Researhers have sequenced the genomes of two living and three extinct rhinoceros species and compared them to existing data from the remaining three living species and a range of outgroups.
A paleoartist’s reconstruction of the three extinct species whose genomes were sequenced by Liu et al.: 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 credit: Beth Zaiken.
“Understanding the relationships among rhinoceros species and when they diverged has been a question addressed by evolutionary biologists since the dawn of the field,” said Dr. Love Dalén, a researcher at the Centre for Palaeogenetics and the Swedish Museum of Natural History, and colleagues.
“Charles Darwin himself discussed the topic in 1842 as one of a handful of examples in his short treatise on evolution that preceded On the Origin of Species in 1859.”
“Although rhinoceroses were once a diverse clade, extant rhinoceroses comprise only five species, all of which are highly endangered and global priorities for conservation.”
“Rhinocerotoidea, the clade including the rhinoceros family Rhinocerotidae, diverged from tapirs 55-60 million years ago in either Eurasia or North America.”
“The family subsequently radiated into at least 100 species distributed across Africa, Eurasia, North, and Central America and included some of the largest land mammals that ever lived.”
“Most rhinocerotids went extinct prior to the Pleistocene, with just nine species surviving into the Late Pleistocene, during which additional extinctions occurred.”
Liu et al. identifed an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of living rhinoceroses. Image credit: Liu et al., doi: 10.1016/j.cell.2021.07.032.
In the study, the scientists analyzed the genomes of five living species: the Indian rhinoceros (Rhinoceros unicornis), the white rhinoceros (Ceratotherium simum simum), the black rhinoceros (Diceros bicornis), the Sumatran rhinoceros (Dicerorhinus sumatrensis), and the Javan rhinoceros (Rhinoceros sondaicus).
They also analyzed the genomes of three extinct species: the Siberian unicorn (Elasmotherium sibiricum), the Merck’s rhinoceros (Stephanorhinus kirchbergensis), and the woolly rhinoceros (Coelodonta antiquitatis).
Their findings show that the oldest split separated African and Eurasian lineages about 16 million year ago.
The authors also found that while dwindling rhinoceros populations today have lower genetic diversity and more inbreeding than they did in the past, rhinoceroses have historically had low levels of genetic diversity.
“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,” Dr. Dalén said.
“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.”
“All eight species generally displayed either a continual but slow decrease in population size over the last two million years, or continuously small population sizes over extended time periods,” said Dr. Mick Westbury, a researcher 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.”
“Rhinos may have purged deleterious mutations in the last 100 years, allowing them to remain relatively healthy, despite low genetic diversity.”
“The findings are partly good news, and partly not,” Dr. Dalén said.
“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.”
“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.”
The study was published in the journal Cell.
Shanlin Liu et al. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell, published online August 24, 2021; doi: 10.1016/j.cell.2021.07.032