My personal and professional adventure into Science

Archives for June 2013

A genome world record – A 700.000 year old horse gets its genome sequenced

I can proudly say that I have been a part of this project for the last two years 🙂

Official press release written by press office at 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.

Credit: Iben Julie Schmidt. http://www.ishot.dk/

Credit: Iben Julie Schmidt.
http://www.ishot.dk/

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 and research, carried out by Dr. Duane Froese, University of Alberta, and his team. 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.

At CBS we have used our supercomputers throughout the last two years to map all the 12 billions DNA fragments that were handed over to us from the people at GeoGenetics. Furthermore, we functionally annotated the donkey genome including the identification of Y chromosome associated contigs and assessed the metagenome of the Middle Pleistocene horse sample.

Link to Nature paper: Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Link to Nature news: First horses arose 4 million years ago

Ludovic Orlando, Aurélien Ginolhac, Guojie Zhang, Duane Froese, Anders Albrechtsen, Mathias Stiller, Mikkel Schubert, Enrico Cappellini, Bent Petersen, Ida Moltke, Philip L. F. Johnson, Matteo Fumagalli, Julia T. Vilstrup, Maanasa Raghavan, Thorfinn Korneliussen, Anna-Sapfo Malaspinas, Josef Vogt, Damian Szklarczyk, Christian D. Kelstrup, Jakob Vinther, Andrei Dolocan, Jesper Stenderup, Amhed M. V. Velazquez, James Cahill, Morten Rasmussen et al., Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) doi:10.1038/nature12323, PDF

Contact:

Dr. Ludovic Orlando: E-mail: orlando.ludovic@gmail.com;  Phone +45 21849646

Professor Eske Willerslev: E-mail: ewillerslev@gmail.com;  Phone +45 28751309

Ancient horse DNA provides new insights into evolution

This post is a teaser for tomorrow’s post and is directly taken and translated from Videnskab.dk, hence all credit should go to Line Fedders who wrote the original article in april 2013 and not me. This is a project I have been so fortunate to be involved in for the last two years 🙂

Horses are one of the species that have had the greatest impact on mankind. As food, transportation, in war and in the daily use and as pets. The horse’s appearance-related evolution from a small animal the size of a dog to today’s powerful beast is also well understood by scientists, but no one has yet looked at how the horse’s DNA has evolved in line with the look.

Credit: Iben Julie Schmidt

Credit: Iben Julie Schmidt
http://www.ishot.dk/

This is what a group of scientists at The Center for GeoGenetics at Copenhagen University is looking at with financial support from DFF.

The group, led by Associate Professor Ludovic Orlando, is currently investigating how the horse’s DNA has evolved, and it can provide new insight into how changes in the environment and man took and the subsequent domestication of horses have changed a species all the way into the DNA.

»Different breeds of horses can be seen as experiments, we humans have made and experimentation have created completely different horses. In this project we are able here to see which genes are changed in each experiment. We will be able to explain the processes, both man-made and environmentally made, biological drives the development of a horse’s appearance, “says Associate Professor Ludovic Orlando.

“We expect that some of the mechanisms we find are similar in all mammals, and thus the horse’s development also tell something more general about evolution,” he adds.

Will restore ancient horses

When Ludovic Orlando says that horses can be seen as experiments, we humans have made, he believes that by selecting certain individuals and give them benefits, such as food, or by direct breeding, selecting for certain traits. For example, size, strength or temperament.

The horse breeds that exist today, almost all bred by humans, and therefore can not be the basis of their DNA say something about how an original horse’s DNA looked.

“With this project here, we want to restore the horses, from before they were domesticated. We will create the profile for what a horse was before we made them the animals they are today, “says Ludovic Orlando.

Comparing across time

If the scientists successful can map the genome of the ancient horses, they will compare it with the genome of modern horse breeds and genome of the so-called Przewalski horse, which is probably the living race that has most in common with the ancient horses. Przewalski horses is an endangered wild horse that lives on the steppes of Central Asia, especially in Mongolia.

