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59 results for “genetic biodiversity”
A plant biodiversity effect resolved to a single genetic locus - datasets
<p>Despite extensive evidence that biodiversity promotes plant community productivity, progress towards understanding the mechanistic basis of this effect remains slow, impeding the development of predictive ecological theory and agricultural applications<em>. </em>Here, we analysed non-additive interactions between genetically divergent Arabidopsis accessions in experimental plant communities. By combining methods from ecology and genetics, we identified a major effect locus that promotes complementarity amongst genotypes and above-ground productivity in mixed communities. In experiments with near-isogenic lines, we show that this diversity effect can act independently of other genomic regions and be resolved to a single locus representing less than 0.3% of the genome. Using plant-soil-feedback experiments, we demonstrate that allelic diversity also causes genotype-specific soil legacy responses in a subsequent growing period. Our work thus shows that positive diversity effects can be linked to single Mendelian factors, and that a range of complex community properties, some of which manifest themselves even after the original community has disappeared<strong>, </strong>can have a simple, single cause. This may pave the way to novel breeding strategies, focussing on phenotypic properties that manifest themselves beyond isolated individuals, i.e. at a higher level of biological organisation.</p>
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework
<p>Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to report the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socioeconomic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5,271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.</p>
Global warming leads to habitat loss and genetic erosion of alpine biodiversity
<p><span><strong>Aim</strong>:</span><span> Species living on steep environmental gradients are expected to be especially sensitive to global climate change. Here, we combined genetic, ecological niche modelling and climatic niche comparisons to investigate the influence of climate on the biogeography of three alpine species with overlapping ranges.</span></p> <p><span><strong>Location</strong>:</span><span> Te Waipounamu (South Island) Aotearoa</span>–<span>New Zealand.</span></p> <p><span><strong>Taxon</strong>:</span><span> Endemic alpine-adapted Cataontopinae grasshoppers.</span></p> <p><span><strong>Methods</strong>:</span><span> We used niche modelling to estimate and project the potential niche of three focal species under past and future climate scenarios.</span><span> Vulnerability assessments were</span><span> performed using </span><span>niche factor analyses. Demographic trends and phylogeographic structure were investigated using samples from 15 mountain tops to generate mitochondrial DNA haplotype networks and population genetic statistics.</span></p> <p><span><strong>Results</strong>:</span><span> Niche models and genetic data suggest suitable habitat for all three alpine species was more widespread and contiguous in the past than today. Demographic analyses indicate in situ survival rather than post-Pleistocene colonisation of current habitat. Population structuring and genetic divergence suggest that mountain uplift during the Pliocene and environmental barriers during Pleistocene glacial and interglacial stages shaped contemporary population structure of each species. Though geographically overlapping, niche analyses suggest these alpine species are not ecologically identical, and each shows similar but distinct responses to environmental change, but all will lose intraspecific diversity through population extinction.</span></p> <p><span><strong>Main</strong> <strong>conclusions</strong>:</span><span> Climatic, biological and geophysical factors controlled population structuring of three cold-adapted species during the Pleistocene with a legacy of spatially separate intraspecific lineages. Ecological niche models for each species emphasise distinct combinations of environmental proxies, but all are expected to experience severe habitat reduction during climate warming. Increased global temperatures drive available habitat to higher elevation resulting in population contractions, range shifts, habitat fragmentation, local extinctions, and genetic impoverishment. Despite alpine species not being ecologically identical, we predict all mountain biota will lose significant genetic diversity due to global warming.</span></p>
Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework
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Global warming leads to habitat loss and genetic erosion of alpine biodiversity
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Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
Figure 11. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 11. - The neighbour-joining tree of available COI sequences. Numbers associated with nodes represent bootstrap values. Length of each sequence is listed in Table 1.
Figure 12. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 12. - The neighbour-joining tree of available 12S sequences. Numbers associated with nodes represent bootstrap values. Length of each sequence is listed in Table 1.
Figure 10b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 10b. - Habitat of Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan.Figure 10a.small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.Figure 10b.landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN. <br> landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN.
Figure 10a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 10a. - Habitat of Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan.Figure 10a.small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.Figure 10b.landscape of the Suygaty Valley (Ili River Depression). Photo taken by KN. <br> small pond where the present leeches were found. Photo taken by Dr Atsushi Tominaga.
Figure 7a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 7a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: at, atrium; ed, ejaculatory duct; ep, epididymis; mg, male gonopore; pes, penis sheet.Figure 7a.dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.Figure 7b.left lateral view of schematic drawing of male median reproductive system. <br> dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.
Figure 7b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 7b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: at, atrium; ed, ejaculatory duct; ep, epididymis; mg, male gonopore; pes, penis sheet.Figure 7a.dorsal view of male median reproductive system including positions of ganglia XI and XII. Scale bar: 0.25 mm.Figure 7b.left lateral view of schematic drawing of male median reproductive system. <br> left lateral view of schematic drawing of male median reproductive system.
Figure 4. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 4. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Ventral view of somites XI and XII. Abbreviations: fp, female gonopore; mp, male gonopore; np, nephridiopore. Scale bar: 0.5 mm.
Figure 2b. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 2b. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Scale bars: 5 mm.Figure 2a.dorsal view.Figure 2b.ventral view. <br> ventral view.
Figure 6. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 6. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Dorsal view of reproductive system including ventral nervous system. Abbreviations: at, atrium; ep, epididymis; ov, ovisac; ts, testisac; vg, vagina. Scale bar: 1 mm.
Figure 2a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 2a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Scale bars: 5 mm.Figure 2a.dorsal view.Figure 2b.ventral view. <br> dorsal view.
Figure 9. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 9. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan. Dorsal view of a live animal, one of the leeches examined in this study, in the field. Photo taken by KN.
Figure 1. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 1. - Localities where Limnatispaluda (Tennent 1859) has been recorded. Open circles indicate collection localities in previous studies. Sources: aBoye and Joshi (1994); bKinzelbach and Rückert (1985); cKuntz and Myers (1968); dMoore (1927a).
Figure 8a. from First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches - Biodiversity Data Journal 3: e5004 (27 April 2015) https://doi.org/10.3897/BDJ.3.e5004
Figure 8a. - Limnatispaluda (Tennent 1859) from Suygaty Valley, Kazakhstan, KUZ Z702. Abbreviations: cod, common oviduct; fg, female gonopore; od, oviduct; ov, ovisac; vg, vagina.Figure 8a.dorsal view of female reproductive system including positions of ganglia XII and XIII. Scale bar: 0.25 mm.Figure 8b.left lateral view of schematic drawing of female reproductive system. <br> dorsal view of female reproductive system including positions of ganglia XII and XIII. Scale bar: 0.25 mm.
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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)
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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.