SciMy Interview: Professor Mark Stoneking (Part I)

Interviewed by Dr. New Jaa Yien

Introduction

Prof Mark StonekingProfessor Mark Stoneking is a world-renowned geneticist in the field of human evolution. He (along with Professor Rebecca Cann and the late Professor Allan Wilson) is known for proposing the Mitochondrial Eve hypothesis in 1987. Analysis of mitochrondrial DNA (mtDNA) of ~150 modern humans from different geographic populations revealed that all of them had stemmed from a woman who lived 200,000 years ago in Africa, and this woman (aka Mitochondrial Eve) is hypothesised to be a common ancestor of all modern humanity . Prof. Stoneking is currently a Group Leader at the Max Planck Institute for Evolutionary Anthropology, and an Honorary Professor of Biological Anthropology at the University of Leipzig, Germany. We caught up with Prof. Stoneking while he was in Malaysia to give a talk at the Monash University Malaysia in March 2015.

Q1. What drew you into anthropology and genetics?

When I started my undergraduate course at the University of Oregon (USA), I wasn’t sure of what to study. So I took several subjects including which include anthropology and it sparked my interest in the field. This further led me into taking other subjects such as human population biology and human genetics. Driven by the fascination that human population history can be studied through genetic methods, I went on to pursue a Masters in Evolutionary Genetics. Upon completion, the first human DNA-based study relating to evolutionary genetics was reported by Professor Allan Wilson (University of California, Berkeley, USA). This prompted me to do a PhD with his group, focusing on mitochondrial DNA variation in evolution. It was an interesting new field to look at as prior to that time, most of the work done in population genetics and evolutionary genetics was focused on protein variation, which was easier to study. Therefore, mtDNA was the very first DNA-based study that takes a closer look at the actual genetic changes that happened.

Q2. With a research career spanning close to three decades, what are the highlights of your career and/or memorable moments?

It was certainly the work on mtDNA. The project was very exciting and it opened up a lot of opportunities for me as a graduate student. The study provided the first genetic evidence that proves the African origin of the human species. It was a fundamental contribution to the field of genetic evolution and I was very fortunate to be involved in it. Another highlight was the work that didn’t involve humans directly but involved human parasites, the lice. Our team studied the origins and the genetic differences between head and body lice. We were able to conclude when clothing became important in human evolution (~72,000 years ago). Another very exciting time occurred between 1996 and 1997, when I was on sabbatical leave from my position at the Pennsylvania State University (USA) and went to the University of Munich (Germany) working with Professor Svante Pääbo. It was at that time when their lab obtained the first mtDNA from the Neanderthal and our laboratory back at Penn State had the opportunity to confirm the findings by doing an independent replication study of the DNA. When the replication was achieved, it was absolutely a highlight to realise that we were finally getting the first DNA sequence from the ancient human.

Q3. You and your colleagues discovered the “Mitochondrial Eve”  – a term that has been popularised by the media. What are the common misconceptions that come with such a provocative term?

The common misconception that arises is that the mtDNA traced back to the only woman who was alive at the time; instead, as a matter of fact, she was a member of a population. They all had mtDNA but of all those individuals, only her mtDNA was somehow passed on to the modern humans. This scenario demonstrates a simple and straightforward application of the evolutionary theory that all life on this planet has a single origin and everything alive today traces back to that single origin. This has to be the case of a single variation on any gene that we look at. It doesn’t matter that whether it is a mtDNA or any other gene, it all has to trace back to a single ancestor at some point in the past. For the majority of our genome, the variations traces back several hundreds thousands or even millions of years well before the appearance of modern humans.

Figure: Unlike nuclear DNA (left), mitochondrial DNA is only inherited from the maternal lineage (right). Image source: “Marshalling the Evidence.” Understanding Evolution. University of California Museum of Paleontology. 22 April 2014. http://undsci.berkeley.edu/article/0_0_0/endosymbiosis_07

Figure: Unlike nuclear DNA (left), mitochondrial DNA is only inherited from the maternal lineage (right). Image source: “Marshalling the Evidence.” Understanding Evolution. University of California Museum of Paleontology. 22 April 2014. http://undsci.berkeley.edu/article/0_0_0/endosymbiosis_07

Q4. Along the same line, how has the term “Mitochondrial Eve” been used against the teaching of evolution?

