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29 results for “museomics”
Figure 4 in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification
Figure 4. Evolutionary parallelism in forest-dwelling sengis, Rhynchocyon (less) and Petrodromus (right). Ŋe geographically widespread P.t.ss lineage (dark blue) mimics the cirnei/stuhlmanni sister pair in Rhynchocyon. Rhynchocyon species: Rch R. chrysopygus (cyan), Rci R. cirnei (dark blue), Rpe R. petersi (red), Rst R. stuhlmanni (dark blue), Rud R. udzungwensis (yellow). Petrodromus lineages: NC/Z Northern coastal/ Zanzibar Archipelago (red), P.t.ss (dark blue), Ud Udzungwa Mountains (yellow).
Data from: Next-generation museomics disentangles one of the largest primate radiations
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HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
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Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea
<p>Natural history collections and tropical tree diversity are treasure troves of biological and evolutionary information, but its accessibility is impeded by several properties. DNA in historical specimens generally occurs in a highly fragmented state, complicating the recovery of high-grade genetic material for scientific studies. Our understanding of hyperdiverse, wide-spread tree assemblages suffers from patchy information on distributions, phenology and paucity of diagnostic characters. This prohibits rapid identification and the strengthening of taxonomic frameworks and in turn, delay the application of downstream conservation actions. Congruently, a sizeable component of botanical collections are sterile, eluding identification and slowing down progress in systematic treatments. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections built up over centuries. </p> <p>Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci for both freshly collected and museum specimens (aged >100 years) of Lithocarpus, a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from museum and recent samples was unaffected by age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach.</p> <p>Phylogenomic inference and biogeographic reconstruction across insular Asia highlights repeated divergence, migration and diversification patterns between continental Lithocarpus and islands species. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. </p> <p><span>We demonstrate the utility of </span><span>MIGseq </span><span>in museomic studies using non-model taxa and present the first range-wide genomic assessment of </span><span>Lithocarpus</span><span> and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.</span><span> </span></p>
Museomics contributes to the spatiotemporal assessment of genetic diversity and structure in wild and ex situ conservation organisms: a case study of three endangered coastal plants in Japan
<p><span>Understanding </span><span>the extent to which </span><span>genetic diversity of wild populations in ex</span> <span>situ</span><span> conservation can be retained is </span><span>crucial</span><span> for the management of </span><span>such</span><span> populations. Wild individuals collected in the target area in the past </span><span>and</span><span> present can be used to estimate the number of alleles lost over time in wild populations and</span><span> thereby</span><span> the number of alleles whose loss could be </span><span>prevented</span><span> by ex</span> <span>situ</span><span> conservation. </span><span>Here</span><span>, we assessed the genetic diversity of wild and ex</span> <span>situ</span><span> conservation populations of three endangered coastal herb species</span><span>,</span><span> <em>Cirsium maritimum</em> Makino (Asteraceae), <em>Linaria japonica</em> Miq. (Plantaginaceae</span><span>) and</span><span> <em>Suaeda glauca</em></span><span><em> </em>(Bunge) Bunge (Amaranthaceae), which are endangered </span><span>species on</span><span> Awaji Island, Hyogo Prefecture, Japan, via multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). We </span><span>incorporated</span><span> the museomics approach, which </span><span>involves conducting</span><span> genetic analyses of museum specimens collected from the targeted wild populations in the past to estimate the temporal transition of genetic diversity in wild populations and the number of alleles maintai</span><span>ned in <em>ex situ</em></span><span> conservation. </span><span>Our </span><span>results </span><span>reveal</span><span> a declining trend in genetic diversity in the wild populations of all </span><span>investigated</span><span> species, although </span><span>this trend is </span><span>not significant. In all the species, </span><span>numerous</span><span> alleles were already lost in current wild populations, </span><span>whereas they</span><span> were </span><span>present</span><span> in the past wild and ex</span> <span>situ</span><span> conservation populations. Our study </span><span>indicates</span><span> that extinct alleles in current wild populations have been maintained in ex</span> <span>situ</span><span> conservation</span><span> by museomics approach. These </span><span>appro</span><span>aches </span><span>were effective in verifying</span><span> the genetic diversity retention effects of <em>ex</em></span><em> <span>situ</span></em><span> conservation populations.</span></p>
Museomics contributes to the spatiotemporal assessment of genetic diversity and structure in wild and ex situ conservation organisms: a case study of three endangered coastal plants in Japan
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Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea
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Fig. 3 in Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment
Fig. 3. Phylogenetic tree from maximum likelihood analysis of 36 taxa based on 378 loci. If the support values are not displayed on the branch, it means it is equal to 100/100.When displayed, numbers are the SH-aLRT support (%)/ultrafast bootstrap support (%).The images are representative species (indicated with numbers; not to scale).The three families are represented by an arrow and a letter. S, Sematuridae; P, Pseudobistonidae; and E, Epicopeiidae.
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
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DANDI Archive for NWB datasets
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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.