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FIGURE 15 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 15. Visma aff. brigalowsum, basiconic sensilla of distal antennal intervals (Type B, Type C indicated). Scale bar: 0.01 mm.
FIGURE 12. Bayesian tree for 28S in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 12. Bayesian tree for 28S data only. Taxon names include BOLD Sample ID, museum accession number and species with locality in parentheses. Numbers above branches are Bayesian posterior probability and RAxML bootstrap percentage, shown only if both numbers are greater than or equal to 0.9 and 70, respectively.
FIGURES 5–9. 5. Visma advenum n in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURES 5–9. 5. Visma advenum n. sp. 6. Visma bundjalung n. sp. 7. Visma bingara n. sp. 8. Visma powellheueri n. sp. 9. Visma xanthorrhoea n. sp.
FIGURE 11 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 11. Bayesian tree for COI data only. Taxon names include BOLD Sample ID, museum accession number and species with locality in parentheses. Numbers above branches are Bayesian posterior probability and RAxML bootstrap percentage, shown only if both numbers are greater than or equal to 0.9 and 70, respectively.
FIGURES 1–4. Visma pallidum n in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURES 1–4. Visma pallidum n. sp. 2. Visma brigalowsum n. sp. Miriam Vale. 3. Visma aff. brigalowsum Yanga. 4. Visma tenebrosum n. sp.
FIGURES 27–32 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURES 27–32. Scales of tibia. 27. Visma aff. brigalowsum. 28. Visma tenebrosum n. sp. 29. Visma bundjalung n. sp. 30. Visma pallidum n. sp. 31. Visma xanthorrhoea n. sp. 32. Visma aff. stilivarians. Scale bar: 0.01 mm.
FIGURE 10 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 10. Method for measuring location of trichobothrial areas and number of combs of two macrochaetae A= distance from anterior margin to anterior trichobothrial area, B = total length of notum, C= comb of two macrochaetae on mesonotum.
FIGURE 14. Visma pallidum n in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 14. Visma pallidum n. sp., slender branched papilla of apical article of maxillary palp. Scale bar: 0.01 mm.
FIGURES 21–26 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURES 21–26. Scales of femora. 21. Visma aff. brigalowsum. 22. Visma tenebrosum n. sp. 23. Visma bundjalung n. sp. 24. Visma pallidum n. sp. 25. Visma xanthorrhoea n. sp. 26. Visma aff. stilivarians. Scale bar: 0.01 mm.
FIGURE 38 in Molecular and morphological studies identify a new genus within the Heterolepismatinae (Zygentoma: Lepismatidae)
FIGURE 38. Visma tenebrosum left anterior corner of frons with large scales over-hanging the anterior margin, clypeus with variety of narrow triangular scales, and labrum with macrochaetae. Scale bar: 0.1 mm.
The common bean aquaporin gene PvXIP1;2 identified by GWAS at seedling stage confers drought and osmotic resistance in transgenic plants
<p>This is the trait data of survival rate used to conduct a GWAS</p>
Wing and bill measurements of Tyrannus round specimens identified to subspecies
<p>Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory, and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations if selection favors improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper, and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants, and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet, and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.</p>
Local ancestry to identify selection in response to trypanosome infection in Baoulé x Zebu crossbred cattle in Burkina Faso
<p><span>The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or resistance against pathogens, and for performances in production traits. Using dense genomic markers from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5% and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21 and 22. Screening for <i>F</i><sub>ST</sub> outliers in trypanosome positive/ negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative SNPs for routine admixture testing. Generally, results will serve as basis for further characterization, conservation and improvement strategies for purebred and crossbred populations. Our results are important not only for conserving the genetic integrity in the indigenous Baoulé cattle, but also for improving community-based breeding programs to increase trypanotolerance in crossbred populations.</span></p>
FIGURE 3 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)
FIGURE 3. Maximum likelihood tree derived from COI sequences of our copepod samples (labeled as P. tortugensis) plus voucher sequences from related copepods in the suborder Ergasilida (see Table 5 for a list). Sequences of copepods confamilial to P. tortugenis (Chondracanthidae) are labelled to species (and shaded blue in the online colour version), and members other taxa are labeled to family (and shaded pink in the colour online version). Support values for bipartitions are indicated, and divergence represented by dark blue scale bar = 3 %.
FIGURE 1 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)
FIGURE 1. Maximum likelihood tree derived from COI sequences of our goby samples plus voucher sequences from all Coryphopterus species except C. punctipectophorus. Voucher sequences are identified by GenBank sequence ID. Sequences from several other goby species are included as outgroups (not all are identified in the figure; see Table 4 for a list). Support values for bipartitions are indicated, and divergence represented by scale bar = 6%.
FIGURE 2 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)
FIGURE 2. Differences in body depth between goby species. A boxplot of body depth (as a % of body length in SL) for the three gobies, with sample sizes in parentheses. For the boxplot: box boundaries represent 25th and 75th percentiles respectively; line inside box indicates the median, lower and upper error lines indicate 10th and 90th percentiles respectively, and circles show data falling outside 10th and 90th percentiles.
A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations
<p>An optimized, high-throughput and cost-effective genotyping method applicable to various crop breeding populations is very important in this genomic era. We have developed an optimized Nextera skim-sequencing (skim-seq) approach to genotype different populations that can be used for genetics studies and genomics-assisted breeding. We performed skim-seq on a variety of populations developed through doubled haploid (DH) technology, inter-specific recombinants developed through introgression, amphidiploid developed through wide crosses, and on known monosomic samples.</p> <p>1. A doubled haploid (DH) population consisting of 48 lines from the cross of spring wheat (<i>Triticum</i> <i>aestivum</i>) cultivars CDC Stanley and CDC Landmark developed by the Crop Development Centre at the University of Saskatchewan. We genotyped these DH with skim-seq and identified the genomic segments contributed by each of the two parental lines.</p> <p>2. A population of 335 back cross generation 1 (BC1) skim-seq samples for wheat-barley recombinants with group 7 translocations and 839 F1 wheat 5D monosomic lines (TA3059) along with 16 standard Chinese Spring lines as internal control.</p> <p>3. A panel of 144 <i>Thinopyrum</i> <i>intermedium</i> x <i>Triticum</i> <i>durum</i> (IWG--durum) lines and 141 <i>Thinopyrum</i> <i>intermedium</i> (IWG) lines were evaluated to assess skim-seq genome coverage as well as amphiploidy levels.</p> <p>The demultiplexed FASTQ files for all samples tested in the experiment are available at NCBI SRA public repository with respective BioProject accessions; DH lines [PRJNA729723], 5D monosomic line [PRJNA742385], wheat-barley recombinants [PRJNA738484], IWG-durum and IWG [PRJNA736976]. An example key file for the 5D monosomic line is also attached. </p> <p>This study indicated that skim-seq is an efficient approach for genomic evaluation of a range of different populations and applications. The scripts have been provided to implement skim-seq data for variant calling, identification of genomic segment dosage and alien introgression. Each step of the pipeline is described and implemented with similar sequencing data from skim-seq libraries.</p>
Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures
<p>Supplementary data for "Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures" by Toray S. Akcan, Matthias Heinig.</p>
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins - Case Studies
<p>Dataset and scripts accompanying the publication "Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins"</p>
Genes with transcripts predicted to be miR-195 or miR-26b targets by all 5 predictive algorithms included in starBase, or experimentally identified as targets by pulldown assay
<p>Genes with transcripts predicted to be miR-195 or miR-26b targets by all 5 predictive algorithms included in starBase, or experimentally identified as targets by pulldown assay</p>
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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.