IN THE NEXT PART, PART III, I SHALL TALK ABOUT THE EGYPTIAN RESULTS AND PRESENT A CRITIQUE
Map showing the male migration routes based on the Y chromosome study of 10,000 indigenous individuals from all over the world (Adam in genetics is a designation given to the common ancestor from which all Y chromosomes descended)[1]
In Part I of this series, The National Geographic Genographic Project on The Egyptian Genetic Make-Up – Part I: The Egyptian Reaction (July 31, 2020), I talked about how the results of the Genographic Project on Egypt was misunderstood by the Arab Egyptian media. To understand the project properly and its results on Egypt, it is mandatory that we look in some detail at the project, which I am doing here.
Introduction
The Genographic Project (GP) was launched on 13 April 2005 by National Geographic, the International Business Machine Corporation (IBM) and the Waitt Family Foundation – all American. It was an ambitious endeavour in genetic anthropology. The last two funded the programme, while IBM acted as a biobank, interpreting the information in the biobank, finding patterns in the genetic data, and providing the computing infrastructure of the project. The project was approved by the University of Pennsylvania Social and Behavioural Sciences Institutional Review Board, and was headed by the American geneticist and anthropologist Spencer Wells.
The GP aimed at collecting 100,000 DNA blood samples from “aboriginal groups” worldwide in five continents and more from the public in an attempt to trace human migration out of Africa in the last 50,000 to 60,000 years.
The decision to make this project privately-funded and not funded by the federal government was a result of the failure of a previous ambitious project, the Human Genome Diversity Project (HGDP), which was conceived in 1991. It was accused of being racist and conducting “imperialist science”, and consequently the US government refused to fund it. $40m (£21m) were set aside for the GP, but that was largely augmented by selling genetic kits to public participants at $99-199 each.[2] Being privately funded was a concern to many, including Kenneth Weiss, a former HGDP organiser. He thought that the GP would not be subject to public scrutiny: “Decisions will be made privately rather than in the kind of open forum that the HGDP was going to for setting ethical standards, for making sure that the populations are not exploited, and that samples are not collected in a hit-and-run kind of way.”[3] For reassurance, Wells answered that the samples would be available for the scientific community to use on a collaborative basis, and that scientists willing to do research could approach the GP with their proposal. He added that the information gathered would not be patented, and would all be in the public domain, accessible to scientists studying human migrations. He also confirmed that the stored DNA would not leave the region where they were collected.[4]
Another HGDP organiser, Kenneth K. Kidd, had two concerns:
- That samples would not be established as cell lines but kept as stored DNA, pointing that these stored samples would not last long, and that the project would not worth the effort and money spent and would not provide that much useful information. Wells answered that many indigenous groups objected to the idea that a piece of their body would live on after their death. Further, he pointed that many geneticists had concerns about the genetic integrity of cell lines.
- As the initial phase of the GP was planned to focus on DNA from Y chromosomes and mitochondrial DNA (mtDNA), results obtained would not reflect the best kind of genetic markers (DNA markers), which are located in the autosomal chromosomes. Wells responded and said that as the project progressed they would expand in the future to include autosomal markers from the stored DNA, which they did in the later stages.[5]
What was known before the GP
Much was known before the GP about human migration and anthropological genetics, but as the reader will see later, the GP expanded that knowledge and improved on it. In this anthropological investigation of human migration, genetics, linguistics and archaeology aided each other, and it was known that the origin of modern humans (Homo sapiens) was in Africa, and for this Africa is known as “the cradle of humanity”.
It was estimated that the first humans appeared roughly 200,000 years ago in Africa. They remained confined to Africa for a long time, but for some reasons around 60,000 years ago humans started migrating out of Africa, mainly through Egypt’s Sinai and Bab al-Mandab Strait in the southern part of the Red Sea. Over time, they spread to Asia and Europe, and then later to the rest of the world. Migrations are usually made possible or prompted by historical events, such as the spread of agriculture from the Middle East into Europe; the appearance of the Roman Empire which brought nations together; the Jewish diaspora after the Fall of Jerusalem in 70 AD; the spread which Islam in the seventh century; and the slave trade up the Nile, particularly after the thirteenth century. These migrations caused the dispersion of regional populations’ genetic patterns.
Geneticists were able to trace this out-of-Africa migration by studying mutations, that served as genetic markers in the Y chromosome and mitochondrial DNA (mtDNA) of contemporaneous humans. The Y chromosome allows the paternal lineage of men to be traced back many generations; the mtDNA, on the other hand, is inherited maternally in both sexes, and was therefore used to trace maternal lineage of men and women. Both of these, the Y chromosome and the mtDNA, are described as non-combinant, meaning that during the process of cell division that gives rise to eggs and sperms no mixing of genetic material occurs between chromosomes, and this makes the tracking back across generations accurate.
