Subscribe free to our newsletters via your
. Energy News .




FLORA AND FAUNA
A 700,000 year old horse gets its genome sequenced
by Staff Writers
Copenhagen, Denmark (SPX) Jun 28, 2013


Dr. Ludovic Orlando and professor Eske Willerslev, both of the Centre for GeoGenetics at the University of Copenhagen, have sequenced the genome of the oldest horse ever found on Earth. Bone fragments from a 700,000 year old nag excavated in Yukon, Canada, had enough DNA in them to reveal new aspects of the evolutionary history of the horse. Credit: Uffe Wilken/University of Copenhagen.

It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit.

They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700.000 years in the permafrost of Yukon, Canada.

By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details. The spectacular results are now published in the international scientific journal Nature.

DNA molecules can survive in fossils well after an organism dies. Not as whole chromosomes, but as short pieces that could be assembled back together, like a puzzle. Sometimes enough molecules survive so that the full genome sequence of extinct species could be resurrected and over the last years, the full genome sequence of a few ancient humans and archaic hominins has been characterized. But so far, none dated back to before 70,000 years.

Now Dr. Ludovic Orlando and Professor Eske Willerslev from the Centre for GeoGenetics have beaten this DNA-record by about 10 times. Thereby the two researchers - in collaboration with Danish and international colleagues - have been able to track major genomic changes over the last 700.000 years of evolution of the horse lineage.

First, by comparing the genome in the 700,000 year old horse with the genome of a 43,000 year old horse, six present day horses and the donkey the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago.

Therefore, the evolutionary radiation underlying the origin of horses, donkeys and zebras reaches back in time twice as long as previously thought. Additionally, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the Last Glacial Maximum, some 20,000 years ago.

The world's only wild horse
The results also put an happy end to a long discussion about the so-called Przewalski's Horse from the Mongolian steppes. This horse population was discovered by the Western world in the second half of the nineteenth century and rapidly became threatened.

It almost became extinct in the wild by the 1970s but has survived until now following massive conservation efforts. The evolutionary origin of this horse, that shows striking physical differences compared to domesticated horses, as well as an extra-pair of chromosomes, remained a mystery.

The researchers reveal now that the Przewalski's horse population became isolated from the lineage leading to the present day domesticated horses about 50.000 years ago.

As the scientists could detect similar levels of genetic diversity within the Przewalski's Horse genome than in the genomes of several domestic breeds, this suggests that the Przewalski's Horses are likely genetically viable and therefore worthy of conservation efforts.

True Single DNA Molecule Sequencing
The geological context and dating information available was very strong and was built on about ten years of field work. Additionally, cold conditions, such as those from the Arctic permafrost, are known to be favourable for DNA preservation. But even so, "Sequencing the first genome from the Middle Pleistocene was by no means straightforward, says Dr Ludovic Orlando who, together with his team, spent the most of the last three years on this project.

The researchers first got excited when they detected the signature of those amino-acids that are most abundant in the collagen as this could indicate that proteins had survived in situ.

They even got more excited when they succeeding in directly sequencing collagen peptides. When they detected blood proteins, it really started looking promising because those are barely preserved. At that stage, it could well be that ancient DNA could also be preserved.

And indeed DNA was present. In tiny amount as the vast majority of sequences generated actually originated from environmental micro-organisms living in the bone. But with Helicos true Single DNA Molecule Sequencing, the researchers managed to identify molecular preservation niches in the bone and experimental conditions that enabled finishing the full genome sequence.

This was methodologically challenging but clearly some parameters worked better than others, says Professor Eske Willerslev. But sequencing was just half the way really.

Professor Willerslev continues, "Because 700,000 years of evolution and damage, it is not something that does come without any modification to the DNA sequence itself. We had to improve our ability to identify modified and divergent ancient horse sequences by aligning them to the genome of present day horses.

Quite a computational challenge, especially when the level of DNA modification outcompasses that seen in any other Arctic horses from the Late Pleistocene. Dr. Orlando explains, "Levels of base modifications were extremely high, for some regions even so high that every single cytosine was actually damaged. This, and the phylogenetic position of the ancient horse outside the diversity of any horse ever sequenced, provided clear evidence that the data was real."

Professor Willerslev adds, "The results of the studies and the applied techniques open up new doors for the exploration of prehistoric living creatures. Now with genomics and proteomics, we can reach ten times further back in time compared to before. And new knowledge about the horse's evolutionary history has been added - a history which is considered as a classical example in evolutionary biology and a topic which is taught in high schools and universities.

The new results are published in the scientific journal Nature. This major scientific advance has been made possible through the collaboration with researchers from Denmark, China, Canada, USA, Switzerland, UK, Norway, France, Sweden and Saudi Arabia and with financial support from the Danish National Research Foundation.

.


Related Links
University of Copenhagen
Darwin Today At TerraDaily.com






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle








FLORA AND FAUNA
Yukon Gold Mine Yields Ancient Horse Fossil
Edmonton, Canada (SPX) Jun 28, 2013
When University of Alberta researcher Duane Froese found an unusually large horse fossil in the Yukon permafrost, he knew it was important. Now, in a new study published online today in Nature, this fossil is rewriting the story of equine evolution as the ancient horse has its genome sequenced. Unlike the small ice age horse fossils that are common across the unglaciated areas of the Yukon ... read more


FLORA AND FAUNA
Remote Norway islands added to national electric grid after blackout

Outside View: Obama's climate action plan masks hidden agenda

Extreme Energy, Extreme Implications: Interview with Michael Klare

Energy Companies Pull a Blackwater

FLORA AND FAUNA
Outside View: Azerbaijan decides Europe's energy security

Jordan seeks energy security with shale oil plant

Philippines, US hold war games near China flashpoint reef

Japan vows to help Philippines amid China sea row

FLORA AND FAUNA
Next step on King Island wind power project welcomed

Chile expands wind power resources

Policy issues plague hydropower as wind power backup

Renewable energy use gaining worldwide: IEA

FLORA AND FAUNA
SolarCity Introduces Energy Explorer

Largest-in-the-Nation Feed-in Tariff Solar Program Kicks Off

Santerno Solar Skids To Be Installed To The Largest Solar Installation In Vermont

ET Solar Supplied Solar Modules to School Projects in Southern California

FLORA AND FAUNA
Japan gets first MOX nuclear shipment since Fukushima

Japan disaster budget given to nuclear operator

Japan gets first MOX nuclear shipment since Fukushima

New radioactive water leak at Fukushima: TEPCO

FLORA AND FAUNA
High-octane bacteria could ease pain at the pump

Novel Enzyme from Tiny Gribble Could Prove a Boon for Biofuels Research

A cheaper drive to 'cool' fuels

When green algae run out of air

FLORA AND FAUNA
Twilight for Tiangong

China calls for international cooperation in manned space program

Shenzhou 10 Returns Safely To Earth

Home of space dreams

FLORA AND FAUNA
Obama says US can lead climate change battle

Australia to forge ahead on climate change?

Climate tug of war disrupting Australian atmospheric circulation patterns

Tunisian woman to be first boss of Green Climate Fund




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement