FOCUS9

0DUFK 1R 1 ( : 6 / ( 7 7 ( 5 2 ) ) ( 0 6 )('(5$7,21 2) (8523($1 0,&52%,2/2*,&$/ 62&,(7,(6

The journey of man, told by bacteria Bacteria tell a lot of stories. In the story of the human migration, the Y-chromosome and mitochondrial DNA (mtDNA) play major roles. Where does microbiology step in? For one, there is evidence that mitochondria were once primitive bacterial cells. Or are descendants of bacteria. Some scientists even argue that mitochondria are bacteria and should be given their own taxonomy.

The mtDNA and the Y-chromosome are what the group of Geneticist and National Geographic Explorer-in-Residence Spencer Wells analyzes to give us a clue on our past as a people. His research points to a Y-chromosomal Adam in Africa as the one who fathered all human beings alive today. Read on as Wells talks about his research and his own DNA. FEMS Focus: During your research, you said that we came from one single ancestor in Africa. Is this correct?

Spencer Wells (SW): Well, we can trace back to a single individual who gave rise

Source: nationalgeographic.com

Spencer Wells is a geneticist and anthropologist, an Explorer-in-Residence at the National Geographic Society, and Frank H.T. Rhodes Class of ‘56 Professor at Cornell University, US. He obtained a Bachelor of Science in Biology from the University of Texas at Austin in 1988, and a Ph.D. in Biology from Harvard University in 1994.

He was a postdoctoral fellow at Stanford University 1994-98, and a research fellow at Oxford University 1999-2000.

Wells did his Ph.D. work under Richard Lewontin, and later his postdoctoral research with Luigi Luca Cavalli-Sforza and Sir Walter Bodmer. His work, which has helped to establish the critical role played

to all Y-chromosomes or the mtDNA types of today. They weren’t the only people alive at that point but they were the ones who were lucky enough to leave their lineage down to the present-day.

by Central Asia in the peopling of the world, has been published in journals such as Science, American Journal of Human Genetics, and the Proceedings of the National Academy of Sciences.

He wrote the book “The Journey of Man: A Genetic Odyssey” in 2002, which explains how genetic data has been used to trace human migrations over the past 50,000 years, when modern humans first migrated outside of Africa. Wells also wrote and presented the PBS/National Geographic documentary of the same name. By analyzing DNA from people in all regions of the world, Wells has concluded that all humans alive today descend from a single man who lived in Africa around 60,000 90,000 years ago, a man also known as Y-chromosomal Adam.

Since 2005, Wells has headed The Genographic Project, undertaken by the National Geographic Society, IBM, and the Waitt Family Foundation, which aims to create a full picture of how our ancestors populated the planet by analyzing DNA samples from around the world.

He also wrote the books “Deep Ancestry: Inside the Genographic Project” in 2006 and “Pandora’s Seed: The Unforeseen Cost of Civilization” in 2010. (source: Wikipedia)

From the Editorial Team In November last year, FEMS had the chance to have a one-on-one interview with famous geneticist and anthropologist Dr Spencer Wells of the National Geographic Society. We talked to him about the journey of man from Africa to all known parts of the world. Wells is the Director of the Genographic Project of the National Geographic Society. He started the project in 2005, collaborating with indigenous peoples with the hope to form the largest database of human genotypes in the world. At the moment, the Genographic team already has more than 200,000 samples of DNA in its possession, from people all over the world. All of these tell that all humans alive today, even those born and living on different continents, share a common ancestor who lived in Africa 60,000 years ago. This story is told by the Y-chromosome and mitochondrial DNA, genetic markers that point to our ancestors. What does this mean to microbiology? That is what this issue is all about!

Tone Tønjum & Chared Verschuur Editors

What caused the migration of the human race?

Why did we leave Africa?

SW: It was probably a population expansion. We see evidence that the human population, after going through a bottleneck effect, whereas it was reduced in size, significantly, there might have been only 2 or 3,000 people alive if we go back to 70,000 years ago. We expanded back from that. We expanded in Africa and some people started to leave. So it’s probably, literally, an expanding population of like, some people beyond Asia and the Americas.

If we all came from Africa, why are our colors different?