Mutations are small variations between a person’s DNA and those around him or her. Basically they are changes that occur in the DNA sequence (the arrangement of the nucleic acids or the building blocks of the gene) that makes up a gene. They are rare, and in nearly all cases occurred once in the past, i.e., they are permanent, and so any two who share a rare mutation must have inherited it from a shared common ancestor. Mutation are therefore carried by all the descendants of the individual in whom the mutation first appeared. It is possible to estimate when or where these mutations happened. They tell us about the individual’s historical and prehistorical events in the individual’s ancestral history, but, even more important, of his or her ancestor’s migration route over thousands of years. Researchers are able to count a person’s individual rare mutations, which are used as genetic markers, and compare them to thousands of other people and so be able to relate him or her to geographical regions of the world, called ancestry regions, where the mutations first appeared and concentrated through marriage between neighbours. Even though the mutation occurred in time in a certain ancestry region, where it is highly concentrated, it is found in the individual who may be living thousands of miles away and in a different continent because his or her ancestors who carried the mutation had migrated in the past to where the individual presently lives.
Through the Y chromosome and mtDNA, and their mutations, the researchers, prior to the GP, were able to piece together a broad-brush picture of which populations moved when in the world and when. The reason that science in the pre-GP period was not able to build a fine picture of human migration was that by that time anthropological genetics was based on DNA samples donated by only around 10,000 “indigenous and traditional” people from around the world. What was available was a broad view of the patterns of human migration, representing just a small sample of humanity’s genetic diversity.
There was obviously a need to obtain a much bigger DNA samples size to get a more accurate and complete picture of human migration. And this is where the GP came. Even though it envisaged testing 100,000 samples at its launch in 2005, it ended in 2019 by testing over a million samples.
The three phases of GP
The GP thus was an ambitious project, aiming at piecing together a more informative picture of how the Earth was colonised, as our ancestors migrated from the African homeland and dispersed across the globe. It aimed at mapping the world migratory patterns dating back some 150,000 years and filling in the gaps in the knowledge of humankind migratory history. It was originally planned to be limited to 5 years but extended to 14 years instead, and went over three phases that were increasingly more sophisticated.
Phase I (Geno 1.0): Launched in 2005
The project enlisted 11 global regional scientific teams, comprising its fieldwork component.[6] It was the job of these teams to collect DNA samples in their continent regions from collaborating indigenous peoples, and then to analyse them.
In addition, another component was set up, called public participation. More than 470,000 members of the public (participants) worldwide took part in this phase. Each participant bought what was called Genographic Project DNA Public Participation Kit, and collected buccal (cheek) samples that contained DNA material and then sent back to a central laboratory based in the US for DNA analysis.[7] In 4-6 weeks, the participant’s results were made available to the participant in the project’s website to learn their personal ancient migratory history. The participant was provided with his or her deep ancestry (that is, their paternal and/or maternal journey)[8] and a customised migration map.
In this stage the project relied on the Y chromosome, the mtDNA and their mutations.
Phase II (Geno 2.0): Launched in 2012
In this phase, more than 270,000 participants joined in. This stage was more sophisticated, and used what was called GenoChip. It studied not only the Y chromosome DNA and the mtDNA but also the X chromosome and, more importantly, autosomal DNA. This provided more information, as mutations in them affect the whole genome and are not restricted to a single chromosome. They enabled the scientists to provide the ancestry regional ancestry of the participants in addition to their deep ancestry. Using an admixture (interbreeding) test, one of the components of autosomal DNA testing, that had been developed by Wells and Elhaik, it was possible to infer the participant’s geographical origins based on analysis of their genetic ancestry. In other words, the GP was able to classify individuals by assessing their proportion of genomic ancestry related to 9 geographical regions (ancestry regions). These ancestry regions were Sub-Saharan African, Southern African, Mediterranean, Northern European, Northeast Asian, Southeast Asian, Southwest Asian, Oceania, and Native American.
