Genomic insights into the persistence of Nubian giraffe (Giraffa camelopardalis camelopardalis) in conflict-affected South Sudan
Daskin, J. H. & Pringle, R. M. Warfare and wildlife declines in Africa’s protected areas. Nature 553, 328–332 (2018).
Stalmans, M. E., Massad, T. J., Peel, M. J. S., Tarnita, C. E. & Pringle, R. M. War-induced collapse and asymmetric recovery of large-mammal populations in Gorongosa National Park, Mozambique. PLoS ONE 14, e0212864 (2019).
Wube, T., Doherty, J. B., Fennessy, J. & Marais, A. Giraffa camelopardalis ssp. camelopardalis. IUCN Red List. Threatened Species. 2018, eT88420707A88420710. https://doi.org/10.2305/IUCN.UK.2018-2.RLTS.T88420707A88420710.en (2018).
Day, C. & Garside, A. Wildlife Management in South Sudan, 1901–2021: Conservation amidst Conflict. Afr. Stud. Rev. 67, 610–631 (2024).
Central Intelligence Agency. South Sudan. The World Factbook 2024 https://www.cia.gov/the-world-factbook/field/population-growth-rate/country-comparison/ (2024).
Gaynor, K. M. et al. War and wildlife: Linking armed conflict to conservation. Front. Ecol. Environ. 14, 533–542 (2016).
IUCN SSC Antelope Specialist Group. Kobus kob ssp. leucotis. IUCN Red List. Threatened Species. 2016, eT11042A50190165. https://doi.org/10.2305/IUCN.UK.2016-2.RLTS.T11042A50190165.en (2016).
IUCN SSC Antelope Specialist Group. Damaliscus lunatus ssp. tiang. IUCN Red List. Threatened Species. 2017, eT6242A50185852. https://doi.org/10.2305/IUCN.UK.2017-2.RLTS.T6242A50185852.en (2017).
Marneweck, C. J. et al. State of Giraffe 2025: An update from the Giraffe Africa Database (GAD). https://doi.org/10.5281/zenodo.15688798 (2025).
Morjan, M. D. et al. Armed conflict and development in South Sudan threatens some of Africa’s longest and largest ungulate migrations. Biodivers. Conserv. 27, 365–380 (2018).
IUCN ESARO. The state of protected and conserved areas in Eastern and Southern Africa, 2nd ed. State of Protected and Conserved Areas Report Series No. 1 https://doi.org/10.2305/VUQC1935 (2024).
Harris, G., Thirgood, S., Hopcraft, J. G. C., Cromsigt, J. P. G. M. & Berger, J. Global decline in aggregated migrations of large terrestrial mammals. Endanger. Species Res. 7, 55–76 (2009).
Brown, M. B., Bolger, D. T. & Fennessy, J. All the eggs in one basket: A countrywide assessment of current and historical giraffe population distribution in Uganda. Glob. Ecol. Conserv. 19, e00612 (2019).
Muller, Z. Rothschild’s giraffe Giraffa camelopardalis rothschildi (Linnaeus, 1758) in East Africa: A review of population trends, taxonomy and conservation status. Afr. J. Ecol. 57, 20–30 (2019).
Muneza, A. B. et al. Updated review of the conservation status of Nubian giraffe (Giraffa camelopardalis camelopardalis) in Kenya. Biodivers. Conserv. 33, 1269–1284 (2024).
Brown, M. B. et al. Assessing the success of conservation translocation establishment: Post-translocation demography of Nubian giraffe (Giraffa camelopardalis camelopardalis) in Uganda. Conserv. Sci. Pract. https://doi.org/10.1111/csp2.70127 (2025).
Coimbra, R. T. F. et al. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol. 21, 215. (2023).
Frankham, R. Genetics and extinction. Biol. Conserv. 126, 131–140 (2005).
IUCN SSC Giraffe and Okapi Specialist Group Taxonomic Task Force. An evaluation of the taxonomic status of giraffe (Giraffa spp.). https://iucn.org/sites/default/files/2025-08/gosgtaxonomictask-force_iucn_giraffetaxonomyassessment_final.pdf (2025).
Muller, Z. Population structure of giraffes is affected by management in the Great Rift Valley, Kenya. PLoS One. 13, e0189678 (2018).