SW: We’ve adapted to different climate regimes around the world. That’s probably the main reason. It’s literally adaptation. Skin color is the best example of that. We evolved in the tropics, in Africa on the Savannahs, with a lot of sunlight distracting our skin so we needed some kind of natural sunscreen.

That’s the reason people living in the tropics, people living in Africa, have darker skin.

As we left the tropics and moved to higher latitudes – people moving into Central Asia, moving into Europe and North-Eastern Asia – you have to lose some of that pigmentation because you have to allow a little bit of light through the deeper layers of your skin so you can synthesize vitamin D which we don’t normally get in our diets. If you don’t do that, then your children get rickets and osteoporosis. If you’re running around making a living as a hunter-gatherer, that’s not a good thing. So we adapted by losing some of the pigmentation. That’s why people in higher latitudes have lighter skin. That played a big role. Probably also something called sexual selection, of course, like Darwin talked about. And that’s the fact that we choose mates on the basis of what we find attractive and that varies according to where you are in the world. So what people find attractive in Scotland is not necessarily what they find attractive in the Philippines or somewhere else. So when people chose little characteristics that they find attractive, these probably helped to mold things like the shape of the nose, the eye shape and so on.

Are you concentrating only on the DNA markers of indigenous peoples and why?

SW: Scientifically, yes, they tend to be more useful because they retain the geographic context in which the genetic pattern origiPutative modern and ancient co-migrations of humans and Helicobacter pylori. Arrows indicate specific migrations of humans and H. pylori populations. BP, years before present.

Source: Falush D et al., Science 299 (5612), 1582-1585, 2003

nated and so they have this link to their geography that most other people have lost because we’ve all moved around. I lived in Washington D.C. but my ancestors all come from Northern and Western Europe. And so, indigenous peoples allow us to look back many generations in the past.

Mitochondrial DNA’s role in evolution DNA is present inside the nucleus of every cell of our body, but also the DNA of the cell’s mitochondria is commonly used to construct evolutionary trees.

Mitochondrial DNA (mtDNA) — maternal DNA — is used to construct evolutionary trees.

Mitochondria have their own genome of about 16,500 bp that exists outside of the cell nucleus.

Each mtDNA contains genes encoding 13 protein, 22 tRNAs and 2 rRNAs, mostly involved in energy metabolism.

They are present in large numbers in each cell, so fewer samples is required. mtDNA is inherited only from the mother, which allows tracing of a direct genetic line. mtDNAs have a higher rate of substitutions (mutations where one nucleotide is replaced with another) than nuclear DNA, making it easier to resolve differences between closely related individuals. mtDNAs don’t recombine. The process of recombination in nuclear DNA (except the Y chromosome) mixes sections of DNA from the mother and the father creating a garbled genetic history.

•

Why focus on just the Y-chromosome and not the X-chromosome?

SW: We focus on the Y-chromosome and mtDNA, so the male and female sides are

• • •

The Genographic Project The Genographic Project is a multi-year research initiative which seeks to chart new knowledge about the migratory history of the human species by using sophisticated laboratory and computer analysis of DNA contributed by hundreds of thousands of people from around the world. In this unprecedented research effort in real time, the Genographic Project is closing the gaps of what science knows today about humankind’s ancient migration stories.

National Geographic Explorer-in-Residence Dr Spencer Wells and a team of renowned international scientists and IBM researchers analyze historical patterns in DNA from participants around the world to better understand our human genetic roots. The three components of the project are: (1) to gather field research data in collaboration with indigenous and traditional peoples around the world; (2) to invite the general public to join the project by purchasing a Genographic Project Public Participation Kit; and (3) to use proceeds from Genographic Public Participation Kit sales to further field research and the Genographic Legacy Fund which in turn supports indigenous conservation and revitalization projects. The Project is anonymous, nonmedical, non-profit and all results will be placed in the public domain following scientific peer publication. (source: www.nationalgeographic.com/genographic) represented, because these are the most useful markers. It’s primarily due to the fact that they don’t go through the shuffling effect of recombination so we can trace on broken lineages back in time. But we’re not limiting ourselves to that. Initially, we’re studying the Y and the mtDNA in all of the samples and we are starting to expand into other areas of the genome as well.

