution ranges for C. capreolus and C. pygargus, and the area of putative current sympatry between the rivers Volga and Don (Hewison & Danilkin, 2001). The question mark indicates the area of further putative presence of C. pygargus. Collection sites are as follows: (FRA) France, (SWE) Sweden, (DEN) Denmark, (AUS) Austria, (ITA) Central-southern Italy, (E-AL) Eastern Italian Alps, (N-SP) Northern Spain, (CS-SP) Central-southern Spain, (GRE) Greece, (ROM) Romania, (POL) Poland, (LIT) Lithuania, (CRI) Crimea, (W-RUS) Western Russia, (KYR) Kyrgyzstan, (NE-CH) North-eastern China, (CE-CH) Central-eastern China, (E-RUS) Eastern Russia. Multiple sampling sites for one population are indicated by the same acronym. See Table 1 for details on precise sampling locations and sample sizes.
Figure 3 in Global phylogeography of the genus Capreolus (Artiodactyla: Cervidae), a Palaearctic meso-mammal
Figure 3. Median-joining network based on the data set of C. capreolus and C. pygargus haplotypes. Branch lengths are approximately scaled to the number of nucleotide substitutions occurring along the branches. White circles represent missing haplotypes. The main haplogroups are indicated by curved lines. The number of mutations are reported only for the main haplogroups.
MAGs generated in "Global scale phylogeography of functional traits and microdiversity in Prochlorococcus"
<p>High quality metagenomic assemblies from the manuscript "Global scale phylogeography of functional traits and microdiversity in <em>Prochlorococcus</em>". Pre-print available at: https://doi.org/10.1101/2023.01.24.525399</p>
Fig. 2 in Predicting the global mammalian viral sharing network using phylogeography
Fig. 2 The predicted viral sharing network predicts observed trends in an independent dataset. In all figures, points are jittered along the x-axis according to a density function; the black points and associated error bars are means ± standard errors. a Species pairs with higher predicted viral sharing probability from our model were more likely to be observed sharing a virus in the independent EID2 dataset. This comparison excludes species pairs that were also present in our training data. b Species that hosted a zoonotic virus in our dataset had more viral sharing links in the predicted all-mammal network than those without zoonotic viruses. c Species that had never been observed with a virus have fewer links in the predicted network than species that were known to host viruses in the EID2 dataset only, in our training data only, or in both. The y-axis represents viral sharing link number, scaled to have a mean of 0 and a standard deviation of 1 within each order for clarity. Black points represent means; error bars represent standard errors. Supplementary Figure 5 displays these same data without the within-order scaling.
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)
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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.