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476 results for “species boundaries”
Imputed Forest Composition Map for New England Screened by Species Range Boundaries 2001-2006
Initializing forest landscape models (FLMs) to simulate changes in tree species composition requires accurate fine-scale forest attribute information mapped contiguously over large areas. Nearest-neighbor imputation maps have high potential for use as the initial condition within FLMs, but the tendency for field plots to be imputed over large geographical distances results in species frequently mapped outside of their home ranges, which is problematic. We developed an approach for evaluating and selecting field plots for imputation based on their similarity in feature-space, their species composition, and their geographical distance between source and imputation to produce a map that is appropriate for initializing an FLM. We applied this approach to map 13m ha of forest throughout the six New England states (Rhode Island, Connecticut, Massachusetts, New Hampshire, Vermont, and Maine). The map itself is a .img raster file of FIA plot CN numbers. To access FIA data from this map, one has to link the mapcodes in this map to FIA data supplied by USDA FIA database (https://apps.fs.usda.gov/fia/datamart/datamart.html). Due to plot confidentiality and integrity concerns, pixels containing FIA plots were always assigned to some other plot than the actual one found there.
Data set: Variations in water economy traits in two Sphagnum species across their distribution boundaries
<p><em>Sphagnum</em> trait data collected (2016-2017) across a climatic gradient in Sweden. Trait data for both shoot and canopy traits. Data for <em>Sphagnum cuspidatum</em> and <em>Sphagnum lindbergii</em>. Also contains data on species occurrence records in Sweden and output from speceis distribution modelling. See published paper for more information.</p> <p>Files contain (i) processed data ("calculated_trait_data...cvs"), (ii) raw data ("Campbell_etal_clim_traits_...cvs"), (iii) their readme files, and (iv) R-scripts to run the analyses. Note that you need the files in the zip-file to run the analyses in the R-script. The zip-file contains all raw data (climate, traits, species occurences), MaxEnt output, and raster files from photogrammetry.</p> <p>More info in paper: <a href="https://doi.org/10.1002/ajb2.16347" target="_blank" rel="noopener">https://doi.org/10.1002/ajb2.16347</a></p>
Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles
Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the <i>breve</i> species group of <i>Bembidion</i>, and vary across broader taxonomic sampling in <i>Bembidion</i> subgenus <i>Plataphus</i>. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of <i>Plataphus</i>. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution.
Fig. 15 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 15. Differences in the posterior part of the surstylus among species of the M. avidus complex. A. UPGMA phenogram constructed using squared Mahalanobis distances. B. Thin-plate spline deformation grids showing overall shape differences between analysed species.
Fig. 14 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 14. Differences in the posterior part of the surstylus among species of the M. avidus complex. A. Scatter plot of individual scores of CV1 vs CV2. B. Scatter plot of individual scores of CV2 vs CV3.
Fig. 11 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 11. UPGMA phenogram constructed using the squared Mahalanobis distances of wing shape for species of the M. avidus complex.
Fig. 12 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 12. Thin-plate spline deformation grids showing wing shape differences between analysed species. Differences between the species have been exaggerated five-fold to make them more visible.
Fig. 10 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 10. Differences in wing shape among species of the M. avidus complex. A. Scatter plot of individual scores of CV1 vs CV2. B. Scatter plot of individual scores of CV2 vs CV3.
Fig. 9 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 9. UPGMA tree based on pairwise genetic distances for four species from the Merodon avidus complex.
Fig. 8 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 8. Median-joining network of the mtDNA 5'-end of the COI gene. Circle sizes are proportional to haplotype frequencies. Each branch represents one mutational step; if more than one mutational step is present, it is denoted by the given number.
Fig. 6 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 6. Maximum parsimony strict consensus tree based on DNA barcode COI sequences. Length 136 steps, Consistency Index (CI) = 93, Retention Index (RI) = 95. Filled circles denote unique changes, open circles non-unique.
Fig. 4 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 4. Merodon megavidus Vujić & Radenković sp. nov., head, antero-lateral view. A. Ƌ. B. ♀. Scale bar = 1 mm.
Fig. 3. Hind leg, lateral view. A–B in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 3. Hind leg, lateral view. A–B. Merodon avidus (Rossi, 1790). A. Ƌ. B. ♀. — C–D. M. megavidus Vujić & Radenković sp. nov. C. Ƌ. D. ♀. Scale bar = 1 mm.
Fig. 2 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species
Fig. 2. Merodon megavidus Vujić & Radenković sp. nov., male genitalia. A. Epandrium, lateral view. B. Left surstylus, anterior view. C. Hypandrium, lateral view. Abbreviations: psl = posterior surstylus lobe; asl = anterior surstylus lobe; c = cercus; ae = aedeagus; ea = ejaculatory apodeme. Scale bar = 0.5 mm.
