Condoleezza Rice, former US Secretary of State and national security adviser, ought to be a tough woman to surprise. Yet when Henry Louis Gates Jr, host of a US television series called Finding Your Roots, revealed that nearly half of her genetic ancestry could be traced to Europe, Rice, an African American, told Gates, “I’m stunned.”
Although it is no secret that many African Americans have some European ancestry — a legacy of the transatlantic slave trade — advances in DNA analysis are beginning to provide more detailed insight for individuals. Commercial ancestry testing, once the province of limited information of dubious accuracy, is taking advantage of whole-genome scans, sophisticated analyses and ever-deeper databases of human genetic diversity to help people to answer a simple question: where am I from?
Until a few years ago, most ancestry tests for individuals relied on short stretches of DNA in cell-powering organelles called mitochondria, which are inherited through the mother, or on the Y chromosome, which a father passes down to his sons. As humans fanned out from Africa some 40,000 to 80,000 years ago and populated the world, mitochondria and Y chromosomes developed specific changes that were tied to different populations. Yet these ‘uniparental markers’, which chart an unbroken chain back through either the maternal or paternal line, are rarely unique to a population.
For example, a set of Y-chromosome markers called Haplogroup R1b is common among Western European men, but a small fraction of North Africans have it, too. Similarly, “if men have a Y chromosome that is more common in Scandinavia than England, they’re convinced they’re a Viking”, says Mark Jobling, a geneticist at the University of Leicester, UK. But that is not necessarily the case. Such nuances are not always conveyed by the companies that offer such services, notes Jobling. What’s more, Y-chromosome or mitochondrial markers trace only one strand in a person’s ancestry.
A more complete picture lurks in the full genome. It is trickier to tease out ancestry information from our 22 pairs of non-sex chromosomes, because whole stretches of DNA in these are mixed up in every generation. But in recent years, researchers have made strides mapping the ancestry of certain populations — including Europeans (J. Novembre et al. Nature 456, 98–101; 2008) and Indians (D. Reich et al. Nature 461, 489–494; 2009) — by simultaneously analysing hundreds of thousands of single DNA letter changes across the genome. These surveys of human genetic diversity, including the International HapMap Project and the 1000 Genomes Project, have provided the data needed for more sophisticated ancestry testing.
Genetics company 23andMe, based in Mountain View, California, was one of the first to offer its customers ancestry analysis based on whole-genome scans, at a cost of US$300–400. The company worked closely with the television network PBS on the latest series of Finding Your Roots, which uses whole-genome analysis to investigate the genealogy and deeper ancestry of figures such as Rice, actor Kevin Bacon and celebrity entrepreneur Martha Stewart.
The discovery that a significant amount of Rice’s genetic ancestry can be traced to Europe came from an analysis called chromosome painting (see ‘Painting your ancestry’), in which genetic variations in small chunks of each chromosome are compared with matching regions in different populations around the world (European, West African and East Asian in the case of 23andMe, although the company is soon due to extend the analysis to 20 populations, including Native American and South Asian).
Carlos Bustamante, a population geneticist at Stanford University in California, advises 23andMe and Ancestry.com, which runs a testing service called AncestryDNA from its base in Provo, Utah. He says that he works with scientists at the companies to make sure that the information they offer customers stands up to scrutiny. For instance, Ancestry.com’s predictions — which include possible connections to customers who might be distant relatives, on the basis of shared stretches of chromosomes — come with confidence estimates. “The important thing is to say ‘here are the limits of what we know’,” says Bustamante.
“If men have a Y chromosome that is more common in Scandinavia, they’re convinced they’re a Viking.”
As ancestry testing trawls deeper into the genome, such cautionary notes will become more important. It may be possible, for instance, to determine more precisely when someone’s ancestors from different populations interbred, says Sarah Tishkoff, a geneticist at the University of Pennsylvania in Philadelphia. But such calculations make assumptions about past population sizes and other demographic factors. Conveying such caveats to personal-genomics customers could prove difficult.
Individuals may soon be able to trace the geographic origins of their ancestors more precisely. An academic project called People of the British Isles has distinguished the genetic signatures of people from neighbouring UK counties. This level of precision was attained by analysing the genomes of people from rural regions, whose ancestors tended to live in the same place, says project leader Walter Bodmer, a geneticist at the University of Oxford, UK. Genome information from these individuals could form a database that others could use to track their distant ancestors.
Tishkoff says that deeper surveys of human genetic diversity are needed elsewhere, particularly in Africa. Angola, for example, where many slaves originated, is not represented in existing surveys, making it impossible for African Americans to trace ancestors who once lived there. “You can’t tell someone they can trace ancestry to a certain region if that region has never been studied,” she says.
