From the once large family of rhinos, five species have survived today, all of which are severely threatened by poaching and the destruction of their habitat. A new study is now using genome analyzes to reveal how the species living today and three extinct species are related to one another. It also shows that the genetic diversity of rhinos was already low long before human influences decimated the animals. That could be good news for conservation efforts – even if diversity has never been as low as it is today.
The rhinoceros family originated around 55 to 60 million years ago and once comprised more than a hundred species that were distributed across Africa, Eurasia, North and Central America. Some of them were among the largest land mammals that ever lived on earth. Today there are still five species of rhinoceros: the white and black rhinoceros in Africa, which both have two horns, and in Asia the two-horned Sumatran rhinoceros and the one-horned armored and Java rhinos.
Expansion thanks to the land bridge
The relationship of these species to each other and to extinct representatives has long been controversial. The so-called horn hypothesis was based on the assumption that the most important distinction is between one-horned and two-horned species. The geographical hypothesis, on the other hand, stated that the main demarcation between the Asian and African species is. To answer this question, a team led by Shanlin Liu from the Chinese Agricultural University in Beijing examined and compared the genome of five living rhino species and three extinct species. To do this, the researchers used high-resolution DNA sequencing, which is more complete and more detailed than previous genomic data.
The result: “We have shown that the main branch in the rhinoceros tree of life runs between the geographical regions, Africa and Eurasia, and not between rhinos with one or two horns,” reports co-author Love Dalén from the Center for Paleogenetics in Stockholm. The African and Eurasian lines separated about 16 million years ago. “The split occurred after the creation of a land bridge between the Afro-Arab and Eurasian land masses around 20 million years ago,” the researchers said. “We suspect that the land bridge enabled expansion with subsequent emergence of new species, as is well documented for many other species.”
Small gene pool
During their analysis, Liu and his colleagues also found that all rhinos, including the extinct ones, have a very low genetic diversity compared to other mammals. “In a way, this means that the low genetic diversity we see in today’s rhinos, all of which are critically endangered, is in part a consequence of their biology,” explains Dalén. Until now, it was assumed that the low genetic diversity of rhinos was only due to the fact that populations had declined sharply within a short period of time due to human influences and inbreeding had increased.
But even if this effect also plays an important role, the new findings show that it is not the only one. “All eight species have shown either a continuous but slow decline in population size or continuously small population sizes over long periods of time over the past two million years,” says co-author Mick Westbury of the University of Copenhagen. “Continuously small population sizes could indicate that rhinos are generally adapted to low diversity.”
Hope for species protection
Normally, in populations that have too small a gene pool, harmful mutations accumulate over time and threaten the survival of the species. The researchers also found individual such mutations in today’s rhinos, for example in a gene that is important for the development and function of the eyes. “This mutation could contribute to the known poor eyesight of the rhinos,” said the researchers. Overall, however, the genomes examined showed significantly fewer harmful mutations than would have been expected given the small gene pool and more frequent inbreeding.
“This could be positive news for conservation, as it means recent declines have had less of an impact on genetic aspects of population viability than previously thought,” the researchers write. “However, we also find that today’s rhinos have less genetic diversity and a higher level of inbreeding than our historical and prehistoric rhino genomes,” says Dalén. “This suggests that recent population decline caused by hunting and habitat degradation has had an impact on genomes.”
The researchers hope that their study can make a contribution to the conservation of the rhinos. “Now we know that the low diversity we see in today’s individuals does not indicate an inability to recover, but is a natural state in the rhinoceros,” says Westbury. “We can better tailor our conservation programs to increasing population size and not individual genetic diversity.”
Source: Shanlin Liu (China Agricultural University, Beijing) et al., Cell, doi: 10.1016 / j.cell.2021.07.032