Data for modeling phylogeographic dynamics of Sindbis virus in Africa

Citation Metadata

Title title

Data for modeling phylogeographic dynamics of Sindbis virus in Africa

Author author

1. Author Name

   Nabatanzi, Maureen

   Author Affiliation

   University of Bonn

   Author Identifier Scheme

   ORCID

   Author Identifier

   Type Name

   authorIdentifier

   Multiple

   False

   Type Class

   primitive

   Value

   https://orcid.org/0000-0002-9801-4210

   Expandedvalue

   Person Name

   Nabatanzi, Maureen

   @id

   https://orcid.org/0000-0002-9801-4210

   Scheme

   ORCID

   @type

   https://schema.org/Person

Dataset Contact datasetContact

1. Dataset Contact Name

   Nabatanzi, Maureen

   Dataset Contact Affiliation

   University of Bonn

   Dataset Contact Email

   s65mnaba@uni-bonn.de

Ds Description dsDescription

1. Ds Description Value

   This 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.

Subject subject

1. Agricultural Sciences
2. Earth and Environmental Sciences
3. Medicine, Health and Life Sciences

Free Keyword freeKeyword

1. Free Keyword Value

   Phylogeography, Sindbis virus, Africa, ecology, biodiversity, land-use change

Publication publication

1. Publication Relation Type

   Cites

   Publication Citation

   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

   Publication IDType

   doi

   Publication URL

   https://doi.org/10.60507/FK2/FWVXDH

Language language

1. English

Grant Number grantNumber

1. Grant Number Agency

   German Research Foundation (DFG)

   Grant Number Value

   458328858

Depositor depositor

Nabatanzi, Maureen

Date Of Deposit dateOfDeposit

2026-03-06

Time Period Covered timePeriodCovered

1. Time Period Covered Start

   1952-08-01

   Time Period Covered End

   2022-01-01

Date Of Collection dateOfCollection

1. Date Of Collection Start

   2025-08-01

   Date Of Collection End

   2025-12-01

Kind Of Data kindOfData

1. Genome sequences
2. GPS Coordinates
3. Raster data

Software software

1. Software Name

   MAFFT

   Software Version

   7

2. Software Name

   R

   Software Version

   4.5.2

Data Sources dataSources

1. a) 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. Poulter, K. Riahi, E. Shevliakova, E. Stehfest, P. Thornton, F. N. Tubiello, D. P. van Vuuren and X. Zhang (2020). "Harmonization of global land use change and management for the period 850–2100 (LUH2) for CMIP6." Geosci. Model Dev. 13(11): 5425-5464. j) Maus, Victor; da Silva, Dieison M; Gutschlhofer, Jakob; da Rosa, Robson; Giljum, Stefan; Gass, Sidnei L B; Luckeneder, Sebastian; Lieber, Mirko; McCallum, Ian (2022): Global-scale mining polygons (Version 2) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.942325 k) Kummu, M., Kosonen, M. & Masoumzadeh Sayyar, S. 2025. Downscaled gridded global dataset for gross domestic product (GDP) per capita PPP over 1990–2022. Scientific Data 12: 178. https://doi.org/10.1038/s41597-025-04487-x l) Joint Research Centre - JRC - European Commission, & Center for International Earth Science Information Network - CIESIN - Columbia University. (2021). 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