Fennessy, J. et al. Multi-locus Analyses Reveal Four Giraffe Species Instead of One. Curr. Biol. 26, 2543–2549 (2016).
Winter, S., Fennessy, J. & Janke, A. Limited introgression supports division of giraffe into four species. Ecol. Evol. 8, 10156–10165 (2018).
Coimbra, R. T. F. et al. Whole-genome analysis of giraffe supports four distinct species. Curr. Biol. 31, 2929–2938e5 (2021).
Bertola, L. D. et al. Giraffe lineages are shaped by major ancient admixture events. Curr. Biol. 34, 1576-1586e.e5 (2024).
Kargopoulos, N. et al. Heads up–four Giraffa species have distinct cranial morphology. PLoS One 19, e0315043 (2024).
Muneza, A. B. et al. Effective conservation and management of giraffe require adopting recent advances of their taxonomy. Biodivers. Conserv. 34, 1211–1229 (2025).
Henderson, D. M. & Naish, D. Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis. J. Theor. Biol. 265, 151–159 (2010).
Petzold, A. et al. First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens. Eur. J. Taxonomy. https://doi.org/10.5852/ejt.2020.703 (2020).
Gašparová, K. et al. Saving the Last West African Giraffe Population: A Review of Its Conservation Status and Management. Animals 14, 702 (2024).
Dawson, N. et al. qgis/QGIS: 3.40.4. Zenodo https://doi.org/10.5281/zenodo.14906438 (2025).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Farré, M. et al. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8, giz090 (2019).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
Picard toolkit. Broad Institute, GitHub repository https://broadinstitute.github.io/picard/ (2019).
Okonechnikov, K., Conesa, A. & García-Alcalde, F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32, 292–294 (2016).
R Core Team. R: A Language and Environment for Statistical Computing https://www.R-project.org/ (R Foundation for Statistical Computing, 2025).
de Jong, M. J., de Jong, J. F., Hoelzel, A. R. & Janke, A. SambaR: An R package for fast, easy and reproducible population-genetic analyses of biallelic SNP data sets. Mol. Ecol. Resour. 21, 1369–1379 (2021).
Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).
de Jong, M. J. et al. Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence. Commun. Biol. 6, 1–16 (2023).
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M. & Wilson, J. F. Runs of homozygosity: Windows into population history and trait architecture. Nat. Rev. Genet. 19, 220–234 (2018).
Frichot, E. & François, O. LEA: An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925–929 (2015).
de Jong, M. J. & Janke, A. DIST: Distance-based Inference of Species Trees. BioRxiv https://doi.org/10.1101/2025.05.02.651899 (2025).
Malinsky, M., Matschiner, M. & Svardal, H. Dsuite – Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).
Coimbra, R. T. F., Winter, S., Mitchell, B., Fennessy, J. & Janke, A. Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe. Genes 13, 221 (2022).
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M. & Luikart, G. Conservation and the Genomics of Populations (3rd ed.). https://doi.org/10.1093/oso/9780198856566.003.0001 (2022).
Colangelo, P. et al. Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique. BMC Ecol. Evo. 24, 29 (2024).
Brenneman, R. A., Bagine, R. K., Brown, D. M., Ndetei, R. & Louis, E. E. Jr. Implications of closed ecosystem conservation management: The decline of Rothschild’s giraffe (Giraffa camelopardalis rothschildi) in Lake Nakuru National Park, Kenya. Afr. J. Ecol. 47, 711–719 (2009).
Fennessy, S., Fennessy, J., Muller, Z., Brown, M. & Marais, A. Giraffa camelopardalis ssp. rothschildi. IUCN Red List Threatened Species 2018, eT174469A51140829. https://doi.org/10.2305/IUCN.UK.2018-2.RLTS.T174469A51140829.en (2018).
Bercovitch, F. B. & Berry, P. S. M. Ecological determinants of herd size in the Thornicroft’s giraffe of Zambia. Afr. J. Ecol. 48, 962–971 (2010).
Brown, D. M. et al. Extensive population genetic structure in the giraffe. BMC Biol. 5, 57 (2007).
Thomassen, H. A., Freedman, A. H., Brown, D. M., Buermann, W. & Jacobs, D. K. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa. PLoS One 8, e77191 (2013).