•

ing to move up from Iberia, from presentday Spain. So it’s a Basque lineage or Spanish lineage that originally came in from Central Asia around 35-40,000 years ago. Before all that, they were in the Middle East and ultimately, of course, in Africa. So it’s all about that long journey.

What can you say is the newest cutting-edge in your field?

Mitochondria are the energy-factories of eukaryotic cells suggested to originate from bacteria.

Mitochondria have their own genome (mtDNA), which is inherited only from the mother.

Source: Dreamstime.com

Do you also analyze that (microbial DNA)?

What is the nature of the coordinated human and microbe molecular clocks and development that is taking place and shaping the current planet features of the earth? Why does each person carry its own strain of i.e. Helicobacter pylori in its stomach?

And how has bacteria affected life on earth and genealogy?

SW: It turns out that humans actually are commensal organisms, so we have a lot of microorganisms moving inside of ourselves as you know and one of those would be H. pylori. It turns out you can actually track the spread of certain strains of H. pylori and they mimic the spread of humans because when we move, the bacteria are moving as well.

That’s another way of looking at human migrations.

So it’s not just DNA? SW: Well, it’s the DNA from those microorganisms. You can analyze it the same way you analyze human DNA.

SW: We don’t, but many people have done that and it’s something that we might consider doing in the future.

SW: Well, the primary effect most recently has been the spread of epidemic diseases -many of those brought about by the domestication of animals. A lot of the diseases we think of as being human have actually been introduced from the animals we domesticated. Bacteria have thereby affected human health of the last 10,000 years. And in some cases, there have been epidemics, the bubonic plague, for instance, the black plague of Europe. They estimate that maybe a third of Europe’s population was killed by that. So it (bacterial migration) has had a significant effect on human population history.

Have you traced your own DNA? If yes, what did you find out?

SW: I have. I have a very typically North Western European Y-chromosome for in-

stance. Obviously, I got it from my father.

His side of the family, his father’s side comes from England ultimately. It’s a lineage we call R1D and it’s carried by about 70% of the men in England and it moved in to England from further South at the end of the last Ice Age so it’s when the ice sheets were retreating after the last glacial maximum it was start-

SW: It’s the ability to analyze hundreds of thousands of single nucleotide polymorphisms (SNPs) at the same time. Genome scans. So you are not limited to old-fashioned DNA sequencing or doing one SNP at a time, you can do many in parallel. We’re starting to explore some of those high through-put technologies and apply them to this kind of work.

The bacterium Helicobacter pylori is the cause of gastric ulcer in humans.

Source: Marina Aspholm

www.fems-microbiology.org RIW EHPM I (

W VERX

7 + ERH XW *)1 REP W +VER S M X E I 2 W

W 7 I *)1P 'SRKV

E

R I S M LMTW .YR 6IK PS[W P I *

VGL IWIE 6

RXW 7 I R Y +VE *)1 .

X W M X GMIR RK 7 M X M W 7 :M .YRI RGI *)1 RHE I X X %

XMRK

1II +VERXW 7 1

*)

V I IQF 7ITX

Links and Resources https://genographic.nationalgeographic. com/genographic http://www.actionbioscience.org/ evolution/ingman.html http://www.ur.umich.edu/9900/ Jan17_00/12.htm http://www.geneticorigins.org/mito/ intro.html http://www.ucl.ac.uk/tcga/ http://www.leipzig-school.eva.mpg.de/ pdf/Stoneking_mtDNA_review.pdf

Register as a FEMS Affiliate!

The FEMS Focus is published by the FEMS Central Office.

Whom to contact? Prof. Dr Tone Tønjum (tone.tonjum@medisin.uio.no).

Design: Zak Princic Production: Ilumina.si FEMS is a registered charity (no. 1072117) and also a company limited by guarantee (no. 3565643). © 2011 Federation of European Microbiological Societies

Online subscription to the full set of FEMS Journals for only 185 euros

Thematic issue now available

FEMS Central Office Keverling Buismanweg 4 2628 CL Delft The Netherlands Tel: +31-15-269 3920 Fax: +31-15-269 3921 E-mail: fems@fems-microbiology.org