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Sequencing of Extinct and Living Elephants Reveals Genetic Admixture

NEW YORK (GenomeWeb) – Led by the Broad Institute, an international group of researchers sequenced the complete genome of both extinct and living elephantid species and saw evidence of genetic admixture among multiple species. In addition, the team found that African forest and savannah elephant exist as separate species.

In the study, published today in Proceedings of the National Academy of Sciences, the authors generated 14 genomes from both living and extinct elephantids, as well as from the American mastodon. They used classic Sanger-sequencing methods to generate a de novo gene assembly from a savannah elephant, while performing deep shotgun sequencing of genomes of additional living elephants and an extinct straight-tusked elephant.

To collect additional data from extinct elephant samples, the team generated low- to medium-coverage genomes from four woolly mammoths, one columbian mammoth, and two American mastodons. Since the mastodon diverged from elephantids around 20 to 30 million years ago, the team believed that the species "represented an appropriate outgroup for studying Elephantidae evolution."

While earlier genetic studies mapped elephantid evolution via separate genealogical trees, the new study demonstrated that interspecies hybridization has been a recurrent feature of elephantid evolution.

"[This paper] will be a reference point for understanding how diverse elephants are related to each other and it will be a model for conducting similar studies in other species groups," co-senior author and Uppsala University comparative genomics professor Kerstin Lindblad-Toh said in a statement.

While noting interbreeding between the North American woolly and Columbian mammoths, the team did not find evidence of recent gene flow between African savannah and forest elephants, demonstrating that they were two genetically distinct species. The team's genome-wide analysis demonstrated that about 500,000 years of isolation occured between ancestors of the African forest and savanna elephants

"Our data shows that these two species have been isolated for long periods of time, making each worthy of independent conservation status," study co-senior author and Harvard Medical School professor David Reach said in a statement.

The Broad Institute generated genomes for all present-day elephants as well as a high-quality genome from an extinct 120,000-year-old straight-tusked elephant obtained from a sample prepared by the University of Potsdam in Germany.

The team was initially confused by a discrepancy between morphological and genetic results of straight-tusked elephants, who were traditionally grouped with Asian elephants because of morphological similarities in their skulls and teeth.

Through sequencing, the researchers found that the straight-tusked elephants descended from a mixture of three ancestral lineages. Most of the species' ancestry derives from an African elephant ancestor, while its remaining ancestry consists of a large contribution from a lineage related to mammoths, and the other related to extant forest elephants.

The researchers' analysis of whole elephant genomes highlights that multiple major interbreeding events occurred between different ancient species.

The team believes future studies should explore whether admixture was not only an important phenomenon in the demographic history of elephantids, but if it also played a biologically important role in their evolution.

The study highlighted included examples such as "facilitating adaptation after migration into new habitats, or in the face of fluctuating climatic conditions and resulting ecological shifts."