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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: Distribution and biogeography of Sanguina snow algae: fine-scale sequence analyses reveal previously unknown population structure
It has been previously suggested that snow algal species within the genus Sanguina (S. nivaloides and S. aurantia) show no population structure despite being found globally (S. nivaloides) or throughout the Northern Hemisphere (S. aurantia). However, systematic biogeographic research into global distributions is lacking due to few genetic and no genomic resources for these snow algae. Here, using all publicly available and previously unpublished Sanguina sequences of the Internal Transcribed Spacer 2 region, we investigate if this purported lack of population structure within Sanguina species is supported by additional evidence. Using a minimum entropy decomposition (MED) approach to examine fine-scale genetic population structure, we find that these snow algae populations are largely distinct regionally and have some interesting biogeographic structuring. This is in opposition to the currently accepted idea that Sanguina species lack any observable population structure across their vast ranges and highlights the utility of fine-scale (sub-OTU) analytical tools to delineate geographic and genetic population structure. This work extends the known range of S. aurantia and emphasizes the need for development of genetic and genomic tools for additional studies on snow algae biogeography.
Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
<p>After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, <i>Etmopterus pusillus</i> in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple <i>E. pusillus</i> samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark <i>Etmopterus joungi</i>. Results confirm the almost global distribution of <i>E. pusillus</i> and suggest <i>E. joungi </i>to be a junior synonym of <i>E. pusillus</i>. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.</p>
FIGURE 8 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 8. Phylogeny of tribe Senecioneae using maximum likelihood analysis based on concatenated ITS and ETS data. Bootstrap values (maximum likelihood/maximum parsimony; MLBS/MPBS) ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95 are indicated above and below branches, respectively. Dashes (-) indicate bootstrap values <70%.
FIGURE 5 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 5. Senecio acutipinnus in the wild (Wenshan county, Yunnan, China). A. Habitat. B. Habit. C. Rhizome and roots. D. Proximal to distal stem leaves. E. Synflorescence. F. Capitula. G. Phyllaries (abaxial side). H. Disc florets. I. Achene and pappus. Photographed by Wen-qun Fei.
FIGURE 6 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 6. Senecio graciliflorus in the wild (Lhünzê, Xizang, China). A. Habitat. B. Habit. C. Rhizome and roots. D. Leaf. E. Synflorescence. F. Capitula. G. Phyllaries (abaxial side). H. Ray florets. I. Disc florets. Photographed by Long Wang.
FIGURE 7 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 7. Mitotic metaphase chromosomes (A–D) and karyotypes (E–H) of Senecio acutipinnus (A, B, E, F), S. graciliflorus (C, G), and S. racemulifer (= Jacobaea racemulifera; D, H). All the three species have 2n = 40 = 40 m. A–C, the same scale; E–H, the same scale.
FIGURE 4 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 4. Selected specimens of Senecio acutipinnus. A. China, Guizhou, Leishan county, X.L. Yu 14111003 (CSF). B. China, Yunnan, Yongde county, E.D. Liu & Z.F. Xu 3422 (KUN).
FIGURE 3 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 3. Senecio racemulifer (= Jacobaea racemulifera) in the wild (Wuqia county, Xinjiang, China). A. Habitat. B. Habit. C. Rhizome and roots. D. Basal to distal stem leaves. E. Synflorescence. F. Capitulum. G. Longitudinal section of involucre. H. Ray florets. I. Disc florets. Photographed by Hui-min Li.
FIGURE 2 in Nuclear ITS/ETS sequence data indicate the membership of Senecio racemulifer, but not S. acutipinnus and S. graciliflorus, within the genus Jacobaea (Asteraceae, Senecioneae)
FIGURE 2. Selected specimens of Senecio racemulifer (= Jacobaea racemulifera) from Wuqia county in Xinjiang, China. A, B. Northwest Inst. Bot. Xinjiang Exped. 1726 (WUK). C, D. H.M. Li & Y.P. Zeng 599 (IBSC).