Data for: Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)
<p class="MsoNormal">Scleractinian corals are the main modern builders of coral reefs, dynamic ecosystems that are hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo-Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi-Atlantic hard coral genus <em>Favia</em>. Coalescent-based species delimitation (BFD* - Bayes factor delimitation) recovered <em>F. fragum </em>and <em>F. gravida </em>as separate species. Although our results agree with depth-related genetic structuring in <em>F.</em><em> frag</em><em>um</em><em>,</em><em> </em>they did not support incipient speciation of the "tall" and "short" morphotypes. The preferred scenario revealed a split between two main lineages of <em>F. gravida</em>, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were supported by analysis of datasets with varying levels of missing data. Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in <em>Favia</em><em> </em>and<em> </em>rejected the long-standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations. </p>
FIGURE 3 in Morphological and molecular species boundaries in the Hyalella species Flock of Lake Titicaca (Crustacea: Amphipoda)
FIGURE 3 Bayesian phylogeny and molecular species delimitation of South American Hyalella based on currently available cox1 mitochondrial data (present work and Barcode of Life DATA Systems (BOLD) repository project TTKK). Nodes with maximum nodal support are remarked with circles. Purple dots on branch tips indicate haplotypes exclusively sampled in South America outside the Altiplano area (see supplementary fig S1 for details). See main text for details on molecular species delimitation methods and results.
FIGURE 1 A in Morphological and molecular species boundaries in the Hyalella species Flock of Lake Titicaca (Crustacea: Amphipoda)
FIGURE 1 A, map of South America showing location of the Andean Altiplano; B, approximate area of the Altiplano showing placement of its main water bodies; C, sampling sites placed outside Lake Titicaca; D, sampling sites at Lake Titicaca itself. Numbers identify sampling stations. See supplementary tables S1 and S2 for precise information on sampling sites. Maps were produced using R ggmap (Kahle & Wickham, 2013) and Google Maps (Google Inc., Mountain View Downloaded, CA). from Brill.com 12/12/2023 03:08:26PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
FIGURE 2 in Morphological and molecular species boundaries in the Hyalella species Flock of Lake Titicaca (Crustacea: Amphipoda)
FIGURE 2 Morphological disparity within the Hyalella species-flock of Lake Titicaca. A, H. robusta; B, H. longipalma; C, H. montforti; D-E, H. crawfordi; F, H. neveulemairei; G-H, H. armata; I, H. knickerbockeri; J, Hyalella n. sp. 1; K, H. lucifugax. See key to species for descriptionDownloadedof precisefrom Brill armature.com 12/12 arrangement /2023 03:08:26PM on each species. [A-C, E: after via ChevreuxOpen (1907 Access);. D, This E: after is an Coleman open & accessGonzález article(2006); distributedG, H: after under the terms González & Coleman (2002); I: modified from Weckel (1910); K: modified from Faxonof(the 1876)] CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
FIGURE 4 in Morphological and molecular species boundaries in the Hyalella species Flock of Lake Titicaca (Crustacea: Amphipoda)
FIGURE 4 Multidimensional scaling plot based on Kimura 2-parameters genetic distances of the 560 unique cox1 haplotypes detected in Hyalella. Dot colours refer to the main Hyalella lineages inferred in the molecular species delimitation analyses. Dots have been numbered according to their MOTU assignment.
Text-fig. 11. Acer Post Hammer species 1, UF 279-34456. a, b: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. c: Crowded alternate intervessel pits, TLS. d: Simple perforation plates, helical thickenings in vessel elements, TLS. e: Rays 2–3-seriate, gum deposit in vessel element, TLS. Acer Post Hammer species 2. UF 279-34466. f: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. g: Alternate intervessel pits, helical thickenings in vessel elements, TLS. h: Rays 1–4(–5)-seriate, TLS. i: Crystalliferous strand, multiseriate ray, TLS. Trochodendron beckii, UF 279-24558. j, k: Distinct growth rings, abrupt transition from earlywood to latewood, vesselless, wide rays noded at growth ring boundaries, TS. l: Rays of two distinct sizes, uniseriate and multiseriates>10-seriate, TLS. m. Scalariform intertracheary pits. RLS. Scale bars: 500 µm in j; 200 µm in a, f, k, l; 100 µm in b, h; 50 µm in c, d, e, g, i, m. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 11. Acer Post Hammer species 1, UF 279-34456. a, b: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. c: Crowded alternate intervessel pits, TLS. d: Simple perforation plates, helical thickenings in vessel elements, TLS. e: Rays 2–3-seriate, gum deposit in vessel element, TLS. Acer Post Hammer species 2. UF 279-34466. f: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. g: Alternate intervessel pits, helical thickenings in vessel elements, TLS. h: Rays 1–4(–5)-seriate, TLS. i: Crystalliferous strand, multiseriate ray, TLS. Trochodendron beckii, UF 279-24558. j, k: Distinct growth rings, abrupt transition from earlywood to latewood, vesselless, wide rays noded at growth ring boundaries, TS. l: Rays of two distinct sizes, uniseriate and multiseriates>10-seriate, TLS. m. Scalariform intertracheary pits. RLS. Scale bars: 500 µm in j; 200 µm in a, f, k, l; 100 µm in b, h; 50 µm in c, d, e, g, i, m.
ScienceDex guides
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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.