Geno 2.0 also found that modern-day populations around the world carry particular genetic blends of ancestry regional affiliations. They were called reference populations. The ancestry regional affiliations are counted as averages of the genetic blends of individuals from the particular country that are kept in the biobank database. These reference populations were mainly set up to compare the participants’ DNA results to these reference populations, and to estimate which of these reference populations are most similar to the participant in terms of the genetic markers the participant carries. Over 50 reference populations were set up including Egyptian, Tunisian, Lebanese, Kuwaiti, Iranian, British, Greek, German, Russian, Northern Indian, Southern Indian, Eastern Indian, Western Indian. As you can see, some of these populations represent countries while others represent geographical areas in the same country or merge with other countries (as the case in India, Pakistan, Nepal, and Bangladesh). What’s more is that some of what is called reference populations are actually ethnic groups within multi-ethnic countries, such as Yoruba people,[9] Khoisan,[10] Luhya,[11] Altaian,[12] Amerindian,[13] Oceanian,[14] and Tatar.[15]
It is clear that the reference populations based on countries were not going to be accurate representation of all in the country, since almost all countries include different racial and ethnic groups that don’t share much in common, including their genetic structure. GP admitted that these reference groups needed further scientific refinement.[16]
Phase III (Geno 2.0 Next Generation): Launched in 2015
GP developed an even more sophisticated chip, which allowed GP to analyse more than 300,000 DNA markers. The GP was thus enhanced by including more ancestral regions, now called “biographical regions”, 18 in total, mainly through dividing the previous larger ancestry regions of Geno 2.0 into smaller ones that are distinguishable by their specific mutations. These were:
- In Africa: Northern Africa, Eastern Africa, West and Central Africa, and Southern Africa.
- In Asia: Asia Minor, Arabia, Central Asia, Southern Asia, Eastern Asia, and Southeast Asia and Oceania.
- In Europe: Great Britain and Ireland, Scandinavia, Finland and Northern Siberia, West and Central Europe, Southern Europe, and Eastern Europe.
- America: Native American.
And another ethnic group, akin to Native American, was added – Jewish Diaspora. It is not clear why these were added (the first in Geno.2 and the second in Geno 2.0 Next Generation) as they do not represent a geographic area.
At the stage of Geno 2.0 Next Generation, GP refined its reference populations, including 60 of them. But while Egyptian remained as it was, other reference groups were divided, so, e.g., while British remained, by which we understand mainly English, a Scottish and an Irish reference groups appeared. This was admittance that in Geno 2.0 the British reference population wasn’t representative of the Scottish or Irish who have different ancestry blend. The Welsh were forgotten altogether. Also, other groups, such as the Bengali, appeared, which were simply included in previous large geographical areas (Eastern India in the Bengali case). Other reference populations which were not included at all in Geno 2.0, made their appearance: some were ethnic groups, such as the Ashkenazi Jews;[17] and some were based on countries, such as Ethiopian, Argentinian and Polish. The addition of these does not show much sophistication, as Ethiopia, Argentina and Poland are multi-ethnic, and their ancestry blend varies significantly from one ethnic group to the other. This is the same problem as we find in Egypt’s case, and other cases, but we will come to this later.
References
- Graciela Flores, New genome project, new controversy (The Scientist, 8 May, 2005).
- Paul Rincon, DNA project to trace human steps (BBC News, 13 April 2005).
- Genographic Project (Britannica Online Encyclopedia).
- Genographic Project (Wikipedia).
- A guide to Exploring Your Journey (Genographic Project).
- FAQ: About the Project (Genographic Project).
- January 2020 Update (Genographic Project).
- Your Regional Ancestry: Regions (Geno 2.0)
- Biogeographical Regions (Geno 2.0 Next Generation).
- Reference Populations (Geno 2.0 Next Generation).
- Molly McLaughlin and Molly K. McLaughlin, National Geographic Geno 2.0 (PCMag, 31 December 2018).
- Genographic Project (ISOGG).
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[1] The Genographic Project.
[2] It was $99 at the Phase I, then $199 at later phases.
[3] Graciela Flores, New genome project, new controversy in The Scientist (8 May, 2005).
[4] Ibid.
[5] Ibid.
[6] The fieldwork was conducted by investigators from research institutions and laboratories worldwide.
[7] The FTDNA Genomics Center in Houston, Texas.
[8] Men got their deep ancestry following both paternal and maternal lines while women got only that of their maternal line.
[9] The Yoruba people are an ethnic group who speak Yorba language, making around 15% of Nigeria’s population.
[10] Khoisan are the non-Bantu indigenous peoples of Southern Africa.
[11] Luhya are Bantu ethnic group in Kenya made up of 19 tribes.
[12] Altaians are a Turkic people living in Russia.
[13] Amerindians are members of one of the indigenous peoples of the Americas.
[14] Oceanians are natives of the islands of Oceania.
[15] Tartars are Turkic descendants of the Tartars who ruled central Asia in the 14th century and live now in Russia.
[16] Genographic Project, A Guide to Exploring Your Journey.
[17] Ashkenazi Jews are Jews of central and eastern Europe, who are part of the Jewish diaspora.