Genotyping-by-sequencing data for a Haitian sorghum breeding program
<p>Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively intercrossed, and subjected to intense selection under SCA infestation. We conducted evolutionary population genomics analyses of 296 post-selection Haitian lines compared to 767 global accessions at 159,683 single nucleotide polymorphisms. Despite intense selection, the Haitian population retains high nucleotide diversity through much of the genome due to diverse founders and an intercrossing strategy. A genome-wide fixation (FST) scan and geographic analyses suggests that adaptation to SCA in Haiti is conferred by a globally-rare East African allele of RMES1, which has also spread to other breeding programs in Africa, Asia, and the Americas. De novo genome sequencing data for SCA resistant and susceptible lines revealed putative causative variants at RMES1. Convenient low-cost markers were developed from the RMES1 selective sweep and successfully predicted resistance in independent U.S. × African breeding lines and eight U.S. commercial and public breeding programs, demonstrating the global relevance of the findings. Together, the findings highlight the potential of evolutionary genomics to develop adaptive trait breeding technology and the value of global germplasm exchange to facilitate evolutionary rescue.</p>
Data set for the paper "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences"
<p>Mineral data set for the paper "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences"</p>
Data set for the paper "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences"
<p>Mineral data set for the paper "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences"</p>
Figure 9 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 9. Photographs of preserved specimens: A, nuchal spines (hooks), I. australiensis; B, thoracic segments with lateral lobes, I. australiensis; C, thoracic segments with lateral lobes, L. giardi; D, abdominal segments with 'proventricle', dorsal view, Sabellaria sp. nov. 2; E, abdominal segments with 'proventricle', ventral view, Sabellaria sp. nov. 2; F, posterior abdominal segments and cauda, Idanthyrsus australiensis. Abbreviations: b, branchia; ca, cauda; ll, lateral lobes; nh, nuchal spines (hooks); pv, proventricle.
Figure 8 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 8. Photographs of preserved specimens: A, operculum and anterior segments, lateral view, Sabellaria sp. nov. 2; B, operculum and anterior segments, lateral view, Lygdamis giardi; C, detail of opercular papillae, Lygdamis indicus; D, head and thoracic appendices, Idanthyrsus australiensis; E, head and thoracic appendices, Sabellaria sp. nov. 2; F, operculum and anterior segments, ventral view, Phalacrostemma sp. nov.; G, head and thoracic appendices, L. giardi; H, head and thoracic appendices, L. giardi; I, median organ with lateral ocelli, I. australiensis; J, head and thoracic appendices, Bathysabellaria spinifera; K, operculum and paleae, dorsal view, Tetreres robustus; L, operculum and thoracic segments, lateral view, B. spinifera; M, operculum and anterior segments, lateral view, T. robustus. Abbreviations: b, branchia; b2, branchia segment 2; bo, building organ; cn 1, cirrus neuropodia segment 1; chn1, chaetae neuropodium segment 1; dap, dorsal papilla; es, eyespots; ip; inner paleae; li, lips; mo, mouth; mor; median organ; mr, median ridge; ns, nuchal spines (hooks); op, outer paleae; opa, opercular papillae; p, paleae; pa, palp; pl, oral plates; tf, tentacular filaments.
Figure 4 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 4. Schematic representation of sabellariid relationships based on maximum-parsimony analyses of the morphological data (constant of concavity k = 4–6) and stylized drawing of opercula from top view, modified from Kirtley (1994). See text for further details.
Figure 6 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 6. Photographs of Idathyrsus australiensis alive: A, complete specimen, dorsal view; B, anterior end, dorsal view; C, anterior end, central view. Abbreviations: ab, abdomen; b, branchia; ca, cauda; g, gut; ip, inner paleae; nh, nuchal hooks; p, paleae; o, operculum; op, outer paleae; tf, tentacular filaments; pa, parathorax.
Figure 5 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 5. Stylized drawing of a sabellariid indicating the body regions and some of the morphological features described in Appendix 2: A, dorsal view; B, ventral view.
Figure 3 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 3. Trees resulting from parsimony analyses of morphological data of members of Sabellariidae and rooted with Spionidae, implementing implied weighting. Unambiguous changes are marked on the topology; black dots: synapomorphies, white dots: homoplastic character states. A, strict consensus of three most-parsimonious trees (constant of concavity k = 3); B, most-parsimonious tree (constant of concavity k = 4–6).
Figure 10 in Systematic revision of Sabellariidae (Polychaeta) and their relationships with other polychaetes using morphological and DNA sequence data
Figure 10. Scanning electron micrographs: A, arrangement of paleae in two rows, Idanthyrsus australiensis; B, paleae giving the appearance of being arranged in three rows with the mid and inner row directed in opposite directions, Sabellaria sp. nov. 2; C, paleae with cylindrical and straight blades, Phalacrostemma sp. nov.; D, paleae with flat, straight and smooth edges blades, Lygdamis giardi; E, paleae with flat, straight blades and denticulated margins, Idanthyrsus sp. nov. 1; F, paleae with flat, straight blades and denticulated margins, Idanthyrsus australiensis; G, paleae with flat, straight blades with smooth lateral margings but denticulated distal margins, Sabellaria sp. nov. 2; H, geniculate and concave paleae, Sabellaria sp. nov. 2; I, bent nuchal spines (hooks) without limbation I. australiensis; J, bent nuchal spines (hooks) without limbation Phalacrostemma sp.; K, parathoracic notopodia with lanceolate and capillary chaetae, I. australiensis; L, parathoracic neuropodia with lanceolate chaetae, of two sizes, I. australiensis; M, mid abdominal neurochaetae, I. australiensis; N, abdominal uncini with double rows of teeth, I. australiensis.
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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.