Don’t be duped by Eidolon dupreanum!

Today we release the genome of the third and last of the three species of Old World Fruit Bat endemic to the island of Madagascar: Eidolon dupreanum.

Eidolon dupreanum. Photo by Cara Brook.

Bats (order: Chiroptera) make up more than one-fifth of mammalian diversity, and they can broadly be classed into two major sub-orders: the largely insectivorous and small-bodied Yangochiropterans—which typically echolocate to catch insect prey and are distributed widely across both the New and the Old Worlds—and the larger-bodied Yinpterochiropterans, including those in the family Pteropodidae (previously known as the ‘megabats’), which use sight and smell to track down fruit and nectar resources. Pteropodids are found only in Africa, Asia, and Australia.

The International Union for the Conservation of Nature classes some 35% of pteropodids under some category of threat, more than three times that of all other bat species combined [1]. These large fruit bats are particularly vulnerable to habitat destruction and land conversion and are also disproportionately hunted as a source of human food. As a result of higher human-bat contact rates resulting from human hunting and fruit bat consumption of domestic crops, Yinpterochiropterans bats have played important roles in the emergence of several recent viruses known to infect humans, including SARS-CoV-2, the cause of COVID-19, which is derived from Rhinolophous spp. horseshoe bats in China.

Eidolon dupreanum. Photo by Cara Brook.

On the Indian Ocean island nation of Madagascar, my team of young researchers, ‘Ekipa Fanihy’ (‘Team Fruit Bat’ in Malagasy), studies three species of pteropodid found nowhere else on Earth: Pteropus rufus, Rousettus madagascariensis, and Eidolon dupreanum. With this final release, we’ve now worked with DNA Zoo to construct genomes for all three endemic pteropodids on the island. (Read the blog posts for P. rufus and R. madagascariensis on dnazoo.org here and here!)

Eidolon dupreanum is noteworthy for being the only known sister species to the famous African Straw-Colored Fruit Bat, Eidolon helvum, which is distributed widely across the African continent and demonstrates the largest panmictic range ever described for any non-marine mammal [2]. (See the chromosome-length upgrade for Eidolon helvum from (Parker et al., 2013) on DNA Zoo website, here!) Sub-populations of E. helvum from Ghana to Kenya to Malawi demonstrate no genetic structure, a reflection of this species’ huge migratory capacity, with important implications for understanding zoonotic threats posed by the fruit bat virome to human communities.

While less is known about the sister species, Eidolon dupreanum, population genetic studies suggest that this bat is also largely panmictic across the Madagascar island but don’t be duped into thinking that these bats are the same! Eidolon dupreanum is highly genetically distinct from E. helvum, with estimates of species divergence times dating back to the mid- to late-Miocene—some ten to five million years ago [3]. Indeed, the two species show considerable dimorphism in size, color, and ecology—with E. dupreanum roosting in caves and crevasses, while E. helvum roosts in large congregations in trees [4]. Other recent work is beginning to shed light on the importance of E. dupreanum for dispersal of native fruit species in Madagascar [5], as well as highlight hunting threats to its population viability [6]. With DNA Zoo, we are excited to contribute one more piece of evidence to the growing knowledge base for this rare and important pteropodid species!

Assembly of this genome was financed by an NIH grant (R01-AI129822-01) administered Dr. Cara Brook of UC Berkeley and Dr. Jean-Michel Héraud of Institut Pasteur of Madagascar (link: http://grantome.com/grant/NIH/R01-AI129822-01).

Bibliography

[1] C.C. Voigt, T. Kingston, Bats in the Anthropocene: Conservation of bats in a changing world, 2016. doi:10.1007/978-3-319-25220-9.

[2] A.J. Peel, D.R. Sargan, K.S. Baker, D.T.S. Hayman, J. a Barr, G. Crameri, R. Suu-Ire, C.C. Broder, T. Lembo, L.-F. Wang, A.R. Fooks, S.J. Rossiter, J.L.N. Wood, A. a Cunningham, Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses, Nat. Commun. 4 (2013) 2770. doi:10.1038/ncomms3770.

[3] J.J. Shi, L.M. Chan, A.J. Peel, R. Lai, A.D. Yoder, S.M. Goodman, A deep divergence time between sister species of Eidolon (Pteropodidae) with evidence for widespread panmixia, Acta Chiropterologica. 16 (2014) 279–292. doi:10.3161/150811014X687242.

[4] A.O. Kamins, O. Restif, Y. Ntiamoa-Baidu, R. Suu-Ire, D.T.S. Hayman, a a Cunningham, J.L.N. Wood, J.M. Rowcliffe, Uncovering the fruit bat bushmeat commodity chain and the true extent of fruit bat hunting in Ghana, West Africa., Biol. Conserv. 144 (2011) 3000–3008. doi:10.1016/j.biocon.2011.09.003.

[5] M. Picot, R.K.B. Jenkins, O. Ramilijaona, P.A. Racey, S.M. Carrie, The feeding ecology of Eidolon dupreanum (Pteropodidae) in eastern Madagascar, Afr. J. Ecol. 45 (2007) 645–650. doi:10.1111/j.1365-2028.2007.00788.x.

[6] C.E. Brook, H.C. Ranaivoson, D. Andriafidison, M. Ralisata, J. Razafimanahaka, J. Héraud, A.P. Dobson, C.J. Metcalf, Population trends for two Malagasy fruit bats, Biol. Conserv. 234 (2019) 165–171. doi:10.1016/j.biocon.2019.03.032.

