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37 results for “museum genomics”
Fig. 1 in Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)
Fig. 1. Recent phylogenetic hypotheses of family relationships within the marronoid clade (in color) from 1991 to 2020 (Platnick et al. 1991, Griswold et al. 1999, 2005, Spagna and Gillespie 2008, Miller et al. 2010, Spagna et al. 2010, Wheeler et al. 2017, Crews et al. 2020).
Supplementary material 1 from: Zúñiga JD, Gostel MR, Mulcahy DG, Barker K, Hill A, Sedaghatpour M, Vo SQ, Funk VA, Coddington JA (2017) Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution. PhytoKeys 88: 119-122. https://doi.org/10.3897/phytokeys.88.14607
List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers. All the sequences are included in the GGI-Gardens BioProject. : Explanation note: List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers.
FIG. 1 in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 1. The range of E. helvum in green and E. dupreanum in brown across Sub-Saharan Africa and Madagascar. Sampling locations from Peel et al. (2013) depicted by white diamonds and samples collected from the American Museum of Natural History depicted by orange circles
FIG. 4. Admixture plots for 1−9 in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 4. Admixture plots for 1−9 populations (K). Abbreviations: ND: no data, Lib: Liberia, IC: Ivory Coast, Cam: Cameroon, EG: São Tomé and Príncipe, Gab: Gabon, DRC – Democratic Republic of Congo, Sud: Sudan, Uga: Uganda, Mad: Madagascar
FIG. 2. A in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 2. A — The Elevation Hypothesis: The Mambila Mountains in the west and the Ethiopian highlands/Katanga Plateau act as barriers to gene flow across the range of E. helvum; B — The River Basin Hypothesis: The Niger River, Congo River, Nile River, and Zambezi River act as rufugia for populations and limit gene flow across the range of E. helvum; C — The Panmixia Hypothesis: E. helvum mates randomly across the range with no limits to gene flow
Data from: Museum genomics: low-cost and high-accuracy genetic data from historical specimens
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Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens
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Data from: Avian mitochondrial genomes retrieved from museum eggshell
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Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens
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Data from: Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species
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Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)
Historical museum specimens are invaluable for morphological and taxonomic research, but typically the DNA is degraded making traditional sequencing techniques difficult to impossible for many specimens. Recent advances in Next-Generation Sequencing, specifically target capture, makes use of short fragment sizes typical of degraded DNA, opening up the possibilities for gathering genomic data from museum specimens. This study uses museum specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae, with a focus on Palpimanoidea. While many previous studies have used target capture techniques on dried museum specimens (for example, skins, pinned insects), this study includes specimens that were collected over the last two decades and stored in 70% ethanol at room temperature. Our findings support the utility of target capture methods for examining deep relationships within Araneomorphae: sequences from both UCE and exonic loci were important for resolving relationships; a monophyletic Palpimanoidea was recovered in many analyses and there was strong support for family and generic-level palpimanoid relationships. Ancestral character state reconstructions reveal that the highly modified carapace observed in mecysmaucheniids and archaeids has evolved independently.
Data from: Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat
<p>Like many carnivore species, European wildcats (<em>Felis silvestris</em>) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck in the beginning of the 20th century. In Germany, the species has managed to survive its near-extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP genotyped and mtDNA sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, e.g., regarding population structure and the delineation of appropriate conservation units, potentially informing todays' species conservation.</p>
FIG. 5 in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 5. Genotypes corresponding to Admixture plot at K = 9
FIG. 3. Graph indicating the appropriate K in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 3. Graph indicating the appropriate K value where CV error is lowest from Admixture
Data from: Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat
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Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)
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Data from: Unlocking the vault: next generation museum population genomics
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