After 5 years of orchestrating my lab's first whole genome sequencing project we finally have published our initial analysis of the first genome sequence for the Sumatran Rhinoceros (Dicerorhinus sumatrensis). This work was only possible with the help of Jim Denvir and the team at the Marshall University Genomics Core Facility, Terri Roth at the Cincinnati Zoo's Center for Conservation and Research of Endangered Wildlife, and our collaborators in Taiwan including Chih-Ming Hung at the Biodiversity Research Center at Academia Sinica and Pei-Jen Shaner at National Taiwan Normal University. This work appears in the January 8 edition of the journal Current Biology and was featured on the BBC News, Nature PBS, Huffington Post, Sci-News, Science Daily, Mongabay.com, and local papers including The Fayette Tribune, Williamson Daily News, and the Herald Dispatch.
Sumatran Rhinoceros is among the most endangered mammals on earth and genome data can give us insight into this species' population history. The Pleistocene was a turbulent time for Sumatran Rhinoceros. During the early to mid-Pleistocene approximately 950,000 years ago their population (effective population size) experienced a dramatic rise. This increase likely was in concert with an expansion of many large mammals from Southeast Asia into an emergent Sundaland (the landmass that today is represented by the Malay Peninsula, and the islands of Sumatra, Java, and Borneo but during the Pleistocene was connected by a broad land corridor). The fossil record indicates that many island endemic mammals went extinct around this time and were replaced by new species arriving from continental Asia and Sumatran Rhinoceros was likely part of this wave of immigrants into the region.
After their heyday in the early to mid-Pleistocene, times were tough for Sumatran Rhinoceros. Our genome data suggested a precipitous decline in their population sometime in the mid-Pleistocene and by the end of the Pleistocene 12,000 years ago their population likely bottomed out and never showed signs of recovery. Shifting climate and especially fluctuations in sea level likely played a role in shaping their demographic history. Sundaland is a region uniquely and dramatically changed by fluctuating sea level, going from a broad subcontinental region to a fragmented archipelago. These changes had profound effects on the biodiversity of the region.
Like any research, ours has some caveats. The analysis we used to infer population history from genome data has a hard time distinguishing population declines from fragmentation and we suspect that likely both were at play in shaping Sumatran Rhinoceros demographic history. Also, recent studies suggest that some of the apparent swings in past population size for other species may be due to selection and that possibility deserves some more attention in Sumatran Rhinoceros. Climate was also only one factor influencing Sumatran Rhinoceros populations during the Pleistocene and early Holocene. Archeological evidence indicates that paleohuman populations were hunting Sumatran Rhinoceros and clearing forest in Borneo around the end of the Pleistocene and therefore potentially having some negative impact on their populations. Good studies will often lead to more questions than they answer and we have a lot of prospects for future followup work.
After bringing in such a great team for this project I'm looking forward to other analyses on this genome data from Sumatran Rhinoceros and to other whole genome sequencing projects on other species. Many species left genetically vulnerable by events in their evolutionary past are today suffering from modern anthropogenic climate change, over-exploitation and habitat loss. Knowing the evolutionary history of endangered species therefore places their current predicament in a broader context and may point to particular management and conservation strategies to preserve their genetic diversity.