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Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa
<p>Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. <i>K</i>= 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise <i>F<sub>ST</sub></i>analysis showed genetic differentiation <i>(P < 0.05)</i>between the village, commercial and wild populations. A per marker per population pairwise <i>F<sub>ST</sub></i>analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.</p>
Figure 5 in A new large and colourful species of the genus Doto (Nudibranchia: Dotidae) from South Africa
Figure 5. Living specimens. (A) Doto coronata (Gmelin, 1791). Specimen from Northern Ireland. Photo by Bernard Picton; (B) Doto cf. coronata. Specimen from South Africa, Cape Province, Oudekraal. Photo by T.M. Gosliner; (C) Doto rosea Trinchese, 1881. Specimen from Catalunia, Spain Photo by Antoni López-Arenas; (D) Doto pinnatifida (Montagu, 1804). Specimen from Northern Ireland. Photo by Bernard Picton.
Figure 2 in A new large and colourful species of the genus Doto (Nudibranchia: Dotidae) from South Africa
Figure 2. Doto splendida nov. sp. Paratype (CASIZ176123), SEM pictures of the radula and penis. (A) Radula, scale bar: 10 μm; (B) detail of the teeth, scale bar: 3 μm; (C) penis, scale bar: 10 μm; (D) detail of the penis, scale bar: 10 μm.
Figure 3 in A new large and colourful species of the genus Doto (Nudibranchia: Dotidae) from South Africa
Figure 3. Reproductive system of Doto splendida nov. sp. Paratype (CASIZ176123). Abbreviations: am, ampulla; fglm, female gland mass; hd, hermaphrodite duct; ov, oviduct; pb, penial bulb; pr, prostate; sr, seminal receptacle; v, vagina; vd, vas deferens. Scale bars, 1 mm.
FIG. 2 in Feasting among Venda-speakers of South Africa: the Late Iron Age fauna from Mutokolwe
FIG. 2. — Location of Mutokolwe and other sites mentioned in the text within South Africa (adapted from Fish [2000:71], and used with permission from the University of the Witwatersrand).
FIG. 1 in Feasting among Venda-speakers of South Africa: the Late Iron Age fauna from Mutokolwe
FIG. 1. — Location of the study areas in north-eastern South Africa: DZ, Dzata; HU, Ha-Tshirundu; MU, Mutokolwe; TA, Tavhatshena; TH, Tshirululuni; TS, Tshitheme.
Conversion of measurements of tree ring gains: Canada, Africa, Mexico, South America from RWL- files to JSON format.
<p>The International Tree Rings Data Bank (ITRDB) is the most comprehensive tree growth database (https://www1.ncdc.noaa.gov/pub/data/paleo/treering).</p> <p>Shoudong Zhao, et al. (2019, 2018) analyzes the representativity of dendrochronological data (ITRDB) and proposes a corrected database with error indications. One of the bottlenecks of data use (ITRDB) is that the data is loaded as a collection of separate files in the Tucson positional format.</p> <p>The purpose of our data presentation is to change the Tucson data format to JSON format and combine the separate files into one.</p> <p>We convert the initial data for the <strong>Canada</strong>, <strong>Africa</strong>, <strong>Mexico</strong> and <strong>Southamerica</strong> rwl-files into Json format of data on tree growth in four files: <strong>canada.json</strong>, <strong>africa.json</strong>, <strong>mexico.json</strong> and <strong>southamerica.json</strong>. The data was converted using the R programming language and the dplR program library Bunn, A. (2008)</p> <p>The experience of developing the structure of dendroclimatic data in JSON format is described in the works of Kachaev A. (2016, 2017, 2020).</p> <p>Description of the structure of JSON data format is attached in the files ReadMe.pdf</p> <p> </p> <p>References</p> <p>Bunn, A. G. (2008). A dendrochronology program library in R (dplR). Dendrochronologia, 26, 115-124. https://doi.org/10.1016/j.dendro.2008.01.002</p> <p>Kachaev, Alexander (2020), "Compact dataset of dendrochronological data of pri-mary metric characteristics of tree rings of Asia.", Mendeley Data, V1, doi: 10.17632 / p9zhpmzgtk.1</p> <p>Kachaev A. V. (2017) Model for describing the structure of dendroclimatic data In the collection: Regional problems of remote sensing of the Earth Materials of the IV international scientific conference. Siberian Federal University, Institute of Space and Information Technologies. p. 120-122. (Russia)</p> <p>Kachaev A. V. (2016) NOSQL Approach for Development of Dendroclimatic Data Bank. In the collection: Regional problems of remote sensing of the Earth. Materials of the III International Scientific Conference. p. 89-91. (Russia)</p> <p>Shoudong Zhao, et al. (2019). The International Tree-Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity. Journal of Biogeography, 46 (2), 355-368. doi: 10.1111 / jbi.13488</p> <p>Zhao, Shoudong et al. (2018), Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity, Dryad, Dataset, https://doi.org/10.5061/dryad.kh0qh06</p>