- Journal name:
- Nature
- Volume:
- 486,
- Pages:
- 17
- Date published:
- ()
- DOI:
- doi:10.1038/486017a

The efforts to identify genotypes associated with smallish geographic regions is all fine and fascinating for those people whose ancestors are a relatively homogeneous bunch, but us poor Americans have a different sort of problem. Condoleeza Rice is an example (although I doubt the accuracy of the data Gates used), but I know my own much better. Most of my ancestors were early settlers (English and Dutch) of the northeastern US states, mixed over the years with a few Irish (for flavor) some of whose forbears came from England. There may even be some Scots in there. I have some idea where many of these people (particularly the Dutch) came from, but really it is a big mishmash of origins throughout the British Isles and the Netherlands. I yearn for the day when we will understand the genotypes well enough for me to sort this out, but I am afraid I may not live to see it. And I would guess that mine is a less complex problem than many other Americans'.
Pinpointing a Genetic Homeland is not too difficult for those of Scottish ancestry given the shared Clan system and well documented Clan territories of Scotland. For those of English ancestry it is certainly more of a challenge, but not impossible, for it to work there must be a link between a surname and the land which is often missing in English surnames. Having said that many English surnames are topographic in origin. I have no experience of Welsh surnames as yet.
I suggest the origins of surnames in England, Scotland and Wales and their genetic homelands is far more complex than this – and ignores much research carried out over many years in Britain. The book by George Redmonds, Turi King and David Hey: Surnames, DNA and Family History, 2011, is a good recent starting point. But it is impossible to have a useful debate on a subject of this complexity on this public forum. There are specific organisations and bulletin boards where this subject is discussed in the necessary detail required.
Dear Sir
I am a scientist and I was curious to know how DNA could shed light on my ancestry. I was curious as to my origins as I grew up in Ireland with a notable 'English' surname (Bowes). What I was looking for was a match to someone who could fill in the blanks of my genealogical paper trail which reached back only 100 years, but what I got instead was the names of many individuals with whom I shared a common male ancestor (via the results of a 37 marker Y-DNA test). There were many people with lots of different surnames represented in those results, and as a scientist I wondered how I can match many individuals with diverse surnames?
The answer is surprisingly quite simple; when surnames became common around 1000 years ago, my direct male ancestor lived in a small area where he picked his surname, surrounded by others some of whom he was related to but who crucially picked other surnames. Jump forward 1000 years and there will be many descendants of that small group some of whom will today undergo commercial ancestral Y-DNA testing. So what you typically see with the results of a Y-DNA test is a snapshot of your medieval ancestors neighbours (when he picked his surname), and given that in early census data surnames could still be found concentrated in the areas they first arose, by examining surname distribution mapping you can pinpoint a 'Genetic Homeland.'
The Genetic Homeland is the very small area where your ancestors lived for 100's if not 1000's of years, where he first picked his surname, and where they left their mark in the placenames of that area and in the DNA of its current inhabitants. To confirm the association one merely needs to DNA test individuals (your distant relatives) who still live in the pinpointed area.
It is a method that is dependent on the quantity and quality of matches so it will not work with everyone. I also advise testing with Family Tree DNA as their database is by far the largest and it is the size of the Y-DNA database (people testing) that allows one to pinpoint a Genetic Homeland.
Dr Tyrone Bowes
www.irishorigenes.com
www.scottishorigenes.com
www.englishorigenes.com
Science Journalists (along with their editors and supervisors at Nature) such as Ewen Callaway should be tasked with having more than a rudimentary level of what they are writing about if their publication seeks monetary compensation from readers.
IMHO, Mr. Callaway completely flubbed the distinctions and nuances and uses for the various forms of Genetic Genealogy DNA tests. The subtitle of his story is: Companies use whole genomes to trace geographical origins
Well, that subtitle and statement is not factual and the Big 3 of Genetic Genealogy companies such as 23andMe / Family Tree DNA / AncestryDNA do not presently offer Whole Genome / WGS tests to their customers to trace geographical family origins or for any other reason related to ancestry and family history.
These 3 companies along with Katherine Borges, the head of ISOGG should seek to clarify this with Mr. Callaway and Nature and ask for a followup story and/or correction/clarification.
I believe such clarification should include information on Genetic Genealogy tests such as: 1. Y-DNA; 2. mtDNA; 3. atDNA; 4. WGS. An under US$1000 WGS (Whole Genome Scan) will eventually be offered (2013?) in various grades or flavors. A. Medical Grade WGS; B. Research Grade WGS; C. Genetic Genealogy WGS. See more at http://genomics.xprize.org/competition-details/frequently-asked-questions
I respectfully disagree with Brian Swann if it is his belief that <em>readers</em> of Nature should serve as <em>surrogate editors</em>. Mr. Swann said: "I think it is only fair to the author of the article to point out the difference between a Whole Genome Scan and a Whole Genome Sequence." I would suggest that this task is the primary job of the editor or supervisor of Mr. Callaway.
As a followup, maybe Mr. Callaway could interview Brian Swann and Katherine Borges of ISOGG along with persons at 23andMe / Family Tree DNA / AncestryDNA. Perhaps he could also look at what a BCG – Board Certified Genealogist is tasked with. See http://www.bcgcertification.org/ and http://legalgenealogist.com/
$199 / Year for Nature is steep compared against FREE from excellent information and opinions from Science Bloggers such as "Dienekes' Anthropology Blog": http://dienekes.blogspot.com/2012/06/how-journals-once-facilitated-and-now.html
Let's see what Nature and ISOGG are going to do. The ball is in your court.
