In the NYT, a story on the frustrations that African-Americans are experiencing with DNA ancestry testing services:

DNA Tests Find Branches but Few Roots

HENRY LOUIS GATES JR., whose PBS special “African American Lives” explores the ancestry of famous African-Americans using DNA testing, has done more than anyone to help popularize such tests and companies that offer them. But recently this Harvard professor has become one of the industry’s critics.

Mr. Gates says his concerns date back to 2000, when a company told him his maternal ancestry could most likely be traced back to Egypt, probably to the Nubian ethnic group. Five years later, however, a test by a second company startled him. It concluded that his maternal ancestors were not Nubian or even African, but most likely European.

Why the completely different results? Mr. Gates said the first company never told him he had multiple genetic matches, most of them in Europe. “They told me what they thought I wanted to hear,” Mr. Gates said.

Telling Gates his ancestors haled from Nubia, on the upper Nile, was a particularly clever scam for the first company since Gates is about the color of a Nubian (thus obviating the need for Gates to have European ancestors), and Gates made a PBS documentary series called "Wonders of the African World," in which he took a camera crew around Africa looking for ancient ruins, and not finding all that many. In general, ancient Africans didn't seem to see much point in slaving in the hot sun to put up some big structure that tourists would someday be impressed with.

But Nubia has lots of cool looking pyramids, temples, and sculptures, complete with an undeciphered written language, at Jebel Barkal, Kush, and Meroe, and conquered Egypt and ruled as the 25th Egyptian Dynasty.

How exactly Gates' ancestors were supposed to get from Nubia (mostly in northern Sudan) to America wasn't explained, but that's all part of the romance of genealogy.

The article goes on to point out that customers' frustrations come not just from finding out that they had white ancestors, (especially in the direct male line, which Y-chromosome tests study), which reputable services warn about upfront, but also in pinning down just where in Africa their direct line male or female line (mitochondrial DNA test) ancestors came from.

From a genetic point of view, studying your direct male or female line ancestors (left or right edges of your family tree) is fairly pointless, since you only get from them, rather than from all your other ancestors, your small Y-chromosome or your mitochondrial DNA (which is separate from the rest of your genome). The main body of your DNA gets reshuffled with each new generation, so even if you are directly descended from Charlemagne or Mansa Musa, king of the gold-rich medieval Mali empire (who was such a big tipper that his famous 14th Century pilgrimage to Mecca lowered the world price of gold), you probably didn't get any useful but distinctive gene variants from the great man himself.

Still, traditional genealogy hobbyists tend to focus upon the direct male line down which surnames are descended (my father's family tree begins with "X Seiler, patriot from Lucern, c. 1290-c.1340") as a way to give focus to the teeming multitudes of ancestors, so there's nothing more or less silly about using DNA to focus on male or female direct line ancestors.

The second, more subtle problem customers find with African DNA analysis is that minor mutations among Africans aren't all that indicative, at least yet, of where any individuals direct male or female line ancestors came from.

Bert Ely, a geneticist at the University of South Carolina, was a co-founder of the African-American DNA Roots Project in 2000, hoping to use DNA tests as a way to find connections between African-Americans and ethnic groups in Africa.

“I originally thought that the mitochondrial DNA test might be a good way for African-Americans to trace their country of origin,” Mr. Ely said. “Now I’m coming to the opposite conclusion.”

Last October, he matched the DNA sequences of 170 African-Americans against those of 3,725 people living in Africa. He found that most African-Americans had genetic similarities to numerous ethnic groups in Africa, making it impossible to match African-Americans with a single ethnic group, as some companies assert they can do.

Mr. Ely also published a paper in which he tried to determine whether the country of origin of native Africans could be found by using mitochondrial DNA tests. Several of the Africans in the study matched multiple ethnic groups. For example, DNA results for a person from Ghana provided genetic matches with people in 20 African countries.

You are always hearing about how Africans are supposedly the most genetically diverse people on earth, but that's true mostly of the more-or-less nonfunctional genes that population geneticists focus upon because they don't want their genealogies messed up by convergent evolution.

What this statement is actually saying is that current sub-Saharan Africans' ancestors didn't go through an Out-of-Africa bottleneck because they've always been in Africa.

On the other hand, a huge fraction of the ancestry of current Africans stems from the "Bantu expansion" of agriculturalists out of the Cameroon-Nigeria region starting several thousand years ago, displacing hunter-gatherers such as Bushmen. When the Dutch arrived at Cape Town in 1652, the Bantu, whose crops weren't acclimated for Mediterranean climate and higher latitudes, hadn't yet reached the bottom of the continent. There are still lots of exotic groups within sub-Saharan Africa, such as Bushmen, tall Dinkas and small Pygmies, but most of the regions from which African-Americans came from are fairly homogeneously populated by farming descendants of the Bantu expansion. So, there hasn't been much time for many local mutations to emerge.

Moreover, there are relatively few physical barriers to movement within Africa, which ranks with Australia as the flattest continent, so Africans have continued to wander about. While some regions are dependent upon rivers for agriculture, such as the inland Niger delta, Africans were less tied down by specific water sources than Middle Easterners, who tended to settle around rivers such as the Nile, Euphrates, and Jordan, or around springs, as is common in the Holy Land. So, there has been a certain amount of movement over time — the rains fail in one place, so a group moves somewhere else. Perhaps because of the high disease burden, Africa was traditionally less densely populated than Europe or Asia, so land availability was less of a factor in creating a Malthusian trap than in Europe or Asia. Thus, it was easier to move about in Africa because other groups were less jealous in guarding their land than, say, the Romans or Chinese were.

Finally, sub-Saharan Africans tended not to exert such tight control over their womenfolk's fertility as Middle Easterners did.

The upshot is that it will take a lot more work to make African DNA analysis satisfyingly accurate for customers.