qdgc South Africa
<p>QDGC tables delivered in geopackage file<br> - - - - - - - - - - - - - - - - - - - - - -<br> QDGC represents a way of making (almost) equal area squares covering a specific area to represent specific qualities of the area covered. The squares themselves are based on the degree squares covering earth. Around the equator we have 360 longitudinal lines , and from the north to the south pole we have 180 latitudinal lines. Together this gives us 64800 segments or tiles covering earth.<br> <br> <br> Within each geopackage file you will find a number of tables with these names:<br> -tbl_qdgc_01<br> -tbl_qdgc_02<br> -tbl_qdgc_03<br> -tbl_qdgc_04<br> -tbl_qdgc_05<br> -etc<br> <br> <br> The attributes for each table are:<br> qdgc Unique Quarter Degree Grid Cell reference string<br> area_reference Country<br> level_qdgc QDGC level<br> cellsize degrees decimal degree for the longitudal and latitudal length of the cell<br> lon_center Longitude center of the cell<br> lat_center Latitudal center of the cell<br> area_km2 Calculated area for the cell<br> geom Geometry<br> <br> <br> Metadata<br> --------<br> Geodata GCS_WGS_1984<br> Datum: D_WGS_1984<br> Prime Meridian: 0<br> <br> <br> Areas are calculated with different versions of Albers Equal Area Conic using the PostGIS function st_area. For the African continent I have used Africa Albers Equal Area Conic which will look like this:<br> - st_area(st_transform(geom, 102022))/1000000)<br> <br> <br> Conditions<br> ----------<br> Delivered to the user as-is. No guarantees. If you find errors, please tell me and I will try to fix it. Suggestions for improvements can be addressed to the github repository: https://github.com/ragnvald/qdgc<br> <br> <br> Thankyou<br> --------<br> The work has over the years been supported and received advice and moral support from many organisations and stakeholders. Here are some of them:<br> - Tanzania Wildlife Research Institute<br> - Dept of Biology, NTNU, Norway<br> - Norwegian Environment Agency<br> - Eivin Røskaft, Steven Prager, Howard Frederick, Julian Blanc, Honori Maliti, Paul Ramsey<br> <br> <br> References<br> ----------<br> * http://en.wikipedia.org/wiki/QDGC<br> * http://www.mindland.com/wp/projects/quarter-degree-grid-cells/about-qdgc/<br> * http://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection<br> * http://www.safe.com</p>
South Africa higher education data 2 - Data sources
<p>GIS-based map visualisation of the data sources providing open data on South African higher education data. Generated as part of research conducted for the 'Use of open data in the governance of South African higher education' research project, in the IDRC/WWWF 'Exploring Emerging Impacts of Open Data in the South' initiative.</p>
FIGURES 3 – 8 in A new species of Stasimopus from the Eastern Cape Province of South Africa (Araneae, Mygalomorphae, Ctenizidae), with notes on its natural history
FIGURES 3 – 8. Stasimopus mandelai sp. nov., holotype male (MY 557). 3, left leg I, retrolateral aspect; 4, left leg I, prolateral aspect; 5, pedipalp, patella to bulb, retrolateral aspect; 6, pedipalp, distal portion, ventral aspect. Paratype male (MY 559). 7, leg I, retrolateral aspect; 8, pedipalp, retrolateral aspect (box showing enlarged view of palpal organ). Scale bars for legs = 2.0 mm; for pedipalps = 1.0 mm.
FIGURES 1 – 2 in A new species of Stasimopus from the Eastern Cape Province of South Africa (Araneae, Mygalomorphae, Ctenizidae), with notes on its natural history
FIGURES 1 – 2. Stasimopus mandelai sp. nov., live habitus images. 1, female; 2, holotype male. Scale bars = 5.0 mm.