“In doing so, we examine whether the Prewalski-horse actually is the last living wild horse. If you look at cave paintings of 22,000 years ago the pictures of horses actually looks like Przewalski horses. By comparing the genomes we can see if they are genetically closer to the true wild horses that lived before the domestication of 5,500 years ago, or on horses today, “explains Ludovic Orlando.

The researchers have so far been mapped genome of a number of horses today to be used for the comparison. They have looked at the American Quarter Horse, thoroughbred horse, arabian horse, the Icelandic horse and the Norwegian horse, also known as North Bagge or Trotter.

“These breeds present all different breeding preferences. By going back in time and look at the family trees we have found horses that are as different as possible, “says the researcher.

Changing the limits for the possible

Ludovic Orlando and his colleagues are using the latest methods in DNA sequencing and repair of very-old DNA found among other fossils.

Scientists have DNA from horses, spanning many thousands of years. Just how ancient DNA, scientists will be looking at, he can not say yet. Scientists are namely in dialogue with the scientific journal Nature on an article, and it requires that they keep close.

“I can say that we are moving back long before the domestication of horses 5,500 years ago. We look at the DNA that is older than what you have done before, “says Ludovic Orlando.

Microbes stand in the way

Working on the ancient DNA takes place roughly at that scientists crusher bone fossils and extract the DNA. But it is not an easy task.

“We will sequence every one of these about six billion DNA letters that we expect the ancient horses DNA to have. However, it is technically challenging. Old DNA can survive, but it gets injured., “Explains Ludovic Orlando.

The hard part is that as soon as a creature dies, the cells explodes and in goes microbes which also contain DNA. Even if there were no microbes in the cell, there is water in the environment and remains of the tissue. The water degrades DNA into small pieces of sequences that break or change.

The researchers’ main job is to make sure that the DNA they look at, are from the horses and not from microbes.

“With our technology we can generate a billion DNA sequences of about five days. But we also get DNA from microbes in the ratio of 1:99. So there is 1% chance that we find what we’re looking for. It looks like a billion sequences, but actually it should be divided by 100, so we need to map a whole lot before we can hope to get everything we’re looking for, “says the researcher.

We want to understand the process

The methods that scientists use is constantly evolving, so they can be better. But it is the goal, not the means that interest Ludovic Orlando.

The methods are cool and innovative, especially for a molecular biologist. But we are looking for the answer. It’s the process we will understand. What we humans and the environment make that change the creatures, “he says.

Ludovic Orlando expects that the project will be started the next three years. The researchers have already come a long way, but there will always new side projects.

“We are studying among other horses who have been living under very cold conditions to see how the environment has affected their DNA. There are probably tons of projects and we are already in contact with lots of people, for example horses breeders in the United States. ”

 

First danish Coursera course – Learn your Computational Molecular Evolution for free

Here at CBS we are very proud to announce that the first danish Coursera course – Computational Molecular Evolution – taught by Professor Anders Gorm Pedersen will start Monday June 24 (www.coursera.org/course/molevol).

Computational Molecular Evolution

Coursera is a platform for Massive Open Online Courses (MOOCs) offered to the world for free (at coursera.org). It was founded last year by two visionary professors from Stanford University, Andrew Ng and Daphne Koller, under the motto: Education should not be a privilege – but a human right. Andrew and Daphne have not been aiming for any kind of education, they have been working hard to secure that only the best universities, offering the best courses by their best instructors, and using the most efficient pedagogical tools are available on Coursera.

Coursera has since at many occasions been referred to as a revolution in higher education, and has in only a little more than a year grown from 0 to almost 4 million students (courserians). Not surprisingly, professor Andrew Ng and Daphne Koller are now among the Time’s top 100 most influential people in the world (time100.time.com/2013/04/18/time-100/slide/andrew-ng-and-daphne-koller).

Computational Molecular Evolution has more than 13,000 students enrolled, and will run for 6 weeks for the first time this summer. It is a transformed version of a course that Professor Anders Gorm Pedersen is teaching at DTU, and the product now available at Coursera is the result of months of hard work by a range of people from both DTU and Coursera.