Brian – I think you would have been really interested by the work People of the British Isles had on show at the International Congress of Human Genetics in Montreal last year. I'm looking forward to the next paper. If you're interested, the abstract "475F People of the British Isles: An analysis of fine-scale population structure in a UK control population." is here: http://www.ichg2011.org/pdf/ICHG%20Poster%20Abstracts.pdf
Whilst I would agree with most of the comments posted by George Jones (R1b-L371) - I think it is only fair to the author of the article to point out the difference between a Whole Genome Scan and a Whole Genome Sequence. The references to 23andMe point to Whole Genome Scans and not Sequencing. This would be impossible at the costs charged by 23andMe, Family Tree DNA or Ancestry.
As a R1b-L371 Jones ... I know my paternal Jones clan and the Jones progenitor originated in Anglesey Wales circa 1067. That's not "Pinpoint Accuracy" ... but it is "Decent Accuracy". L371 is a terminal Y-DNA SNP.
Perhaps Nature and this reporter can explain their headline: Ancestry testing goes for pinpoint accuracy. They appear to be focusing on Geographic accuracy to the exclusion of other types of accuracy in Genetic Genealogy.
There are 3 major components to Genetic Genealogy accuracy: 1. Place or Geographic accuracy; 2. Timeframe / Generation Number accuracy; 3. Clan or Population accuracy.
1. "Geographic Pinpoint Accuracy" ... is it for a defined Geographical area such as: a Continent? / a Country? / a County?
2. "Time Pinpoint Accuracy" in what time frame: 500BC or in the 1500s when looking at SNP or Y-DNA STR mutation rates?
3. Is it for a Ref./Sample Population group based upon:
a. DNA analysis of atDNA or MtDNA or Y-DNA / Y-STR?
b. Surname analysis ?
c. Genealogical analysis ?
d. Anthropology analysis ?
e. Language analysis ?
f. Climate analysis ?
g. Historical analysis
Many are relying way too much on a DNA test and analysis. This analysis often from companies with PhDs in Population Genetics that don't see the entire elephant! This goes specially for companies such as 23andMe which appears to be more concerned with Health & Medical Genetics than Genetic Genealogy.
Nature needs to run a correction. A $299 23andMe atDNA test is far from being a "Whole or Full Genome" test as the article stated: "The company worked closely with the television network PBS on the latest series of Finding Your Roots, which uses whole-genome analysis ..."
The Finding Your Roots team used a 23andMe admixture analysis for Condoleeza Rice based on her atDNA test.
This 3 Part BGA Population analysis revealed that her genetic makeup is "estimated" as: 51% African, 40% European and 9% Native American / East Asian. It appears a good part of the 40% European is on her paternal side.
The European percent is on average 22% for African Americans. So Rice has about twice that amount of European / White admixture ancestry ... maybe that is what stunned her. http://www.nytimes.com/2012/01/03/science/genome-research-points-to-adaptation-among-early-african-americans.html?pagewanted=all
What I find interesting is this from the Nature reporter: " ... in which genetic variations in small chunks of each chromosome are compared with matching regions in different populations around the world (European, West African and East Asian in the case of 23andMe, although the company is soon due to extend the analysis to 20 Populations, including Native American and South Asian).
Persons like Razib Khan have been all over 23andMe for using just 3 Ref./Sample Populations. He wrote about this in a blog posting: "Finding Fake Roots" http://blogs.discovermagazine.com/gnxp/2012/05/finding-fake-roots/
So when is 23andMe going to formally announce they will start using 20 Ref/Sample Populations versus their current 3? Have these Ref/Sample Populations been peer reviewed?
Did Carlos Bustamante help develop these 20 Ref/Sample Populations for 23andMe?
Did he also do similar work on this for AncestryDNA which is just launching their atDNA tests?
How do these "new 23andMe" 20 Ref/Sample Populations compare to what Family Tree DNA is using?
Also, it appears that Ancestry.com is trying to put itself up for sale ... and that Google might be in the market for it. http://www.forbes.com/sites/ericsavitz/2012/06/06/ancestry-com-for-sale/ Who else could be going after Ancestry.com?
The People of the British Isles Project is almost certainly unable to distinguish counties in Britain – except in certain specialist cases. Counties towards the margins of the British Isles, like Cornwall and Devon, may have genetic features in their populations back in time which can be used to identify them. Others such as Warwickshire or Norfolk may prove a lot more problematical.
Also great care has to be taken to distinguish between the various DNA tests for family history and what they can and cannot deliver. It is important to get unbiased advice about testing companies before jumping in. This article actually mentions three types of DNA test for ancestry and two companies – but does not include the recognised leader in the industry – Family Tree DNA of Houston, Texas.
The International Society of Genetic Genealogy (ISOGG) can help in this respect.
Brian P. Swann
ISOGG Regional Co-ordinator, England & Wales