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315 results for “gene diversity”
Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient
Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city (Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site-level but not at the nest-level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.
Data from: Evolutionary analyses of visual opsin genes in frogs and toads: diversity, duplication, and positive selection
<p>Data from: Evolutionary analyses of visual opsin genes in frogs and toads: diversity, duplication, and positive selection</p>
Raw data and metadata associated with the manuscript: "Organ and ontogeny-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two Solanum dulcamara leaf chemotypes"
<p>Raw LC-MS and RT-qPCR data and metadata associated with the manuscript: "Ontogeny and organ-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two <em>Solanum dulcamara</em> leaf chemotypes", accepted at Plant Biology.</p>
FIGURE 6 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 6. Distribution of the five species of the N. melanoleuca complex. A full list of voucher specimens beyond those included in multivariate analyses and Appendix 2 is available on request from the first author.
FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.
FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).
FIGURE 4 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 4. Ordination of individual specimens and OTU centroids of four of the mitochondrially defined candidate species of the N. melanoleuca complex along the first two canonical variates. CS5-peroescobari was omitted due to the small available sample size. Canonical variates 1 and 2 account for 57.9 and 22.8% of total variance, respectively. Enlarged symbols indicate OTU centroids.
FIGURE 3 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 3. Ordination of individual specimens in a Principal Coordinates Analysis of standardised multilocus distances of PRLR and UBN1 scnDNA sequence data. (a) All specimens; (b) Analysis repeated under exclusion of CS2 and CS3.
FIGURE 8 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 8. Naja (Boulengerina) melanoleuca. Adult specimens from Yaoundé, Cameroon (left—photo J.-F. Trape) and Tsibilé, Gabon (right—photo L. Chirio). Note the diffuse but distinct hood mark that is often present in this species, and the combination of broad main bands and narrow accessory bands on the ventral side.
FIGURE 9 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 9. Naja (Boulengerina) subfulva. Variation in colour and pattern. Top left: specimen from Kakamega, western Kenya, illustrating the typically deep black and white specimens with strong facial markings from the periphery of Lake Victoria. Bottom left: specimen from Chuka, Mount Kenya, Kenya, illustrating an extreme of the brown forebody and reduced facial pigmentation typical of the species in much of its range. Photos W. Wüster, courtesy Royjan Taylor / Bio-Ken snake farm live collection, Watamu, Kenya. Right: specimen from Bamenda, Cameroon, representing the form described by Stucki-Stirn (1979) as Naja melanoleuca aurata. Note the indistinct ventral bands and the lack of accessory ventral bands, as is typical of this species. Photo J.-F. Trape.
FIGURE 7 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 7. Naja (Boulengerina) savannula sp. nov. Top row and bottom left: holotype, MNHN 2018.0002. Bottom right: live specimen from Kindia, Guinea, showing conspicuous, broad dorsal bands and ventral banding, including narrow accessory bands (not vouchered). Photos J.-F. Trape.
FIGURE 2 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 2. Haplotype networks for single copy nuclear loci. (a) PRLR; (b) UBN1. Small black circles indicate unsampled haplotypes.
Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies"
<p>The following repository contains both the genomic and functional annotations for 4 Ithomiini species. Data that was used in GBE paper "Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies".</p>
FIGURE 7 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 7. MultiPip analysis showing overall sequence similarity of plastid genomes based on complete plastome alignment using Capparis spinosa var. spinosa as a reference sequence. Levels of sequence similarity are indicated by red (75±100%), green (50±75%), and white (<50%). Arrows indicate gene losses.
FIGURE 6 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 6. Nucleotide diversity and hotspot regions in genus Capparis. The X-axis represents the nucleotide position and Y-axis represents nucleotide diversity (Pi). 6a. Interspecific variation among four taxa of Capparis. 6b. Intraspecific variation among two varieties of Capparis spinosa viz. var. spinosa and var. herbacea.
FIGURE 2 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 2. Plastome maps of Capparis spinosa var. spinosa and Capparis spinosa var. herbacea. Genes shown outside the circles are transcribed clockwise and those inside are transcribed anticlockwise. Genes belonging to different functional groups are in various colours. The dashed area in inner circles indicates the GC content of plastome. ORF – Open reading frame. Asterisks indicate genes containing introns.
FIGURE 5 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 5. Comparison of SSRs in four Capparis taxa viz. C. spinosa var. herbacea, var. spinosa, C. versicolor and C. urophylla. 5a. Types of SSRs; 5b. Size of SSRs; 5c. Number of SSR repeats in LSC, SSC and IRs. Numbers above each bar represents the number of repeats.
FIGURE 4 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 4. Codon usage of four taxa of Capparis viz. Capparis spinosa var. spinosa, var. herbacea, C. versicolor and C. urophylla. Xaxis: Amino acid, Y- axis: codon usage in percentage. * indicates stop codon.
FIGURE 1 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 1. Map depicting distribution and altitudinal ranges of seven varieties of Capparis spinosa. (as per Jacobs 1965, Fici 2014, and POWO 2019).
FIGURE 3 in Plastome data provide insights into intra and interspecific diversity and ndh gene loss in Capparis (Capparaceae)
FIGURE 3. Comparison of LSC, SSC and IR borders of Capparaceae with members of Cleomaceae (Tarenaya hassleriana) and Brassicaceae (Aethionema arabicum). Numbers in boxes indicate total length of the particular region; numbers below the arrows show base pair shift or overlapping regions. Gene and IR lengths are not to scale.
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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.