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FIGURE 7 in Geographic structure of genetic variation in the Parachute Gecko Ptychozoon lionotum Annandale, 1905 across Indochina and Sundaland with descriptions of three new species
FIGURE 7. Holotype of Ptychozoon cicakterbang sp. nov. LSUHC 10648 from Gunung Jerai, Kedah, Peninsular Malaysia. Photograph by L. L. Grismer.
The population genetics of structural variants in grapevine domestication
<p><strong>The genome assembly: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.fa.fasta?versionId=86a512b8-12a6-4f4d-ac5d-acc26d74589f">Chardonnay.fa.fasta</a> </p> <p><strong>The gene annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_sorted.gff.gz?versionId=2e5878bc-cf53-489b-ac71-2602f9ba4d2e">Chardonnay.annotation_sorted.gff.gz</a></p> <p><strong>The TE annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_te_sorted.gff3.gz?versionId=95780497-e0e7-4a7b-8860-74072d7f7bb2">Chardonnay.annotation_te_sorted.gff3.gz</a></p>
Genetic differences between Coccidioides spp. and closely related nonpathogenic Onygenales
<p><strong>Abstract: </strong><em>Coccidioides</em> spp. are dimorphic, pathogenic fungi that can cause severe human and animal disease. Like the other primary fungal pathogens, animal infection results in a morphologic transformation from the environmental mycelial phase to a tissue phase, known as a spherule. The sequencing and annotation of <em>Coccidioides</em> spp. and the genomes of several nonpathogenic Onygenales species allows orthology comparisons that may provide clues about the <em>Coccidioides</em> spp. genes involved in pathogenesis. There were a number of differences in the characterization of the genes that are <em>Coccidioides</em> spp.-specific and those that are found in both <em>Coccidioides</em> spp. and non-pathogenic Onygenales. Many more <em>Coccidioides </em>spp.-specific genes are up-regulated expression in spherules. <em>Coccidioides </em>spp.-specific genes more often lacked functional annotation, were more often classified as orphan genes and had SNPs with higher non-synonymous/ synonymous ratios. Review of individual genes in the <em>Coccidioides</em> spp.-specific group identified two genes in the Velvet family, a histidine kinase, two thioredoxin genes, a calmodulin gene and ureidoglycolate hydrolase. Velvet genes have been found to be important for mycelium differentiation to yeast in <em>Histoplasma capsulatum</em>. Hopefully, identification of these genes will be useful for pursuing potential <em>Coccidioides</em> spp. virulence genes in the future.</p> <p>This is Supplemental Table 1 from that manuscript</p>
FIGURE 5 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 5. Plots of effective size trends through time generated by Vareff. The x-axis represents time to the past expressed as the product of the generation time (T) by the mutation rate. The y-axis represents the effective size expressed as the log10 of theta, where theta = 4Neu. For abbreviations, see Fig. 1.
FIGURE 1 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 1. Geographic location of the 15 naturally occurring vernal pools sampled in Baja California, México. The main map
FIGURE 7 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 7. Phenotypic traits variation between sexes of B. sandiegonensis individuals in Baja California, México. Asterisks indicates significant differences between sexes at the P<0.0001 level.
FIGURE 6 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 6. Phenotypic trait variation of B. sandiegonensis individuals across the four geographic regions sampled in Baja California. Data with different uppercase letters are significantly different at the P<0.05 level, according to Tukey post-hoc tests. For abbreviations, see Fig. 1.
FIGURE 3. a in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 3. a, Bayesian phylogenetic tree of B. sandiegonensis based on analysis of mitochondrial COI sequences, showing the two major clades: Clade A and Clade B (sensu Bohonak 2005). The 31 samples obtained in this study are denoted by rectangles, with colors corresponding to the region of collection. The 54 sequences downloaded from GenBank lack colored rectangles, and all are from the northern portion of the species' range in the USA (GenBank accession numbers: FJ439689-FJ439743). The tree was rooted with Branchinecta lynchi (GenBank accession numbers HM568501-HM568505). Numbers on branches indicate Bayesian posterior probabilities ≥0.8. b, Median-joining haplotype network based on 568 bp of the mitochondrial COI sequences. Circle size is proportional to haplotype frequencies; line length is roughly proportional to the estimated number of steps between haplotypes. Each geographic region is represented in a different color. For abbreviations, see Fig. 1.
FIGURE 2 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 2. Definition of the six morphometric traits measured on 232 individuals of B. sandiegonensis. Drawing modified from Fugate (1993) and morphometric features based on Timms (2012). a, total body length. b, thorax length. c, abdomen length. d, cercopod length. e, antennule length. f, right antenna length for males, and f1 for females.
FIGURE 4. a in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 4. a, Principal components analysis of the individual genotypes, where the region was used as class factor for the analysis. Colors correspond to the region. b, Edwards genetic distance Dendrogram. The colors below names correspond to the region. c, plots of the genetic clusters inferred by STRUCTURE (K=2, 3, 4). Each vertical column represented an individual, and pools are indicated by the legend. For abbreviations, see Fig. 1.
Using Noninvasive Genetic Sampling to Survey Rare Butterfly Population
<p><strong>Supplementary Table 1.</strong> Sanger sequencing and NCBI BLAST results for exemplar amplicons from each treatment of the proof-of concept study.</p> <p>From: Using Noninvasive Genetic Sampling to Survey Rare Butterfly Populations</p>
FIGURE 4 in Acricotopus indet. morphotype incurvatus: Description and genetics of a new Orthocladiinae (Diptera: Chironomidae) larval morphotype from the Tibetan Plateau
FIGURE 4. Maximum likelihood tree of 18S and 28S sequences, with the small subset chironomid taxa from different subfamilies. The numbers near nodes represent bootstrap supports (100 replications). The taxa in bold represent herein described species, Acricotopus indet. morphotype incurvatus. Forcipomyia brevipennis Macquart represents the outgroup.
