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352 results for “Data Enrichment”
Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci was similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.
Data from: Biochar from "Kon Tiki" flame curtain and other kilns: effects of nutrient enrichment and kiln type on crop yield and soil chemistry
Biochar application to soils has been investigated as a means of improving soil fertility and mitigating climate change through soil carbon sequestration. In the present work, the invasive shrub "Eupatorium adenophorum" was utilized as a sustainable feedstock for making biochar under different pyrolysis conditions in Nepal. Biochar was produced using several different types of kilns; four sub types of flame curtain kilns (deep-cone metal kiln, steel shielded soil pit, conical soil pit and steel small cone), brick-made traditional kiln, traditional earth-mound kiln and top lift up draft (TLUD). The resultant biochars showed consistent pH (9.1 ± 0.3), cation exchange capacities (133 ± 37 cmolc kg-1), organic carbon contents (73.9 ± 6.4 %) and surface areas (35 to 215 m2/g) for all kiln types. A pot trial with maize was carried out to investigate the effect on maize biomass production of the biochars made with various kilns, applied at 1% and 4% dosages. Biochars were either pretreated with hot or cold mineral nutrient enrichment (mixing with a nutrient solution before or after cooling down, respectively), or added separately from the same nutrient dosages to the soil. Significantly higher CEC (P< 0.05), lower Al/Ca ratios (P< 0.05), and high OC% (P<0.001) were observed for both dosages of biochar as compared to non-amended control soils. Importantly, the study showed that biochar made by flame curtain kilns resulted in the same agronomic effect as biochar made by the other kilns (P > 0.05). At a dosage of 1% biochar, the hot nutrient-enriched biochar led to significant increases of 153% in above ground biomass production compared to cold nutrient-enriched biochar and 209% compared to biochar added separately from the nutrients. Liquid nutrient enhancement of biochar thus improved fertilizer effectiveness compared to separate application of biochar and fertilizer.
Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)
Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31 Chrysomeloidea, four outgroup taxa: two Curculionoidea and two Cucujoidea) included exemplars of all families and 23 of 30 subfamilies of Chrysomeloidea (18 of 19 non-chrysomelid Chrysomeloidea), with a focus on the large family Cerambycidae. Our results reveal a monophyletic Cerambycidae s.s. in all but one analysis, and a polyphyletic Cerambycidae s.l. When monophyletic, Cerambycidae s.s. was sister to the family Disteniidae. Relationships among the subfamilies of Cerambycidae s.s. were also recovered with strong statistical support except for Cerambycinae being made paraphyletic by Dorcasomus Audinet-Serville (Dorcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon – Chrysomelidae, Disteniidae, Vesperidae and Orsodacnidae – were monophyletic, but Megalopodidae was rendered paraphyletic by Cheloderus Gray (Oxypeltidae). Our study corroborates some relationships within Chrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon-sampled, phylogenetic and evolutionary studies of the families and subfamilies of Cerambycidae s.l. and other Chrysomeloidea.
Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
LiDAR Data Enrichment By Fusing Spatial and Temporal Adjacent Frames
<p>This is an accompanying video for the manuscript 'LiDAR Data Enrichment By Fusing Spatial and Temporal Adjacent Frames'. This video shows the comparison between the original LiDAR point cloud and the enriched LiDAR point cloud.</p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
Data from: A new genus in the diverse Andean Pedaliodes complex uncovered using target enrichment (Lepidoptera, Nymphalidae)
<p>A new genus of Neotropical Satyrinae butterflies, <em>Viloriodes </em>Pyrcz & Espeland gen. n. is described in the <em>Pedaliodes </em>complex comprising 11-13 genera and more than 400 species. Support for the new genus is provided by a phylogenetic analysis based on target enrichment data (TE) including 618 nuclear loci with a total of 248 940 nucleotides, and the mitochondrial gene COI. Five species, whose DNA sequences were obtained by TE during this study, form a strongly supported clade sister to the large clade comprising <em>Pedaliodes </em>Butler<em> </em>and other four genera. Complementary COI analysis confirms the monophyly of <em>Viloriodes </em>gen. n., with the above five plus eight other species clustering in highly supported clades in both Bayesian Inference (BI) and Maxium Likelihood analyses, and a TE+COI concatenated tree. Based on molecular and morphological data, 30 species are assigned to <em>Viloriodes </em>gen. n. The new genus can be recognized by a set of subtle morphological of colour patterns characters, male and female genitalia. The shape of the valva is diagnostic, with a finger-like tip and, in some species, an ampulla produced into an elongated process. The female genitalia are characterized by the ductus bursae having a strongly sclerotized 'keel' with a bifurcate terminus. An analysis of divergence times indicates that <em>Viloriodes</em> gen. n. and <em>Steromapedaliodes</em> Forster<em> </em>separated around 5.9 Mya. <em>Viloriodes</em> gen. n. has a wider geographic distribution than any other genus of the <em>Pedaliodes </em>complex, being found from central Mexico to northern Argentina and to the Guyana Shield, typically occurring at lower elevations than <em>Pedaliodes</em>.</p>