This course is about molecular evolution – the evolution of DNA, RNA, and protein molecules. The focus is on computational methods for inferring phylogenetic trees from sequence data, and the course will give an introduction to the fundamental theory and algorithms, while also giving the student hands-on experience with some widely used software tools. Since evolutionary theory is the conceptual foundation of biology (in the words of Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evolution”), what you learn on this course will be relevant for any project you will ever do inside the life sciences. A phylogenetic tree will almost always help you think more clearly about your biological problem.

A special emphasis is put on methods that employ explicit models of the evolutionary process (maximum likelihood and Bayesian approaches), and we will explore the role of statistical modeling in molecular evolution, and in science more generally. A mathematical (statistical) model of a biological system can be considered to be a stringently phrased hypothesis about that system, and this way of thinking about models will often be helpful. In addition to model-based methods, you will also learn about other approaches, such as those based on parsimony and genetic distance (e.g., neighbor joining).

Often, the evolutionary tree is the result we are interested in – knowing how a set of sequences (or organisms) are related can provide us with important information about the biological problem we are  investigating. For instance, knowing which organisms are most closely related to a newly identified, uncharacterized, pathogenic bacterium will allow you to infer many aspects of its lifestyle, thereby giving you important clues about how to fight it. In other cases, however, inferring the structure of the tree is not the goal: for instance, our main focus may instead be the detection of positions in a protein undergoing positive selection (indicating adaptation) or negative selection (indicating conserved functional importance). However, even in these cases, the underlying phylogenetic tree will be an important part of our hypothesis about (model of) how the proteins have been evolving, and will help in getting the correct answer.

Although the study of molecular evolution does require a certain level of mathematical understanding, this course has been designed to be accessible also for students with limited computational background (e.g., students of biology)

The team is very excited about the launch, and hope that interested students around the world will enjoy it.

Computational Molecular Evolution

Media coverage:

Text in danish:Dr.dk: 14.000 studerende fra hele verden følger DTU-kursus
http://karriere.jobfinder.dk/artikel/dtu-professor-foerste-dansker-paa-gratis-undervisningsportal-272

Bpetersen.dk is now on Facebook

Just for the fun of it, and to connect with people I am not connected with at my private Facebook page, I have now created a Facebook page for the blog. It can be found here: https://www.facebook.com/Bpetersendk. Feel free to share the link.

Bpetersen.dk on Facebook

Assistant Professor – and now what?

It’s been quite some time since I last wrote a post here. The reason is that a lot of things has been going on in both my private and professional life. Most of it has changed now, so I will try to improve and post more often 🙂

Since the first of May I have had a new title, finally I can call myself Assistant Professor within Bioinformatics (Adjunkt in danish). This has been on the way after a 6 years Masters degree, three years as a PhD student, 2 years of PostDoc and now I am here, awesome 🙂 The contract I am on, is so far, a two-year contract on a FoodGenomics project, which I will write about in another post.

Not much has changed in my work life, yet, except that I am now secured for two more years, which is fantastic! Workplace is still the same (CBS), I still work in the most awesome group at CBS (Metagenomics), Office is still the same, which means that I fortunately still have the same office mates who makes my every working day so happy and cheerful and I still have the same course responsibilities.

Currently I am co-responsible for two courses at DTU, a 13-weeks course in Introduction to Bioinformatics (#27611) and the same course condensed to a 3-weeks course (#27622). 27622 is currently running, going into second week tomorrow and 27611 ended a few weeks ago with a four-hour written exam. This means that I now have 75 exam sets I need to correct, fortunately I am only responsible for correcting 40% of each exam-set as we were four people creating the exam-sets. It’s a lot of work and I still have all the other projects running in parallel with deadlines coming up 🙂

I guess that’s the life of Academia but I still love it! The fact that every morning I wake up, I am looking forward to get to work, should say it all 🙂

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