Data for modeling phylogeographic dynamics of Sindbis virus in Africadoi:10.60507/FK2/VUMWZIbonndata2026-07-081Nabatanzi, Maureen, 2026, "Data for modeling phylogeographic dynamics of Sindbis virus in Africa", https://doi.org/10.60507/FK2/VUMWZI, bonndata, V1Data for modeling phylogeographic dynamics of Sindbis virus in Africadoi:10.60507/FK2/VUMWZINabatanzi, MaureenMAFFTR458328858bonndataNabatanzi, MaureenNabatanzi, Maureen2026-03-06Agricultural SciencesEarth and Environmental SciencesMedicine, Health and Life SciencesThis dataset comprises Sindbis virus (SINV) sequences, their locations of sample collection and ecological variables used to conduct continuous phylogeographic and phylodynamic analysis of SINV dispersal in Africa. There are 23 complete and near-complete SINV genomes sampled across Africa between 1952 and 2022. Ecological variables comprise 26 potential predictors with suspected associations with viral discovery and dispersal. Sequences and location data were used to generate time-calibrated phylogenies, its spatiotemporal dispersal history and dispersal dynamics. We assessed the impact of the predictors on viral dispersal position, direction, and velocity.1952-08-012022-01-012025-08-012025-12-01Genome sequencesGPS CoordinatesRaster dataa) CRU-TS 4.09 (Harris et al., 2020) downscaled with WorldClim 2.1 (Fick and Hijmans, 2017). Fick, S.E. and R.J. Hijmans, 2017. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37 (12): 4302-4315.https://www.worldclim.org/data/monthlywth.html b) Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, v1 c) Center For International Earth Science Information Network-CIESIN-Columbia University. (2018). <i>Gridded Population of the World, Version 4 (GPWv4): Population Count Adjusted to Match 2015 Revision of UN WPP Country Totals, Revision 11</i> (Version 4.11) [Data set]. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). https://doi.org/10.7927/H4PN93PB Date Accessed: 2025-11-10 d) World Health Organization. IHR eSPAR scores (2020). Available at https://extranet.who.int/e-spar/ e) https://www.nature.com/articles/nature25181 f) BirdLife International (2025) Digital boundaries of Important Bird and Biodiversity Areas (IBAs) and Key Biodiversity Areas (KBAs) identified for birds. September 2025 version. BirdLife International, Cambridge, UK. Available at: https://datazone.birdlife.org/contact-us/request-our-data g) Adriana De Palma; Sara Contu; Gareth E Thomas; Connor Duffin; Sabine Nix; Andy Purvis (2024). The Biodiversity Intactness Index developed by The Natural History Museum, London, v2.1.1 (Open Access, Limited Release) (from The Biodiversity Intactness Index developed by The Natural History Museum, London, v2.1.1 (Open Access, Limited Release)) [Data set resource]. Natural History Museum. https://data.nhm.ac.uk/dataset/bii-developed-by-nhm-v2-1-1-limited-release/resource/c4c281c4-befa-4e1b-a162-ba2f25e5ae82 h) Friedl, M., Sulla-Menashe, D. (2022). MODIS/Terra+Aqua Land Cover Type Yearly L3 Global 500m SIN Grid V061. NASA EOSDIS Land Processes Distributed Active Archive Center. Accessed 2025-11-11 from https://doi.org/10.5067/MODIS/MCD12Q1.061. Accessed November 11, 2025. i) Hurtt, G. C., L. Chini, R. Sahajpal, S. Frolking, B. L. Bodirsky, K. Calvin, J. C. Doelman, J. Fisk, S. Fujimori, K. Klein Goldewijk, T. Hasegawa, P. Havlik, A. Heinimann, F. Humpenöder, J. Jungclaus, J. O. Kaplan, J. Kennedy, T. Krisztin, D. Lawrence, P. Lawrence, L. Ma, O. Mertz, J. Pongratz, A. Popp, B. 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Global Human Settlement Layer: Population and Built-Up Estimates, and Degree of Urbanization Settlement Model Grid. Retrieved from: https://doi.org/10.7927/h4154f0w m) NSAL, F. a. A. O.-. (2024). GLW 4: Gridded Livestock Density (Global - 2020 - 10 km) [mapDigital]. Retrieved from: https://data.apps.fao.org/catalog/iso/9d1e149b-d63f-4213-978b-317a8eb42d02 n) National Center for Biotechnology Information, NCBI Virus [Internet]. National Library of Medicine. 