There are others who try to put a biblical term of “Eve”, however, people have to recognise that even if we use the term “mitochondrial Eve”, the genetic evidence indicates that the mitochondrial ancestor lived somewhere around 150-250 thousand years ago.  This is well beyond anything where people who follow the biblical version of events would accept. So it was not initially misused but I think people need to look beyond just the simple “Eve” description and realise that it is not at all compatible with the biblical version of events.

Q5. With the advent of next-generation sequencing and faster computing power, what are the key questions in human evolution that remain unsolved to date?

I would say that among the key questions that remained unresolved are the extent to which the ancestry to modern humans today can be traced back to a single population of African origin versus the ancestry contributed by integrating with the archaic humans. So far from the genomic sequencing evidence, we know that there is a non-African population signal of the Neanderthal- related ancestry. We also know that there is another type of archaic human that we didn’t even know existed and these are known as the Denisovans. They have contributed to the ancestry of the Oceania populations, particularly those in East Asia. That raises another question on what other types of archaic human were present at that time and did they also contribute to the ancestry of the modern humans. This is a question that is currently being pursued by scientists who are trying to obtain genomic information from ancient fossils.

Another big question is trying to understand the big genetic changes that were involved in making humans, human, and the origin of modern humans. The nearest living relatives of modern humans are the chimpanzees, and modern humans and chimpanzees diverged from the common ancestors somewhere around 7-8 million years ago or so. So, in principle, if we compare the genome sequence of modern humans and chimpanzee, we will have all the genetic differences between the two, and we should be able to figure out the genetic changes that gave rise to the species divergence. The problem is that there are about 30 million genetic differences between the human and the chimpanzee sequences and we still don’t know which are the important ones and which are the trivial ones. Figuring out the important fundamental changes that make modern humans remains a major hurdle.

Q6. What are the main challenges you face in your line of work?

Sample collection is always an ongoing issue that comes in two different ways. Firstly, getting access to fossils for DNA work is always a difficult task. It is understandable that these are very valuable fossils and the nature of the DNA work is destructive. You have to destroy a small part of the fossil to obtain the DNA. It is for this reason that curators are usually reluctant to allow scientists to have access to fossils and the former are very protective of the fossils.

The second part of the work is that my group does a lot of investigations on the genetic variation of modern human populations. This involves approaching different human populations and asking people if they are willing to provide samples for our work. One thing that makes things a lot easier compared to the past decade is that rather than having to stick a needle to collect blood, we just provide tubes for people to obtain a sample of their saliva and we can perform all the necessary genetic tests. Nevertheless, we still have to communicate with them and make them understand about our work. There are also certain groups that understandably don’t want to be involved, not comfortable with the idea of Europeans coming to collect samples from them, and that’s their right that you have to respect. In addition, there are various levels of government regulations and ethical approval that you have to go through and it is getting more and more difficult.

Despite these issues, I think more and more work in human evolutionary genetics are being done. Many of the communities are pleased and happy to see someone is taking interest in their genetic history, to learn and to study about them. Although these works are challenging, it is doable.

Prof Mark Stoneking

This interview was conducted by Dr. New Jaa Yien, a lecturer at the School of Science, Monash University Malaysia after a talk given by Prof. Mark Stoneking at Monash University Malaysia.

Part 2 of this interview will be published in the next issue, please stay tuned!

This article first appeared in the Scientific Malaysian Magazine Issue 11. Check out other articles in Issue 11 by downloading the PDF version for free here: Scientific Malaysian Magazine Issue 11 (PDF version)

References

[1] Cann, RL, Stoneking, M, Wilson, AC (1987). Mitochondrial DNA and human evolution. Nature, 325:31-36.

[2] http://www.nature.com/nature/journal/v325/n6099/abs/325031a0.html.

[3] http://www.telegraph.co.uk/news/science/evolution/10297124/Sir-David-Attenborough-Humans-have-stopped-evolving.html

Background Reading

http://en.wikipedia.org/wiki/Mark_Stoneking

http://io9.com/5879991/the-scientists-behind-mitochondrial-eve-tell-us-about-the-lucky-mother-who-changed-human-evolution-forever