Data for: Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Satyrinae, Nymphalidae)
<p>The diverse, largely Neotropical subtribe Euptychiina (Satyrinae, Nymphalidae) is widely regarded as one of the most taxonomically challenging groups among all butterflies. Over the last two decades, morphological and molecular studies have revealed widespread paraphyly and polyphyly among genera, and a comprehensive, robust phylogenetic hypothesis is needed to build a firm generic classification to support ongoing taxonomic revisions at the species level. Here, we generated a dataset which includes sequences for up to nine nuclear genes and the mitochondrial COI 'barcode' for a total of 1280 specimens representing 449 described and undescribed species of Euptychiina and 39 outgroups, resulting in the most complete phylogeny for the subtribe to date. In combination with a recently developed genomic backbone tree this dataset resulted in a topology with strong support for most branches. </p>
Enriched OpenAlex Data for Colombia
<p>See https://github.com/colav-playground/advanced_user_tests</p>
FIGURE 39 Modica confusa comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 39 Modica confusa comb.n. (a–d) male genitalia (dissection KW-21-64), lateral (a) with posterior view juxta, dorsal (b), aedeagus lateral (c) and aedeagus dorsal (d); (e–h) female genitalia (dissection KW-21-65), lateral view exterior tip abdomen (e), ventral view exterior tip abdomen (f), dorsal view interior abdomen (g), corpus bursae perpendicular to signa (h). Scale bars 1 mm.
FIGURE 36 Deltaya gen.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 36 Deltaya gen.n. Species diversity mapped on a 2 degree grid. Colours ranging from dark green to red represent increasing diversity.
FIGURE 33 Deltaya ocypete comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 33 Deltaya ocypete comb.n. (a) male wing venation; (b and c) male (FLMNH-MGCL-209681) dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
FIGURE 30 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 30 Occulta ocnus comb.n. (a) male wing venation; (b and c) male (LEP-10408) dorsal (b) and ventral (c); (d and e) female (ST ocnus) dorsal (d) and ventral (e), with specimen labels. Scale bars 1 cm.
FIGURE 35 Deltaya ocypete comb.n. A-E in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 35 Deltaya ocypete comb.n. A-E, male genitalia (dissection KW-21-66), lateral (a) with posterior view juxta, dorsal (b), aedeagus lateral (c) and aedeagus dorsal (d), vesica everted showing cornuti (e); (f–i) female genitalia (dissection KW-21-67), lateral view exterior tip abdomen with 8th segment retracted (f), lateral view exterior tip abdomen with 8th segment extended (g), ventral view exterior tip abdomen (h), dorsal view interior abdomen (i). Scale bars 1 mm.
FIGURE 31 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 31 Occulta ocnus comb.n. (a and b) male genitalia (dissection SN-19-157), lateral (a) with posterior view juxta, aedeagus lateral (b); (c–e) female genitalia (dissection NHMUK010402850), lateral view exterior tip abdomen (c), ventral view exterior tip abdomen (d), dorsal view interior abdomen (e), corpus bursae perpendicular to signa (f). Scale bars 1 mm.
FIGURE 27 Trico tricolor fulgoracomb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 27 Trico tricolor fulgoracomb.n. (a and b) male dorsal (a) and ventral (b); (c and d) female dorsal (c) and ventral (d). Scale bars 1 cm.
FIGURE 23 Xenovena murryae comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 23 Xenovena murryae comb.n. (a) male wing venation; (b and c) male dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
FIGURE 19 Argentaria itonis comb.n. A-E in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 19 Argentaria itonis comb.n. A-E, male genitalia (dissection KW-21-41), lateral tip abdomen (a), lateral (b) with posterior view juxta, dorsal (c), aedeagus lateral (d) and aedeagus dorsal (e); (f–i), female genitalia (dissection KW-21-60), lateral view exterior tip abdomen (f), ventral view exterior tip abdomen (g), dorsal view interior abdomen (h), corpus bursae perpendicular to signa (i). Scale bars 1 mm.
FIGURE 21 Taguaiba drogoni comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 21 Taguaiba drogoni comb.n. (a) male wing venation; (b and c) male dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
FIGURE 28 Trico tricolor comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 28 Trico tricolor comb.n. (a and b) male genitalia, lateral (a) with posterior view juxta, aedeagus lateral (b); (c and d) female genitalia, ventral view exterior tip abdomen (c), dorsal view interior abdomen (d). Scale bars 1 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)
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.