2024. Available from: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide<a href="http://creativecommons.org/licenses/by/4.0">CC BY 4.0</a>Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, V1Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, V1AccessCity.tifAccessibility as travel time in minutes required to reach the nearest city if walking-only or using motorized transport in 2015.image/tiffAccessHealth.tifAccessibility as time in walking minutes to nearest healthcare facility in 2015.image/tiffBII.tifBiodiversity Intactness Index (BII) are percentage values between 0 and 100, indicating the intactness of the ecosystem in 2020.image/tiffBio1.tifAnnual Mean Temperature (°C) for 2022image/tiffBio12.tifAnnual Precipitation (mm), the sum of 12 months precipitation for 2022image/tiffBio5.tifMaximum Temperature (°C) of Warmest Month for 2022image/tiffBuilt.tifBuilt-Up areas given by the proportion of the building footprint area within the total size of the grid cell for 2014image/tiffCropland.tifSum of annual crops, perennial crops, annual crops, perennial crops and nitrogen-fixing crops in 2015.image/tiffCulexP.tifCulex pipiens presence for 2015. Values range from highest certainty (4) to least certainty (0) of presence.image/tiffCulexU.tifCulex univittatus presence for 2015. Values range from highest certainty (4) to least certainty (0) of presence.image/tiffDistanceKBA.tifDistance to nearest Key Biodiversity Area created from KBA dataset by computing Euclidean distances from each cell to the nearest KBA cell; 2025.image/tiffForest.tifSum of forested primary land and potentially forested secondary land in 2015.image/tiffGDP.tifGross Domestic Product per capita for 2020.image/tiffHumanpop.tifHuman population distribution by number of people per grid cell for 2015image/tiffIBA.tifImportant Bird and Biodiversity Areas (IBAs); boundaries of sites that are significant for the long-term viability of naturally occurring bird populations in 2025.image/tiffIHR.tifInternational Health Regulations (IHR) capacity score given by the electronic IHR States Parties Self-Assessment Annual Reporting Tool (eSPAR). An annual self-assessment of country capacity and compliance with the IHR. eSPAR total average capacity scores for 2020.image/tiffKBA.tifKey Biodiversity Areas (KBA); boundaries of sites of significance for the global persistence of biodiversity in 2025.image/tiffLivestock.tifLivestock density in 2020. Animals or birds/pixel.image/tiffMammals.tifGrid cell values represent the number of mammalian species. Data from International Union for Conservation of Nature (IUCN) are dated April 2013.image/tiffMining.tifLand used by mining industry between 2000 - 2017.image/tiffNonForest.tifForested primary land and potentially non-forested secondary land in 2015.image/tiffPastureland.tifSum of managed pasture and rangeland in 2015image/tiffReadme.txttext/plainRoads.tifTotal road density in meters per km² in 2018.image/tiffS1_Video.mp4Video animation of the results of continuous phylogeographic spread of SINV in Africavideo/mp4SINV_aligned.fastaComplete and near-complete genome sequences of SINV sampled in Africa between 1952 and 2022 and downloaded from the National Center for Biotechnology Information (NCBI) on 9/08/2025. They were aligned in MAFFT (version 7), an online multiple sequence alignment program, and can be opened with a text editor and most sequence alignment software.application/octet-streamSmod.tifHuman settlement model grid for 2015. Grid cells assigned with 2-digit codes in the following classes: 30 = "Urban Centre"; 23 = "Dense Urban Cluster"; 22 = "Semi-dense Urban Cluster"; 21 = "Suburban or peri-urban grid cells"; 13 = "Rural cluster"; 12 = "Low Density Rural grid cells"; 11 = "Very low density rural grid cells"; 10 = "Water grid cells"image/tiffTraits.txtTraits file comprising sequence identifiers and their geo-location of samplingtext/plainUrban.tifUrban land as a unit fraction of a grid cell in 2015.image/tiffWetlands.tifMCD12Q1_V61 Land Cover Type 1: Annual International Geosphere-Biosphere Programme (IGBP) dataset for 2020; class 11.image/tiff