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563 results for “genetic differentiation”
Non-genetically-based intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae
<p>We used next-generation sequencing to study DNA methylation and gene expression changes in plants from four clonal populations of the metallophyte moss <em>Scopelophila cataractae</em> experimentally exposed to either Cd or Cu. For this we performed reduced representation bisulfite DNA sequencing and RNA sequencing. </p>
Even short‐distance dispersal over a barrier can affect genetic differentiation in Gyraulus, an island freshwater snail
<p>Supplementary dataset for a published paper, "Saito T., Sasaki T., Tsunamoto Y., Uchida S., Satake K., Suyama Y., <em>et al.</em> (2022). Even short‐distance dispersal over a barrier can affect genetic differentiation in <em>Gyraulus</em> , an island freshwater snail. <em>Freshwater Biology</em> <strong>67</strong>, 1971–1983. <a href="https://doi.org/10.1111/fwb.13990">https://doi.org/10.1111/fwb.13990</a>"</p>
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests
Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.
Data from: Discordant patterns of genetic and phenotypic differentiation in five grasshopper species co-distributed across a microreserve network
<p>Conservation plans can be greatly improved when information on the evolutionary and demographic consequences of habitat fragmentation is available for several co-distributed species. Here, we study spatial patterns of phenotypic and genetic variation among five grasshopper species that are co-distributed across a network of microreserves but show remarkable differences in dispersal-related morphology (body size and wing length), degree of habitat specialization and extent of fragmentation of their respective habitats in the study region. In particular, we tested the hypothesis that species with preferences for highly fragmented microhabitats show stronger genetic and phenotypic structure than co-distributed generalist taxa inhabiting a continuous matrix of suitable habitat. We also hypothesized a higher resemblance of spatial patterns of genetic and phenotypic variability among species that have experienced a higher degree of habitat fragmentation due to their more similar responses to the parallel large-scale destruction of their natural habitats. In partial agreement with our first hypothesis, we found that genetic structure, but not phenotypic differentiation, was higher in species linked to highly fragmented habitats. We did not find support for congruent patterns of phenotypic and genetic variability among any studied species, indicating that they show idiosyncratic evolutionary trajectories and distinctive demographic responses to habitat fragmentation across a common landscape. This suggests that conservation practices in networks of protected areas require detailed ecological and evolutionary information on target species in order to focus management efforts on those taxa that are more sensitive to the effects of habitat fragmentation.</p>
Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)
<p>This dataset provides the raw data for the population genetic analyses for the article: "Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)" by Benoit Pujol; Juliette Archambeau; Aurore Bontemps; Mylène Lascoste; Sara Marin; and Alexandre Meunier found in the journal "Botany Letters", Vol 164 pp. 111-119 (DOI: 10.1080/23818107.2017.1310056).</p> <p>Link to journal open access article: http://www.tandfonline.com/doi/pdf/10.1080/23818107.2017.1310056</p> <p>Link to Zenodo article reporsitory: https://zenodo.org/record/801169</p> <p>The datafile includes three data sheets:</p> <p>Data, which contains for each plant : the name of the population, the name of the sampled individual, the subspecies, the latitude of the population, the longitude of the population, the altitudinal elevation of the population in meters, and the microsatellite genotype of each plant. Genotype data is recorded by locus (two columns for the two alleles at one locus). Locus name is found as the title of the column. The record for each allele is its allele size.</p> <p>valleys 1 and valleys 2, which contains the association between populations and valleys following the two scenarios that we analyzed in the paper.</p> <p>Microsatelite loci were developed during previous work: see the following paper for more details: Debout, G., E. Lhuillier, P.-J. Malé, B. Pujol, and C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4:75-79.</p>
Figure 8 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 8. Daphnia tanakai sp. nov., male from Lake Midori-ga-ike, Japan. A, lateral view. B, caudal spine. C, head. D, E, armature of antero-ventral and posterior portion of valve. F, G, postabdomen and postabdominal claw. H, male antenna I. I, tip of male seta ('flagellum') on antenna I. J, K, limb I and its distal portion. L–O, distal-most endite of limb II.
Figure 7 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 7. Daphnia tanakai sp. nov., thoracic limbs of parthenogenetic female from Lake Midori-ga-ike, Japan. A, B, limb I. C, D, anterior seta on its endite 3 and 2. E, limb II. F, G, stiff seta on its inner-distal end. H, gnathobase II. I, J, limb III and its inner-distal portion. K, L, limb IV and its inner-distal portion. M, N, limb V and distal portion of its exopodite.
