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Geneticists map the rhinoceros family tree

The relationships among the world’s five living rhinoceros species has been a question all the way back to Darwin’s time. Now, researchers have helped to fill the gaps in the rhino evolutionary family tree by analyzing genomes of all five living species together with the genomes of three ancient and extinct species.

Utdöda arter av noshörning
A paleoartist's reconstruction of the three extinct species whose genomes were sequenced as part of the study. In the foreground is a Siberian unicorn (Elasmotherium sibiricum), and close behind are two Merck’s rhinoceroses (Stephanorhinus  kirchbergensis).  In  the  far background is a woolly rhinoceros (Coelodonta antiquitatis). Image by Beth Zaiken.

The findings, reported in the journal Cell, show that the oldest split separated African and Eurasian lineages about 16 million year ago. They also find that – while dwindling populations of rhinos today have lower genetic diversity and more inbreeding than they did in the past – rhinoceroses have historically had low levels of genetic diversity.

Love Dalén
Love Dalén

“We can now show that the main branch in the rhinoceroses’ tree of life is among geographic regions, Africa versus Eurasia, and not between the rhinos that have one versus two horns,” says Professor Love Dalén at the Centre for Palaeogenetics, which is a collaboration between Stockholm University and the Swedish Museum of Natural History. “The second important finding is that all rhinoceroses, even the extinct ones, have comparatively low genetic diversity. To some extent, this means that the low genetic diversity we see in present-day rhinos, which are all endangered, is partly a consequence of their biology."

 

Adapted to low levels of diversity

“All eight species generally displayed either a continual but slow decrease in population size over the last 2 million years, or continuously small population sizes over extended time periods,” says Mick Westbury at the University of Copenhagen. “Continuously low population sizes may indicate that rhinoceroses in general are adapted to low levels of diversity.”

This notion is consistent with an apparent lack of accumulated deleterious mutations in rhinos in recent decades. Westbury says that rhinos may have purged deleterious mutations in the last 100 years, allowing them to remain relatively healthy, despite low genetic diversity.

Love Dalén says that the findings are “partly good news, and partly not.” It appears that low levels of genetic diversity in rhinos is part of their long-term history and hasn’t led to an increase in health problems related to inbreeding and disease-causing mutations.

“However, we also find that present-day rhinos have lower genetic diversity, and higher levels of inbreeding, compared to our historical and prehistoric rhinoceros genomes,” he says. “This suggests that recent population declines caused by hunting and habitat destruction have had an impact on the genomes. This is not good, since low genetic diversity and high inbreeding may increase the risk of extinction in the present-day species.”

 

Requires a very clean environment

Johanna von Seth
Johanna von Seth

Working on ancient DNA requires a very clean environment to reduce the risk of contamination with modern DNA.

“At the Centre for Palaeogenetics the researchers have access to a state-of-the art laboratory that has made it possible to extract and sequence DNA from three extinct rhinoceros species, the woolly rhinoceros, the Siberian Unicorn and Merck’s rhinoceros,” says Johanna von Seth, Ph D student at Stockholm University and working at the Centre for Palaeogenetics.

According to Nicolas Dussex, postdoc at Stockholm University and working at the Centre for Palaeogenetics, the new study will play an important role in rhinoceros conser-vation.

Nicolas Dussex
Nicolas Dussex

“The new generation of genomic resources will simulate future DNA based monitoring, conservation management and environmental DNA studies of rhinoceros. For instance, having a reference genome for extant rhinoceros will facilitate sequencing and analyses of a large number of specimens for each species. These new data will in turn allow to assess how their genetic diversity has been affected by habitat changes characteristic of the Anthropocene, especially over the past 200 years.”

“Moreover, because understanding the effects of inbreeding on individual health is essential for species conservation, assessing the ‘genomic quality’ of several individuals per population, will also greatly contribute to rhinoceros management such as transloca-tion and breeding programmes.”

Researchers at SciLifeLab in Sweden have also contributed to the study.

Article in Cell, August 24 2021: “Ancient and modern genomes unravel the evolutionary history of the rhinoceros family”

Centre for Palaeogenetics