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).

Conservation

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).

Assembly

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!

References

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: https://doi.org/10.1016/j.celrep.2022.111839

2. Borchert P. November 29, 2022. A roadmap to reversing the decline of southern Africa’s elephants. https://www.ifaw.org/people/opinions/reversing-decline-southern-africas-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:e2354https://doi.org/10.7717/peerj.2354

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. https://dx.doi.org/10.2305/IUCN.UK.2021-2.RLTS.T181008073A204401095.en.

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. https://dx.doi.org/10.2305/IUCN.UK.2021-1.RLTS.T181007989A204404464.en.

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. https://doi.org/10.1371/journal.pone.0175942

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

A top-notch blotch

Common side-blotched lizards (Uta stansburiana) are a ubiquitous lizard of the North American deserts. These lizards inhabit an extraordinarily broad range across the United States and northern Mexico from California’s Channel Islands to central Texas, and from the southern tip of Baja California to central Washington state. Throughout this range, these lizards demonstrate a wide variety of colors and patterns on their back, likely to better blend in with the diverse backgrounds where they live. In fact, these lizards are often a critical food source for other desert species and are sometimes referred to as the “food of the desert.”

Female side-blotched lizard (Uta stansburiana) by Samuel Fellows

This species is best known for alternative mating strategies associated with throat color in both male and female lizards in some populations. Orange-throated females lay many small eggs while yellow- and blue-throated females lay fewer but larger eggs. Male lizards, in contrast, demonstrate a “rock-paper-scissors” strategy where orange-throated males singly guard a harem of females, blue-throated males cooperatively guard a small group of females, and yellow-throated males sneak into harems guarded by the orange-throated males to mate. Orange-throated males out-compete blue-throated males, blue-throated males out-compete yellow-throated males, and yellow-throated males out-compete orange-throated males.

These evolutionarily stable strategies make common side-blotched lizards an excellent species in which to begin to understand the ways in which these alternative throat colors, mating strategies, and background-matching patterns can persist within and among populations in the same species. They also can help understand the ways in which these same factors promote speciation. This genome will help reveal the genetic underpinnings for throat color, mating strategy, and the beginning stages of speciation.

Today, we release the chromosome-length assembly for the side-blotched lizards (Uta stansburiana). The draft assembly was generated by Sam Fellows and Dr. Danielle Edwards using long-read sequencing data generated by the University of California Davis DNA Technologies and Expression Analysis core on two Pacific Biosciences Sequel II SMRT-cells, and was assembled with Hifiasm (Cheng et al. 2021). The Hi-C data was generated by DNA Zoo and applied to upgrade the draft to chromosome-length using methods described here.

The sample used for this genome assembly came from an orange-throated male from Wright’s Point, Harney County, Oregon, U.S.A. collected by Dr. Pete Zani. The animal comes from a large population of common side-blotched lizards that occupies sagebrush-steppe habitat in the northern Great Basin. The population persists on a volcanic lava flow surrounded on three sides by the Malheur wetlands national wildlife refuge. This population has been the subject of an 18-year long mark-recapture study which has demonstrated that lizards at this site are much longer-lived than those farther south (up to 7 years, in contrast to 1-2 years elsewhere), and that lizards at this location do not demonstrate the rock-paper-scissors mating behaviors associated with other populations.

Check out the 17 chromosomes (2n=34) of the common side-blotched lizard in the interactive Juicebox.js session below, and find out more information about the new reference on the corresponding assembly page.

A short furrytail

Off the coast of southern California, there is a group of small islands - Channel Islands. About 7000 years ago, mainland grey foxes (Urocyon cinereoargenteus) got onto these islands (and we still do not know how exactly). The foxes thrived, and are now their own separate species called the island fox (U. littoralis).

Island fox by Christian Schwarz, [CC BY-NC], via inaturalist.org

Over the centuries, the foxes got smaller in size; average weight is only about 2 kg (~4 lb) making them the smallest fox in North America! They also lost a few tail vertebrae making their tails shorter. The island foxes are docile and are not afraid of humans. They enjoy life in woods, grasses, and on the beaches of islands by hunting mostly at dawn and dusk on small mammals (deer mice), insects (crickets), lizards, birds (and their eggs), and frogs.

The Santa Catalina Island fox (U. littoralis catalinae) is one of six subspecies of the island gray fox. The Santa Catalina population was almost wiped out in 1999 by the devastating outbreak of canine distemper virus. The epidemic left less than 100 foxes alive. The severe bottleneck has decreased the levels of genetic diversity in the fox population and increased the frequency of potentially deleterious variants. It is likely that these variants are responsible for the unusually high occurrence of ear tumors (ceruminous gland carcinoma) in these foxes after the distemper epidemic (Hendricks et al., 2022).

Over the last two decades enormous conservation efforts of Santa Catalina Island Conservancy together with the National Park Service, The Nature Conservancy, and the Institute for Wildlife Studies brought the number of foxes back to over 2000. Catalina Island fox survival is a remarkable tribute to well-planned science-based conservation strategies: fox vaccinations, captive breeding, radio-collar monitoring, predator control (Golden eagle), strict limits on mainland-derived pets, wildlife, parasites, and human impact monitoring etc. We hope that the genome assembly we share today will contribute to these conservation efforts including long-term monitoring of the carcinoma alleles as well as overall genetic diversity, and provide crucial information for the long-term persistence of the threatened fox population.

The ear sample that was used for this genome assembly was kindly provided by Julie King from the Catalina Island Conservancy and was collected with Winston Vickers. The primary fibroblast cell line ULI-623 was established by Polina Perelman from the biopsy of the 10-year-old female Catalina Island fox #36966 (affected by ceruminous gland carcinoma) at the Laboratory of Genomic Diversity led by Stephen O’Brien. Passage #3 was used to construct the short-read DNA-Seq and Hi-C libraries. We thank Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, and David Goldman for preserving LGD cell line collection.

Browse the 33 chromosomes of the island fox in the interactive Juicebox.js session below, and check out the assembly page for more information about this genome!

References

https://www.catalinaconservancy.org/

Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae). Genes (Basel). 2022 Aug 22;13(8):1496. doi: 10.3390/genes13081496.