FIGURES 16 – 19 in A new species of Stasimopus from the Eastern Cape Province of South Africa (Araneae, Mygalomorphae, Ctenizidae), with notes on its natural history
FIGURES 16 – 19. Stasimopus mandelai sp. nov., trapdoor and architecture of excavated burrow. 16, trapdoor closed, top view; 17, trapdoor open, lateral view; 18, closeup view of inside trapdoor, the arrow is pointing to small pits; 19, trapdoor open, oblique view.
FIGURE 16 in Cryptopeniculus nigrosetus n. g., n. sp. (Coleoptera: Ptinidae) from the Namaqualand region of South Africa
FIGURE 16. Currently known distribution of Cryptopeniculus nigrosetus in western South Africa near the coast as indicated by the circles.
FIGURES 1 – 3. Cryptopeniculus nigrosetus external views. 1 in Cryptopeniculus nigrosetus n. g., n. sp. (Coleoptera: Ptinidae) from the Namaqualand region of South Africa
FIGURES 1 – 3. Cryptopeniculus nigrosetus external views. 1, dorsal habitus; 2, lateral habitus; 3, dorsal view of the pronotum.
FIGURE 3 A, C in A new species of Strongylodesma Lévi, 1969 (Porifera; Demospongiae; Poecilosclerida; Latrunculiidae) from Aliwal Shoal on the east coast of South Africa
FIGURE 3 A, C. Skeletal architecture of the holotype (SAM H 5083) (A, 100 X; C, 50 X); C. Skeletal architecture showing the clear mesohyl region below the paratangential layer of anisostrongyles (100 X); B. Skeletal architecture of the paratype (SAF 94 23) (50 X); D. Skeletal architecture showing the region of convoluted tracts of anisostrongyles (100 X).
FIGURE 2. A in A new species of Strongylodesma Lévi, 1969 (Porifera; Demospongiae; Poecilosclerida; Latrunculiidae) from Aliwal Shoal on the east coast of South Africa
FIGURE 2. A. Gross morphology of Strongylodesma aliwaliensis sp. nov. (SAM H 5083); B. A close up frame of the fungiform areolate porefields and cylindrical oscules of Strongylodesma aliwaliensis sp. nov. (SAM H 5083); C. Smooth anisostrongyles with one end narrower within Strongylodesma aliwaliensis sp. nov. (Anisostrongyles) (1000 X).
FIGURES 14 – 19. Pamexis hantam n in A remarkable new lichenophilous Pamexis species from the Hantam Karoo of South Africa (Neuroptera: Myrmeleontidae: Palparini)
FIGURES 14 – 19. Pamexis hantam n. sp. Male Genitalia. 14, Gonarcus & Parameres complex dorsal; 15, ventral; 16, lateral; 17, Hypandrium internum dorsal; 18, lateral; 19, ventral. Gb = Gonarcal bulla, Gs = Gonarcus, Pa = Parameres.
FIGURES 22 – 26. 22, Pamexis hantam n in A remarkable new lichenophilous Pamexis species from the Hantam Karoo of South Africa (Neuroptera: Myrmeleontidae: Palparini)
FIGURES 22 – 26. 22, Pamexis hantam n. sp. Female Terminalia, Pregenitalae. Ga = Anterior gonapophyses, Prg = Pregenitale. 23, Pamexis namaqua, Thorax and abdomen male; 24, female; 25, Pamexis hantam Thorax and abdomen male; 26, female.
FIGURES 20 – 21. Pamexis hantam n in A remarkable new lichenophilous Pamexis species from the Hantam Karoo of South Africa (Neuroptera: Myrmeleontidae: Palparini)
FIGURES 20 – 21. Pamexis hantam n. sp. Female Terminalia. 20, Lateral. Note: paired ectoprocts. 21, Spermatheca. Epr = Ectoprocts, Ga = Anterior gonapophyses, Gl = Lateral gonapophyses, Spt = Spermatheca.
FIGURES 9 – 10. Pamexis hantam n in A remarkable new lichenophilous Pamexis species from the Hantam Karoo of South Africa (Neuroptera: Myrmeleontidae: Palparini)
FIGURES 9 – 10. Pamexis hantam n. sp. Showing variability in wing markings, female specimens. Photos: M. W. Mansell ©
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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)
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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.