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25 results for “Hotspot analysis”
Data for: Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
<p>Ticks in the family Ixodidae are recognized as important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from the <em>Borreliella</em> (<em>Borrelia</em>) <em>burgdorferi</em> sensu lato (<em>Bbsl</em>) complex. The blacklegged tick (<em>Ixodes scapulars</em>) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated with <em>I. scapularis</em> in Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adult <em>I. scapularis</em> (N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within an LD hotspot near Kingston, Ontario. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and a <em>Babesia</em> sp. intracellular parasite. We show that β-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing were also discriminatory for dissected tissues only, including a <em>Borrelia</em> from the <em>Bbsl</em> complex, <em>Borrelia miyamotoi</em>, and <em>Anaplasma phagocytophilum. </em>Importantly, we find co-infection of <em>I. scapularis</em> by multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (<em>B. burgdorferi</em> sensu stricto).</p>
Data for: Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
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Analysis of global evapotranspiration datasets reveal hotspots of low and high agreement
<p><span>Evapotranspiration (ET) is a key component of the water cycle and varies widely across the globe. With increasing efforts to create multi-year global gridded products using a multitude of approaches, there is a need to understand where datasets agree and disagree to pinpoint where our collective understanding may fall short. We processed and homogenized fourteen gridded datasets from 2000-2019 to find hotspots of low and high dataset agreement world-wide as well as over different biomes, land cover, IPCC reference regions, elevation classes and ET intensity classes. The use of standardized quartile ranges and distribution testing established two complementary angles of collective agreement. We identified hotspots with low agreement, such as cold dry regions, as well as regions with high agreement. In regions with high agreement, we identified product-specific outliers. These regions can be of high interest for developers and inform users on product selection. </span></p>
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
<p><span>Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera <i>Microcebus</i> and <i>Cheirogaleus</i>, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, </span>as might be expected if they have each evolved to respond to specific stimuli<span>. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus <i>Mus</i>) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."</span></p>
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
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Data for: Characterizing multi-criteria decision analysis, risk stratification, and hotspot analysis methods to optimise disease policymaking and evidence translation for medicines in low- and middle-income countries: A scoping review
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Data from: Evidence of extreme habitat stability in a Southeast Asian biodiversity hotspot based on the evolutionary analysis of neotenic net-winged beetles
The diversification of neotenic beetle lineages has not been studied, despite the potential for defining biodiversity hotspots and elucidating the history of regional faunas. Additionally, neotenics may provide insight into the process of speciation in small populations with extremely low dispersal ability and a limited range. Here, we used two rDNA and three mtDNA markers to investigate the phylogeny of Scarelus, a neotenic lineage endemic to Southeast Asian rainforests. Most genetic differentiation was associated with Palaeogene geographic divisions, which remain distinct despite temporary connections. Dispersal events were rare, with only two inferred for Scarelus: from Borneo to the Philippines 28.3 million years ago (mya) and from Sumatra to Java 13.9 mya. The reproductive isolation depended on allopatric range fragmentation, and Scarelus diversified readily when conditions were favorable; in this case, at different times in the eastern (19.3–39.1 mya) and western (3.5–13.9 mya) parts of Sundaland. The observed strong phenotypic similarity was preserved under speciation through complete allopatry. Neotenic Lycidae have survived for a long time in very stable habitats, and extremely low dispersal activity has not limited their existence; however, the long-term diversification rate of neotenics is low and diversification is nonexistent under stable conditions. The modern ranges of neotenic lineages are indicative of ancient rainforest refugia, and may be used in biodiversity conservation management. Most neotenics are at risk of extinction due to small ranges and a low dispersal potential.
Figure 4 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 4. Diversity estimates based on Hill's series (1973), for the phytophysiognomies freshwater swamp forests (MDB), cerradão (CER) and semidecidual seasonal forest (FES), present in the Municipal Botanical Garden of Bauru, SP (p <0.05). q = 0: species richness; q = 1: estimate of abundant species; q = 2: estimate of dominant species.
Figure 6 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 6. Cumulative richness of Cerambycidae species collected in the phytophysiognomies freshwater swamp forests (MDB), cerradão (CER) and semideciduous seasonal forest (FES). (a) Cumulative richness of MDB; (b) cumulative richness of CER; (c) cumulative richness of FES; (d) total cumulative richness.
Figure 3 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 3. Correlation between abundance of Cerambycidae and climatic variables in the Municipal Botanical Garden of Bauru. (a) Correlation between abundance and average temperature; (b) correlation between abundance and accumulated precipitation. Source: UNESP Bauru Meteorological Institute (2021).
Figure 2 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 2. Seasonality for Cerambycidae species in the phytophysiognomies freshwater swamp forests (MDB), cerradão (CER) and semidecidual seasonal forest (FES), present in the Municipal Botanical Garden of Bauru, from October 2019 to September 2020.
Figure 1 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 1. New records of Cerambycidae species for São Paulo state, Brazil. (a) Eburodacrys elegantula Gounelle, 1909; (b) Compsibidion maronicum (Thomson, 1867); (c) Macroeme sobrina (Gounelle, 1909); (d) Acorethra aureofasciata Gounelle, 1911; (e) Eclipta nigriventris (Melzer, 1934); (f) Eclipta seminigra (Gounelle, 1911); (g) Odontocera albicans (Klug, 1825); (h) Ceralocyna militaris (Gounelle, 1911); (i) Aegoschema migueli Monné and Mermudes, 2007. Scale bar, 5mm.
Figure 5 in Faunistic analysis of longhorn beetles (Cerambycidae: Coleoptera) in Cerrado and Atlantic Forest areas: biodiversity hotspots of Brazil
Figure 5. Cluster similarity analysis for the phytophysiognomies freshwater swamp forests (MDB), cerradão (CER) and semideciduous seasonal forest (FES), present in the Municipal Botanical Garden of Bauru, based on species composition.
FIGURE. Phylogram of Panus generated from Maximum likelihood analysis of ITS sequence data. Lentinus crinitus (MK408650) was selected as the outgroup taxon. Maximum likelihood bootstrap values greater than 60% are indicated above the nodes. The new record Panus similis (HKAS 121668) is in black bold. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Phylogram of Panus generated from Maximum likelihood analysis of ITS sequence data. Lentinus crinitus (MK408650) was selected as the outgroup taxon. Maximum likelihood bootstrap values greater than 60% are indicated above the nodes. The new record Panus similis (HKAS 121668) is in black bold.
Data from: Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus
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Data from: Evidence of extreme habitat stability in a Southeast Asian biodiversity hotspot based on the evolutionary analysis of neotenic net-winged beetles
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Data from: A comparative analysis of common methods to identify waterbird hotspots
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Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization
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Multi-omics analysis reveals single-cell meiotic hotspot dynamics and epigenomic regulations in female mammals
GEO Series GSE226475. Mus musculus. 280 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies
GEO Series GSE164365. Homo sapiens. 20 samples. Type: Methylation profiling by high throughput sequencing.
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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.