Old and new DNA from elephants clarify their evolution and provide knowledge about their future

6 March 2018

Female elephant Swazi at San Diego Zoo who has contributed DNA to the study.

A new study shows that the flow of genes between different species of elephant – both extinct and those living today – has been more extensive than was previously thought. Moreover, the study indicates that the African savannah elephant and forest elephant should be viewed as being two different species. The article will be published today in the scientific journal PNAS.

The elephant – the largest terrestrial mammal – began to walk on the surface of the earth 5–10 million years ago in Africa. Today, there are fewer than 500,000 elephants in the world and they are therefore protected species, especially in Africa where they continue to be under threat from the ivory trade. The diminishing elephant population has therefore developed into an “isolated branch” with only three living species: the Asian elephant, the African savannah elephant, and the African forest elephant.

Approximately 50,000 elephants are killed every year by poachers which is posing a threat to many populations. Mastodons and mammoths, which were closely related, have vanished. Knowledge about the elephant’s genetic heritage could play a valuable role in future conservation efforts to prevent these animals from becoming extinct.

An international consortium headed by senior researchers from the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, the University of Potsdam and McMaster University, has used advanced sequencing technology to study the genetic material of both living and extinct elephant species. In the article which is now being published in PNAS, the authors present an extensive portrait of the genomes of existing elephant species, mammoths, extinct elephants with straight tusks, and the American mastodon, an extinct relative of the elephant family. The article shows that gene flow (genetic mixture) among elephant species has been a common occurrence during the history of the elephant which contradicts earlier studies which described their lineage as simple trees.

“Over the years, it has been debated whether the African savannah elephant and the forest elephant are two different species,” says Kerstin Lindblad-Toh who works at the Broad Institute and is professor of comparative genomics at Uppsala University which was one of the key organisers of the Elephant Genome Project (EGP) when it was started up in 2008. “Our data show that these two species have been isolated for long periods of time and therefore both of them should be preserved.”

The article confirms that the African savannah elephant and the forest elephant are two different species and therefore it can be argued that both species should be protected.

The researchers mapped the genomes for all elephant species currently alive and a high-quality genome for an extinct 120,000-year-old elephant with straight tusks, and generated common genome data from several prehistoric mastodon and mammoth genomes.

“The combined analysis of common genome data from all these prehistoric elephants and mastodons has given us knowledge about the history of the elephant population and revealed a complexity that we have previously been completely unaware of,” says Lindblad-Toh.

Traditionally, the extinct elephants with straight tusks have been grouped together with today’s Asian elephant on the basis of morphological similarities in their skulls and teeth. However, an article published last year by a team led by Michael Hofreiter showed that elephants with straight tusks are on average more closely related to the African forest elephant than the Asian elephant.

“We were puzzled by the difference between the morphological and genetic results but our analyses show that the ancestry of elephants with straight tusks was very complex and included three different components,” says Eleftheria Palkopoulou, the main author of the article.

The article shows that the extinct elephant has descended from a mixture of prehistoric African elephant, woolly mammoth and today’s forest elephant.

“The results were extremely surprising,” says Palkopoulou. “The ancestry of the elephant population could not be explained by simple divisions which gave clues so the evolution of these iconic species could be understood.”

Instead, her analysis revealed several occurrences of cross-breeding among different prehistoric species which is a strong indication that a mixture of divergent species is a fundamental characteristic of the evolution of the elephant. This raises the question of how widespread mixtures are among other groups of species.

Full article: Paper cited: Palkopoulou E, et al. A comprehensive genomic history of extinct and living elephants. PNAS. Online February 26, 2018. DOI:10.1073