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69 results for “Candidate species”
Data from: Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)
There has been considerable debate regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from proposed candidate loci on a common set of samples. In this study, we evaluated main candidate plastid regions (rpoC1, rpoB, accD) and additional plastid markers (psbB, psbN, psbT exons and the trnS-trnG spacer) as well as the nuclear ribosomal spacer region (ITS1-5.8S-ITS2) in a group of land plants belonging to the mahogany family, Meliaceae. Across these samples, only ITS showed high levels of resolvability. Interspecific sharing of sequences from individual plastid loci was common. The combination of multiple loci did not improve performance. DNA barcoding with ITS alone revealed cryptic species and proved useful in identifying species listed in Convention on International Trade of Endangered Species appendixes.
Biofloc removal by the oyster Crassostrea gasar as a candidate species to an Integrated Multi-Trophic Aquaculture (IMTA) system with the marine shrimp Litopenaeus vannamei
<p>Currently, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/aquaculture">aquaculture</a> seeks to implement production models that keep up with the global demands for sustainability and reduced environmental impacts. One of the options adopted is integrated multi-trophic aquaculture (IMTA), which cultivates species of different <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/trophic-level">trophic levels</a>, improving the use of nutrients and increasing the economic profitability of the system. On the other hand, the <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/biofloc-technology">Biofloc Technology</a> system (BFT) has also been highlighted as an important eco-friendly activity. In an attempt to reduce total suspended solids (TSS) and in accordance with the IMTA principles, the present work evaluated the action of the oyster <a href="https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/crassostrea"><em>Crassostrea</em></a><em> gasar</em> on the reduction of TSS and its influence on the <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/microbial-communities">microbial community</a> present on the bioflocs. An experiment with two treatments (With and Without Oyster) was carried out in waters from an ongoing marine shrimp crop. The experiment lasted for 5 days, when water samples and oyster stomach content were collected for analysis of microorganisms. The water quality parameters did not show significant differences. The TSS and aggregates number also showed no differences between treatments, indicating that the presence of oysters did not influence the amount of total suspended solids. However, the predominance of flagellates in the stomach contents of the bivalves indicates a prey selectivity by <em>C. gasar</em> by this microorganism. Thus, it is likely that <em>C. gasar</em> is not an effective tool to reduce suspended solids in IMTA, but this organism can highly benefited from <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/protozoa">protozoan</a> present in BFT system.</p>
Figure 2 in Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans
Figure 2. Cline analyses across the almogavarii/pertinax hybrid zone. (A) Cline fitting from a northeast-southwest transect, separately for the genome average (thick black line; 95% CI in red), mtDNA (thick dash line), and 89 species-diagnostic SNPs (thin grey lines). (B) Selective coefficient s ∗ calculated from the cline widths, for a range of dispersal rates (σ). Twelve diagnostic SNPs featured clines with w ∼ 0 km, 11 with w = 2-4 km, while the rest span around the genome average.
Figure 1 in Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans
Figure 1. Mitochondrial phylogeny of Alytes obstetricans (left, adapted from Gonçalves et al., 2015), distribution of the main lineages (inset map, adapted from Gonçalves et al., 2015; grey: unclear), and population genomics (433 SNPs) of the Catalonian hybrid zone (right). On the tree, the attributed subspecies (and species, see discussion) are indicated; note that lineage E segregates in almogavarii populations from the Pyrenees, but lacks nuclear differentiation (ghost mtDNA lineage, Maia-Carvalho et al., 2018). The lineages studied here are highlighted in bold. The Catalonian map displays the average nuclear ancestry of each population, based on the STRUCTURE analysis (K = 2). The barplots show individual nuclear and mitochondrial assignments. Photo: Alytes obstetricans (CD).
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
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Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’
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Data from: Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)
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Data from: Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis)
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Assessing candidate DNA barcodes for Chinese and internationally traded timber species
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Data from: Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species
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Data from: Thermal tolerance in the keystone species Daphnia magna –a candidate gene and an outlier analysis approach
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Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery
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Data from: Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens
Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced ca. 17,000-32,000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed.
Fig 3 in Development of Microplitis similis (Hymenoptera: Braconidae) on two candidate host species, Spodoptera litura and Spodoptera exigua (Lepidoptera: Noctuidae)
Fig 3. Daily head-capsule width of parasitized and non-parasitized Spodoptera exigua (A) and S. litura (B). Each datum is shown as a mean ± SE. The asterisk means the referred columns differ significantly. Non-parasitized S. exigua larvae pupated on days 6 and 7, and thus for these 2 days no head-capsule width data for them are shown.
Figure 9 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 9 - Drawings of the preserved DNA voucher tadpole of Boophis sibilans (FGZC 2956-ZSM 1631/2007): A Dorsal view B Lateral view C Oral disc.
Figure 7 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 7 - Drawings of the preserved DNA voucher tadpole of Boophis schuboeae (FG/MV 2003.1800-ZSM 978/2004): A Dorsal view B Lateral view C Oral disc.
Figure 8 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 8 - Drawings of the preserved DNA voucher tadpole of Boophis albipunctatus (ZCMV 4946-ZSM 82/2008): A Dorsal view B Lateral view C Oral disc.
Figure 6 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 6 - Drawings of the preserved DNA voucher tadpole of Boophis ankaratra (ZCMV 4917-ZSM 876/2007): A Dorsal view B Lateral view C Oral disc.
Figure 5 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 5 - Drawings of the preserved DNA voucher tadpole of Boophis andohahela (T 428-ZSM 998/2007): A Dorsal view B Lateral view C Oral disc.
Figure 4 from: Randrianiaina R, Strauss A, Glos J, Vences M (2012) Diversity of the strongly rheophilous tadpoles of Malagasy tree frogs, genus Boophis (Anura, Mantellidae), and identification of new candidate species via larval DNA sequence and morphology. ZooKeys 178: 59-124. https://doi.org/10.3897/zookeys.178.1410
Figure 4 - Drawings of the preserved DNA voucher tadpole of Boophis englaenderi [Ca23](FGZC 2957-ZSM 1632/2007): A Dorsal view B Lateral view C Oral disc.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.