Elephant history rewritten by ancient genomes


Ewen Callaway, Nature

Date Published

The genome of a mysterious ancient fossil has shaken up the elephant
family tree.

Modern elephants are classified into three species: the Asian elephant
(Elephas maximus) and two African elephants — the forest-dwellers
(Loxodonta cyclotis) and those that live in the savannah (Loxodonta
africana). The division of the African elephants, originally
considered a single species, was confirmed only in 2010.

Scientists had assumed from fossil evidence that an ancient
predecessor called the straight-tusked elephant (Paleoloxodon
antiquus), which lived in European forests until around 100,000 years
ago, was a close relative of Asian elephants.

In fact, this ancient species is most closely related to African
forest elephants, a genetic analysis now reveals. Even more
surprising, living forest elephants in the Congo Basin are closer kin
to the extinct species than they are to today’s African
savannah-dwellers. And, together with newly announced genomes from
ancient mammoths, the analysis also reveals that many different
elephant and mammoth species interbred in the past.

“It’s mind blowing,” says Tom Gilbert, an evolutionary geneticist at
the Natural History Museum of Denmark in Copenhagen. The
straight-tusked elephant is little-known even among experts, he says.
“And the first thing we hear about it is: here’s the genome.”

Love Dalén, a palaeogeneticist at the Swedish Museum of Natural
History in Stockholm, says that the study will force a reshuffle of
the elephant family tree. “Basically Loxodonta is not valid as a genus
name,” he says. He thinks that taxonomists may need to come up with
new names for the different species, to better represent the
relationship between savannah, forest and straight-tusked elephants.

The results were announced at the 7th International Symposium on
Biomolecular Archaeology meeting in Oxford, UK, on 15 September. A
team led by evolutionary geneticist Eleftheria Palkopoulou and
population geneticist David Reich, both at Harvard Medical School in
Boston, Massachusetts, together with evolutionary geneticist MIchael
Hofreiter at the University of Potsdam in Germany, conducted the
study. It was based on the genomes of two 120,000-year-old
straight-tusked elephant samples from Germany.

Ancient interbreeding

Palkopoulou and her colleagues also revealed the genomes of other
animals, including four woolly mammoths (Mammuthus primigenius) and,
for the first time, the whole-genome sequences of a Columbian mammoth
(Mammuthus columbi) from North America and two North American
mastodons (Mammut americanum).

The researchers found evidence that many of the different elephant and
mammoth species had interbred. Straight-tusked elephants mated with
both Asian elephants and woolly mammoths. And African savannah and
forest elephants, who are known to interbreed today — hybrids of the
two species live in some parts of the Democratic Republic of Congo and
elsewhere —  also seem to have interbred in the distant past.
Palkopoulou hopes to work out when these interbreeding episodes

The study represents a landmark in ancient genomics, scientists at the
meeting say. The straight-tusked elephants aren’t the oldest ancient
genomes — that record belongs to the genome from a horse bone, between
560,000 and 780,000 years old, found frozen in the Canadian Arctic —
but they do represent the oldest whole genomes from a warm
environment. The fact that one of the straight-tusked elephant genomes
was of such high quality — with each DNA letter sequenced on average
15 times — left many scientists awestruck.

“These things are the realm of palaeontology,” says Gilbert. “It’s a
sign of where we are today.”

“No one had dared to think about sequencing straight-tusked elephants
before,” says Dalén. “It’s just insane to go that far back in time.”