Figure 6 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 6. Daphnia tanakai sp. nov. from Lake Midori-ga-ike, collected on August 30, 2004 by S. Tanaka (A–F, K–O) and Lake Kagami-ike, collected on September 01, 2004 by S. Tanaka (G–J, P–R); both lakes are in Hida Mountain Range, Honshu Island, Japan. A, parthenogenetic female, lateral view. B, head of parthenogenetic female. C, D, armature of postero-ventral and posterior region of valve. E, postabdomen. F–I, postabdominal claws of adults. J, postabdominal claw of juvenile. K, L, antenna I in lateral and distal view. M, N, distal portion of basal segment in posterior and anterior view. O, swimming seta. P, Q, ephippial female and postero-dorsal portion of its carapace. R, ephippium.
Figure 3 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 3. Daphnia curvirostris, large parthenogenetic female from Lake Glubokoe, Moscow area, European Russia, collected on August 9, 2004 by AAK. A, lateral view. B, caudal spine. C–E, head. F, G, armature of postero-ventral and posterior region of valve. H, postabdomen. I, J, postabdominal claw. K, L, antenna I in lateral and posterior view.
Figure 5 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 5. Daphnia curvirostris from Lake Glubokoe, Moscow area, European Russia, collected on September 9, 2004 by N. N. Smirnov. A, B, ephippial female and its postero-dorsal region. C, fresh ephippium. D, adult male. E, male head. F, G, armature of ventral margin of valve. H, armature of posterior portion of valve. I, J, postabdomen and abdomen. K, antenna I. L, antenna II. M, N, limb I and its distal portion. O, armature of distal portion of largest seta of outer distal lobe. P, innerdistal portion of limb II.
Figure 2 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 2. Mapping the characters of chromosome number and postabdominal claw morphology onto the Daphnia ND2 consensus tree (Fig. 1). A, the left cladogram shows the evolution of chromosome number. Black line denotes 2n = 22, white line denotes 2n = 20 and dot line denotes 2n = 24. B, the right cladogram shows the evolution of postabdominal claw morphology. Black line denotes variable phenotype between the longispina-claw and pulex-claw types, white line denotes the longispina- claw type, dot line denotes the pulex-claw type and grey line denotes equivocal.
Figure 4 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 4. Daphnia curvirostris, appendages of parthenogenetic female from Lake Glubokoe, European Russia. A, coxal part of antenna II. B, distal portion of basal segment and basal portion of branches. C, distal portion of endopod. D, swimming seta. E, maxilla I. F, limb I: ODL indicates outer distal lobe; IDL indicates inner distal lobe. G–I, limb II, second seta on its inner-distal end, and gnathobase II. J–L, limb III, its inner-distal portion and filtering seta of gnathobase. M, N, limb IV and its inner-distal portion. O, limb V.
Figure 1 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 1. ME bootstrap consensus tree of Daphnia ND2 sequences. The numbers on each branch show support values of the branch. Upper numbers indicate ME, and ML bootstrap support values for nucleotide sequences. Middle numbers indicate MP bootstrap support values and Bayesian clade credibility values for nucleotide sequences. Lower numbers indicate MP bootstrap support values and Bayesian clade credibility values for amino acid sequences. Asterisks indicate no support values.
Fig. 4 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene
Fig. 4. Distribution of pairwise values of genetic distances amongst species with allopatric areas: 1 — for the Western Palearctic genus Sylvaemus; 2 — for the Eastern Palearctic genera Apodemus and Alsomys; 3 — for the Palearctic Muridae as a whole, including species of genera Micromys and Mus.
Fig. 3 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene
Fig. 3. Distribution of pairwise intraspecies genetic distances within: 1 — the Western Palearctic genus Sylvaemus; 2 — the Eastern Palearctic genera Apodemus and Alsomys; 3 — in general for the Palearctic Muridae, including Micromys and Mus.
Fig. 2 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene
Fig. 2. Phenogram of genetic distances (Tamura, Nei, 1993) calculated from cytb sequences amongst representatives of the genera/subgenera Alsomys, Apodemus and genera Micromys, Mus, Rattus, constructed using the UPGMA algorithm. Representatives of the Arvicolidae and Cricetidae as well as S. s. dichrurus, S. flavicollis, S. (K.) mystacinus and S. (K.) epimelas were taken as outgroups.
Fig. 5 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene
Fig. 5. Distribution of pairwise genetic distances amongst taxa: 1 — Western Palearctic genus Sylvaemus, 2 — Eastern Palearctic genera Apodemus, Alsomys, 3 — Western Palearctic genus Sylvaemus and contrarily Eastern Palearctic genera Apodemus, Alsomys.
Fig. 1 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene
Fig. 1. Phenogram of genetic distances calculated from cytb sequences amongst representatives of the genera Sylvaemus, Rattus, constructed using the UPGMA algorithm, as mentioned above. Microtus arvalis (Arvicolidae) and Cricetus cricetus (Cricetidae) are used as outgroups.
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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.