FIGURE 1. Acricotopus indet. morphotype incurvatus 4 in Acricotopus indet. morphotype incurvatus: Description and genetics of a new Orthocladiinae (Diptera: Chironomidae) larval morphotype from the Tibetan Plateau
FIGURE 1. Acricotopus indet. morphotype incurvatus 4th instar larva. a) Mentum. b) Mandible with seta subdentalis. c) Labrum with premandibles, S I and pecten epipharyngis. d) Sclerotized plate.
FIGURE 3. Acricotopus indet. morphotype incurvatus 4 in Acricotopus indet. morphotype incurvatus: Description and genetics of a new Orthocladiinae (Diptera: Chironomidae) larval morphotype from the Tibetan Plateau
FIGURE 3. Acricotopus indet. morphotype incurvatus 4th instar larva, scanning electron microscope pictures. a) Head capsule. b) Antenna. c) Anterior parapods. d) Labro-epipharyngeal region with S I. e) Pecten epipharyngis with S I. f) Posterior parapods.
FIGURES 14,15 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURES 14,15. Males of Rhyacophila spp. 14a–14e, R. kykladica Malicky & Sipahiler 1993: 14a, general view of genitalia, left lateral; 14b, apicodorsal lobes and preanal appendages, dorsal; 14c, structures of segment X, ventral; 14d, left inferior appendage, left lateral. 14e, left paramere, left lateral. 15a–15e, R. fasciata Hagen 1859: 15a, general view of genitalia, left lateral; 15b, apicodorsal lobes and preanal appendages, dorsal; 15c, structures of segment X, ventral; 15d, left inferior appendage, left lateral; 15e, left paramere, left lateral. Scale bars: 14a–14d, 15a–15d = 0.5 mm. 14e, 15e = 200 µm.
FIGURES 12,13 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURES 12,13. Larvae and females of Rhyacophila spp. 12a–12e, R. kykladica Malicky & Sipahiler 1993: 12a, larva, dorsal view of head and prothorax, * = setae #6, + = setae #12; 12b, larva, terguite IX. 12c–12e, segments VIII–XI of female: 12c, dorsal; 12d, left lateral; 12e, ventral. 13a–13d, R. fasciata Hagen 1859: 13a, larva, dorsal view of head and prothorax, * = setae #6, + = setae #12; 13b, larva, terguite IX. 13c–13e, segments VIII–XI of female: 13c, dorsal; 13d, left lateral; 13e, ventral. Scale bars: 0.5 mm.
FIGURE 17 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURE 17. Distribution of Rhyacophila kykladica Malicky & Sipahiler 1993 in Greece (context in square).
FIGURE 16 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURE 16. Neighbour-joining tree of some species of the Rhyacophila fasciata Group: Rhyacophila sociata (Rsoc) (16a), Rhyacophila denticulata (Rden) (16b), Rhyacophila fasciata (Rfas) (16c), Rhyacophila kykladica (Rkyk) (16d) together with Rhyacophila relicta (Rrel) (16e) and Rhyacophila palmeni (Rpal) (16f) as outgroup, based on mitochondrial COI sequence data. Bootstrap values of main branches are shown; data for specimens are summarized in Table 1. RsocSpa = Rhyacophila sociata specimens from Spain, RsocFra = Rhyacophila sociata specimens from France, RdenFra = Rhyacophila denticulata specimens from France, RfasGer = Rhyacophila fasciata specimens from Germany, RfasBel = Rhyacophila fasciata specimens from Belgium, RfasFin = Rhyacophila fasciata specimen from Finland, RkykGre = Rhyacophila kykladica specimens from Greece, RrelSpa = Rhyacophila relicta specimen from Spain, RpalGre = Rhyacophila palmeni specimen from Greece. Scale bar: 1% divergence.
FIGURES 10, 11 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURES 10, 11. Male and female genitalia of Rhyacophila kykladica Malicky & Sipahiler 1993. 10, male: 10A, 2nd segment of left inferior appendage, left lateral; 10BV–10BL, parameres: 10BV, ventral view of parameres and aedeagus; 10BL, left paramere, left lateral. 10CL–10CD, aedeagus (phallicata) and lateroventral lobes: 10CL aedeagus and ventral lobe, lateral; 10CD, aedeagus and lateroventral lobes, dorsal. 10DD–10DV, apicodorsal lobes of segment IX, preanal appendages, and bodies of segment X: 10DD, apicodorsal lobes and preanal appendages, dorsal; 10DV, bodies of segment X, ventral. 11, female segments VIII–XI: 11L, left lateral; 11D, dorsal; 11V, ventral. Scale bars: unlabelled = 1 mm; O = 0.5 mm; * = 200 µm.
FIGURES 1–6 in The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features
FIGURES 1–6. Larva of Rhyacophila kykladica Malicky & Sipahiler 1993. 1a–1d, head: 1a, dorsal; 1b, right lateral; 1c ventral; 1d, frontoclypeus, dorsal. 2D–2V, mandibles from last instar larval exuviae, left (l) and right (r): 2D, dorsal; 2V, ventral. 3, labrum, dorsal. 4a–4b, prothorax: 4a, dorsal; 4b left hemisclerite, left lateral. 5, dorsal sclerite of abdominal segment IX. 6a–6c, details of anal prolegs: 6a, right anal claw, right lateral; 6b, detail of claw, right lateral; 6c, detail of basolateral plate with sword process and basoventral hook, right lateral. Scale bar: unlabelled = 1 mm; O = 0.5 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.