Zoom lens on the human family

Mathures Paul reports on a project that will map world migratory patterns dating back some 150,000 years and fill in the huge gaps in our knowledge of humankind’s migratory history

WHERE do we come from? Where are we headed? The objective of the Genographic Project, led by National Geographic explorer-in-residence Dr Spencer Wells, who is working with a team of renowned international scientists and IBM researchers, is to analyse historical patterns in DNA from participants around the world to better understand our human genetic roots. Dr Ajay K Royyuru, project leader, Computational Biology Centre, IBM Research (Watson Research Centre), shares some insights into IBM’s Genographic Project and discusses how IBM’s India Research Laboratory is contributing to the project. Excerpts:

Major findings so far…
A common origin of the entire human population was established on the basis of genetic evidence well before the Genographic Project. We are all Africans. The human species appeared in the 2.5 million years before the present time frame, in Africa. Human migration within and out of Africa has occurred substantively in the last 100,000 years. On the basis of genetic markers, one defines population groups that share a common ancestry. Such data can be analysed as a phylogeny (tree). Populations on close by branches share more recent common ancestors. The branches labelled “L-haplogroups” from mitochondrial DNA analysis are indeed the ones connected closest to the root, therefore these are populations ancestral to all other (non-L) populations. A majority of the present day L-population is in the African continent.

The current status of the project…
As of August 2008, over 40,000 samples have been collected. The resulting data will map world migratory patterns dating back some 150,000 years and will fill in the huge gaps in our knowledge of humankind’s migratory history. This data will eventually comprise the largest database of its kind.
In addition to the field research component, the general public around the world is invited to participate in the study by purchasing a Genographic Public Participation Kit. By sending in a simple cheek swab sample, a participant will learn about his or her own deep ancestry while contributing to the overall project. So far, over 265,000members of the general public have joined by purchasing Participation Kits from over 130 countries — two and a half times our five-year goal in the first three years!
In essence, it is a zoom lens on who we are and how we moved around the world. The Genographic Project will result in the creation of a global database of human genetic variation and associated anthropological data (language, social customs, etc). This database will serve as an invaluable scientific resource for the research community. Many indigenous and traditional populations around the world are facing strong challenges to their cultural identities. The Genographic Project will provide a snapshot of human genetic variation before we lose the cultural context necessary to make sense of the genetic data. Ultimately, we hope that the findings from the project will underscore how closely related we are to one another as part of the extended human family.

If humans have their origin in Adam, why are our skin tones different?
The origin of human species was on the African continent. “Adam” is just a short hand notation, has no particular ethnic or racial significance. Through the course of the last 100,000-plus years as the human species has expanded and migrated, populations have moved to varying latitudes and climates, resulting in various genetic adaptations. One such adaptation is the loss of pigmentation on skin (lighter skin), in northern latitudes, allowing for greater absorption of sunlight from skin, a crucial ingredient for synthesis of vitamin D.

While talking about the migratory history of the human species, Spencer Wells said there is a common male ancestor for all humans. How was the conclusion reached? Does the genetic Adam relate to the Adam of the Bible?
Phylogenetic analysis — reconstructing the family tree — from human genetic data provides the conclusive evidence of most recent common ancestry. Analysis of Y chromosome data allows inference of male ancestry, since the Y chromosome is carried exclusively by males. Such evidence points overwhelmingly towards the origin of the human species in Africa, since the genetic diversity in African populations far exceeds that outside Africa. Genetic “Adam”is simply a label, a short hand notation to refer to Most Recent Common Ancestor, a scientific term as explained above.
Inferring ancestry from present population will always fail to detect historical lineages that had no progeny. Therefore, one must conclude that in the time frame of the most recent common ancestor, there were many other individuals whose descendants have not made it into the present sampled population. Also, reconstructing the family tree to a most recent common ancestor does not imply that there was exactly one individual as the ancestor. Instead, it implies a population of ancestors that are genetically unresolved on the basis of current used genetic markers.
I am not a Biblical scholar, so I cannot comment on who the Biblical Adam was. All I can say is genetic evidence points to common human origin in Africa, dating to about 200,000 years before the present.

Where does IBM fit into the project?
This is the most ambitious genetic anthropology research initiative in history, with plans to gather one of the largest collections of DNA samples to map how humankind populated the planet. Our role in the partnership will be to handle all aspects of storage and analysis of this complex data. Ten of the world’s leading geneticists, working with indigenous and traditional peoples from across the globe, use our (IBM) technology to collect and analyse samples. Data gathered is analysed by IBM research, which generates conclusions about humanity’s migratory history.
IBM supports the Genographic Project in three main ways…
— First, the scientists use a novel IBM client solution that allows for simpler data collection in the field and allows the scientists to securely transmit this data to a central repository;
— Second, IBM designed and built a solution called the DNA Analysis Repository that houses the genetic information of hundreds of thousands of volunteers who have donated DNA to the Genographic Project, as well as data submitted by the scientists;
— Third, IBM’s Computational Biology Centre, one of the world’s foremost life sciences research facilities, is helping to analyse the data to infer patterns of ancestry, including eventually opening this massive database to researchers around the world at the conclusion of the five-year Genographic Project.
IBM has developed client software that allows the Principal Investigators in the field to collect, store and transfer the data that they are collecting. By creating a simple user interface and linking the software with genotyping equipment from Applied Biosystems, the Genographic client software allows the PI to create expeditions, manage phenotyping and genotyping, and then securely transmit that data back to a central repository to allow for further study from the entire Genographic Consortium. Currently, we have 11 scientists working in the field and have collected tens of thousands of DNA samples from participating indigenous groups, whose partnership is a vital component of the Genographic Project.
As this project is an international effort, a central DNA repository is critical to its success. IBM has developed a solution to manage this unprecedented mountain of genetic information — the DNA Analysis Repository. The Dar sits at National Geographic headquarters in Washington, DC, and is comprised of a Linux BladeCenter and a host of IBM software, including DB2 and Websphere. This central repository, and an IBM reporting interface to query it, allows for scientists all over the world to analyse this data to draw the migratory paths of our species back tens of thousands of years.
At the conclusion of the Genographic Project, this database will be made available to scientists to encourage further study.
IBM’s Computational Biology Centre provides critical analysis on the gathered data to infer patters of descent and shed light on the migratory paths of our species. The IBM CBC team, along with the rest of the Genographic Project Consortium, has authored several papers detailing the findings from the Genographic Project, with many more on the way.

In India, are experiments restricted to Madurai and Delhi?
Professor Rasamswamy Pitchappan at Madurai Kamraj University is leading the field research for the project in India. He has conducted several expeditions within India, to obtain samples from selected indigenous populations. He has already gathered samples from Tamil Nadu, Kerala, Andhra Pradesh, Orissa, Chattisgarh, Assam. And plans are underway to gather samples from all across the Indian subcontinent.

Does the project state anything about the people of eastern and north-eastern India?
Evidence from recorded history (for instance, cultural, anthropological, linguistic) and the limited genetic evidence gathered from prior studies indicates that the Indian subcontinent has a high diversity of populations and holds significant clues to global migratory patterns. Professor Pitchappan and Dr Spencer Wells’ prior work, for instance, revealed the migration of Australian indigenous population from Africa, via southern India. We hope to uncover many such patterns in global migration, by relating and analysing the data from different regions of the world.