Dolphinitely a gray area

The Risso’s dolphin, Grampus griseus, sets some impressive #travelgoals. Some estimates say that the Risso’s dolphin may spend as much as 77% of their lives traveling [1]! Their geographical range is spread across the world, although they prefer deeper waters over the coast. From temperate to tropical waters, the Risso’s dolphin can be found in pods of 10-30 individuals [2].

Sometimes called the gray dolphin, the coloring of this species changes with age. Risso’s dolphins start their lives as black or dark gray in color and then lighten to a gray/white as they mature. The skin of this species is often marked by many scars, usually caused by teeth raking from other dolphins [3].

Unlike most cetaceans, the Risso’s dolphin lacks any upper teeth but instead can have several rows of peg-like teeth on their lower jaw. These teeth are useful in catching their preferred prey the cephalopods and also may play a role in mating behavior [4].

Risso's Dolphin, Grampus griseus by Robin Agarwal, [CC BY-NC 2.0], via flickr.com.

Today, we share the chromosome-length assembly for the Risso’s dolphin. This is a $1K de novo genome assembly with a contig N50 = 62 Kb and a scaffold N50 = 93 Mb. See Dudchenko et al., 2018 for details on the assembly procedure.

The sample for this genome assembly was provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center prides itself on gathering and providing open research data that is free to access, reuse, repurpose and redistribute in service to ocean conservation and marine mammal health.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

Want to compare this genome against other members of the Delphinidae family? You’re in luck as this is the DNAZoo’s 8th genome assembly of a dolphin species! Check out the assembly pages for the bottlenose dolphin and the Commerson’s dolphin.

We thank Barbie Halaska, Laura Sherr, Giancarlo Rulli and Ben Neely for their help with this genome assembly!

Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the TMMC website at MarineMammalCenter.org.

Scaling up genomes of scaly pangolins

Pangolins are some of the most interesting animals on the planet both from the perspective of biology as well as pangolins being the most illegally trafficked mammal in the world. Pangolins are the sole members of the mammalian order Pholidota (which is Greek for “horny scale”), which is split into three genera: the Asian pangolins (genus Manis), the African tree pangolins (genus Phataginus), and the African ground pangolins (genus Smutsia).

Due to the illegal wildlife trade for pangolin scales, which are highly valued in the Asian traditional medicine markets, populations of pangolin species in both Africa and Asia are rapidly decreasing. The Asian species are typically smaller than their African counterparts, with tens of thousands of animals trafficked illegally each year. The eight known pangolin species are listed as either Vulnerable, Endangered, or Critically Endangered according the IUCN Red List of Threatened Species. Many international efforts on both policy and scientific fronts are aiming to prevent the extinction of these species and you can learn more about pangolin conservation efforts by visiting the Save Pangolins website.

Time-calibrated, molecular phylogenetic tree of pangolins, summarizing their distribution and revised classification. Time to most recent common ancestors (in million years) are indicated at the tree nodes. From Gaubert et al. (2017).

Recently, we released a chromosome-length assembly for the African tree pangolin, here. Today, we follow-up with chromosome-length assemblies for two Asian species of pangolins: the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These genome assemblies are upgrades from the drafts published by (Choo, Rayko et al., 2016).

Manis pentadactyla. Photo credit to Ms. Sarita Jnawali of NTNC – Central Zoo [CC BY 2.0], via flickr.com.

Manis javanica, photo by budak [CC BY-NC-ND 2.0], via flickr.com.

The Chinese pangolin can be found in northern India and Southeast Asia as well as southern China, while the Malayan pangolin can be found throughout Southeast Asia.

In contrast to the previously reported tree pangolin (Phataginus tricuspis) genome assembly (https://www.dnazoo.org/assemblies/Phataginus_tricuspis), which possess 57 (!) chromosome pairs making the tree pangolin the mammal with one of the largest chromosome count out there, the Malayan pangolin possesses only 19 chromosome pairs while the Chinese pangolin possess 20 chromosome pairs. See how the chromosomes of the three species relate to each other in the whole-genome alignment plot below.

Whole-genome alignments between the new chromosome-length genome assemblies of the the Malayan (ManJav1.0_HiC), the Chinese (M_pentadactyla-1.1.1_HiC) pangolin and the tree pangolin (Jaziri_pseudohap2_scaffolds_HiC).

According to Gaubert et al. 2018, the genus Manis split from the African genera roughly 38 million years ago and the split between the Malayan and Chinese pangolin is estimated at about 13 million years ago. This makes Pholidota a remarkable group in studying genome rearrangements and the role of chromosome numbers in diversification and speciation.

Lastly, pangolins are susceptible to coronaviruses, and there have been many mentions of pangolins in the media in relation to COVID-19 as a possible intermediate host for the transmission of SARS-CoV-2 to humans. The data does not seem to link pangolins directly to the current outbreak, but a virus related to pangolin coronavirus may have donated a receptor-binding domain to SARS-CoV-2 (Xiao et al., 2020). More generally, pangolin coronaviruses could represent a future threat to public health if wildlife trade is not effectively controlled.

If you happen to have samples for the African ground pangolins, please reach out. We’d love to work together to fill in the gaps in the pangolin phylogeny!