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Decoding the big five

African elephants of which there are two species (the savanna elephant Loxodonta africana, and its smaller cousin, the forest elephant Loxodonta cyclotis), are the largest terrestrial animals on Earth. African savanna elephants, for which we provide an upgraded chromosome-level genome assembly, are found in 24 sub-Saharan African countries and occur in a variety of habitats from open and wooded savanna to desert (Gobush et al. 2021). Along with the lion, leopard, black rhinoceros and African buffalo, the African savanna elephants are part of the Big Five, a term used to describe the most iconic of Africa's large mammals.

A group of elephants at the Addo Elephant National Park, South Africa. This population is known for the high number of tuskless females (Whitehouse, 2002). RJ van Aarde, Conservation Ecology Research Unit, University of Pretoria (South Africa).

Afrotheria phylogeny

Afrotheria (from Latin Afro- "of Africa" + theria "wild beast") represents one of the most eutherian mammals’ ancient clades that includes six mammalian orders all with an Afro-Arabian origin. The group comprises golden moles, elephant shrews, tenrecs, aardvarks, hyraxes, elephants and sea cows (dugongs and manatees). The afrotherian species exhibit extreme morphological diversity and niche preference, which is thought to result from the long period of isolation when Africa was an island continent 105-125 mya (Meredith et al., 2011). Genome organization within Afrotheria is diverse, with diploid numbers ranging from 2n = 54 in the African and Asian elephants to 2n = 20 in the aardvark (Robinson and Seiffert, 2004; Ruiz-Herrera et al. 2012).


Concerns about Africa’s elephant numbers have led to savanna elephants being categorized as Endangered, and forest elephants as Critically Endangered by the IUCN (International Union for Conservation of Nature) (Gobush et al. 2021a and 2021b). The greatest threat to Africa’s elephants is ivory poaching and habitat loss, primarily through agriculture, often leading to human-elephant conflict (Borchert 2022). The increasing fragmentation of suitable elephant habitat due to altered land-use led to suggestions that ~70% of their current distribution may fall outside of protected areas, and that savanna elephants may persist in only 15 percent of their historic pre-agricultural range (Chase et al. 2016).

The effects of habitat alteration and poaching extend beyond the threat of possible elephant extinction. Elephants play a significant role in savanna ecosystems by altering the physical environment, facilitating seed dispersal and though the creation of microhabitats¾it seems inescapable that declining elephant densities will result in a cascade of consequences for other savanna species (Robson et al. 2017).


Today, we share the upgraded chromosome-level genome for the savanna elephant Loxodonta africana! This genome assembly was based on the Loxafr3.0 draft genome assembly generated by the Broad Institute (Di Palma, F., Heiman, D., Young,S., Johnson,J., Lander, E.S. and Lindblad-Toh, K.). The Hi-C data was generated from cryopreserved fibroblast cell cultures that form part of the South African National Biodiversity Institute Biobank collection (Alvarez-Gonzalez et al. 2022). For more details on our assembly procedure, please see our Methods page. Finally, don't forget to check out the interactive Juicebox.js session below featuring the chromosomes (2n=54) of the African savanna elephant below!


  1. Álvarez-González L, [ARHM1] Arias-Sardá C, Montes-Espuña L, Marín-Gual L, Vara C, Lister NC, Cuartero Y, Garcia F, Deakin J, Renfree MB, Robinson TJ, Martí-Renom MA, Waters PD, Farré M, Ruiz-Herrera A (2022) Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals, Cell Reports 41, 111839. DOI:

  2. Borchert P. November 29, 2022. A roadmap to reversing the decline of southern Africa’s elephants.

  3. Chase MJ, Schlossberg S, Griffin CR, Bouché PJC, Djene SW, Elkan PW, Ferreira S, Grossman F, Kohi EM, Landen K, Omondi P, Peltier A, Selier SAJ, Sutcliffe R. 2016. Continent-wide survey reveals massive decline in African savannah elephants. PeerJ 4:e2354

  4. Gobush, K.S., Edwards, C.T.T, Balfour, D., Wittemyer, G., Maisels, F. & Taylor, R.D. 2021. Loxodonta africana (amended version of 2021 assessment). The IUCN Red List of Threatened Species 2021: e.T181008073A204401095.

  5. Gobush, K.S., Edwards, C.T.T, Maisels, F., Wittemyer, G., Balfour, D. & Taylor, R.D. 2021. Loxodonta cyclotis (errata version published in 2021). The IUCN Red List of Threatened Species 2021: e.T181007989A204404464.

  6. Meredith, R.W., Janecka, J.E., Gatesy, J., Ryder, O.A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simao, T.L.L., Stadler, T., et al. (2011). Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334, 521–524. 10.1126/science.1211028

  7. Robinson, T.J., and Seiffert, E.R. (2004). Afrotherian origins and interrelationships: New views and future prospects. Curr. Top. Dev. Biol. 63, 37–60. 10.1016/S0070-2153(04)63002-X.

  8. Robson AS, Trimble MJ, Purdon A, Young-Overton KD, Pimm SL, van Aarde RJ (2017) Savanna elephant numbers are only a quarter of their expected values. PLoS ONE 12: e0175942.

  9. Ruiz-Herrera, A., Farré, M., and Robinson, T.J. (2012). Molecular cytogenetic and genomic insights into chromosomal evolution. Heredity 108, 28–36. 10.1038/hdy.2011.102.

  10. Whitehouse, A. (2002). Tusklessness in the elephant population of the Addo Elephant National Park, South Africa. Journal of Zoology 257: 249-254. doi:10.1017/S0952836902000845


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