Gene researchers reveal insights into equid evolution

Two pieces of the 700,000 year-old horse metapodial bone, just before being extracted for ancient DNA.
Two pieces of the 700,000 year-old horse metapodial bone, just before being extracted for ancient DNA. © Ludovic Orlando

Danish researchers who made headlines this week for mapping the complete genetic makeup from the frozen remains of a 700,000-year-old horse have also mapped the genomes of several Pleistocene horses.

Several species of horse became extinct toward the end of the Pleistocene epoch during an extinction pulse that saw the demise of many large mammals. The mass extinctions, centered on North America, resulted in the loss of mammoths, ground sloths, dire wolves and woolly rhinos, among others.

The University of Copenhagen’s Centre of GeoGenetics, which this week announced it had mapped the genome – the entire hereditary information of an organism – from the 700,000-year-old remains of a horse taken from permafrost in the Yukon, Canada, also revealed it had completed the genomes of several Pleistocene horses, together with those of a variety of modern domestic breeds. They also characterized the donkey genome.

The researchers said this represented an unprecedented genome sequence dataset for equids.

“We are currently scanning those genomes in order to identify the genetic changes that were specifically selected during horse domestication,” the centre said.

“Those changes contributed to major changes in human history, as mounted riding provided an unquestionable military advantage and has facilitated the exploration of novel territories.”

DNA molecules can survive in fossils well after an organism dies – not as whole chromosomes, but as short pieces that can be assembled back together, like a puzzle.

The lab, which officially started in April 2010, has carried out pioneering work in the extraction of ancient DNA. Its research has also helped piece together the complex puzzle that makes up horse evolution and the extinction of many equid species.

In March, researchers from the centre said they had characterized the full mitochondrial genome variation of all contemporary equids, as well as three extinct species: the Sussemione, New World stilt-legged horse, and the quagga.

Today’s equids do not have the rich diversity of species of the past.

Fossil horse bones extracted for ancient DNA.
Fossil horse bones extracted for ancient DNA. © Ludovic Orlando

A long history of over 55 million years is documented in the fossil record, showing drastic changes in body size and morphology over time and providing some of the most famous textbook examples of evolution in action.

Despite this, many aspects of the evolutionary history of equids remain controversial. How the different extant species are related to each other, and also the reasons for  extinctions in the late Pleistocene, remain matters of scientific debate.

The survival of traces of DNA in fossils makes it possible to retrieve genetic information from extinct animals and identify the living species to which they are most closely related, providing a unique opportunity to link past and present biodiversity.

Research at the centre also showed, in 2009, that woolly mammoths and prehistoric horses grazed on the North American plains for several thousand years longer than previously thought.

This was revealed by samples of ancient DNA, analysed by an international team of research scientists under the leadership of Professor Eske Willerslev.

Analyses of ancient DNA challenged the results of more common methods of dating, such as carbon 14 analysis of bone and tooth remains from extinct animals. These methods had previously dated the extinction of mammoths and prehistoric horses in Central Asia to within 13,000 to 15,000 years ago.

But with the DNA-test methods of Willerslev and his colleagues, the boundary has now moved between 2600 and 5600 years closer to present day for when the last mammoths and prehistoric horses grazed on the North American Plains.

Probing Alaska's permafrost.
Probing Alaska’s permafrost. © Center for Permafrost Studies (CENPERM), University of Copenhagen

The ancient DNA that formed the basis for result was discovered by scientists in samples of soil from the permafrost tundra surrounding the windswept town of Stevens Village on the bank of the Yukon River in Central Alaska.

Professor Eske Willerslev said of the finding: “In principle, one can take a pinch of soil and uncover which living creatures, animals and plants lived in the area half a million years back in time.

“With ancient DNA analysis, we are completely independent of skeletons, bones, teeth and other macro-fossil evidence from extinct animals. This greatly increases the possibility of finding evidence of the existence of a species through time.

“Whilst an animal leaves only a single corpse when it dies, it leaves quantities of DNA traces through urine and faeces whilst it is still alive. It is these DNA traces which we find in the soil.”

When the remains of the last member of an extinct species were hard to find, Willerslev and a team of international research scientists decided to carry out an expedition to Central Alaska to solve the riddle of “The last surviving mammoths” using ancient-DNA tests from permafrost soil.

Surprisingly, the scientists found that the later samples with mammoth DNA could be dated back to between 10,500 and 7500 years ago, between 2600 and 5600 years after the supposed extinction of the mammoths from mainland Alaska.
It is believed these animals, threatened with extinction, survived in small, isolated enclaves, where suitable living conditions were intact.

The findings breathe new life into the debate about why prehistoric animals, such as sabre-toothed tigers, giant sloths, woolly rhinos, and mammoths apparently suddenly disappeared from the face of the earth.

“Our findings show that the mammoth and the horse existed side by side with the first human immigrants in America for certainly 3500 years and were therefore not wiped out by human beings or natural disasters within a few hundred years, as common theories otherwise argue.

“The technique behind ancient-DNA analysis has the potential to greatly contribute to the debate about the extermination of prehistoric species, but can also be used to gather knowledge of contemporary animal species which are so shy that they are hard to detect. Not to mention the forensic possibilities opened up by the technique.”


Node ages as estimated from BEAST analyses given in years and with 95% HPD. Shown is the averaged results from the three analyses excluding outgroups
Node ages as estimated from BEAST analyses given in years and with 95% HPD.
Shown is the averaged results from the three analyses excluding outgroups.

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