Newsletter #13

Cousin Marriages Produce More Children

Science 8 February 2008:
Vol. 319. no. 5864, pp. 813 - 816

An Association Between the Kinship and Fertility of Human Couples

Agnar Helgason et al.

Previous studies have reported that related human couples tend to produce more children than unrelated couples but have been unable to determine whether this difference is biological or stems from socioeconomic variables. Our results, drawn from all known couples of the Icelandic population born between 1800 and 1965, show a significant positive association between kinship and fertility, with the greatest reproductive success observed for couples related at the level of third and fourth cousins. Owing to the relative socioeconomic homogeneity of Icelanders, and the observation of highly significant differences in the fertility of couples separated by very fine intervals of kinship, we conclude that this association is likely to have a biological basis.


Female Perogative
Male Presumption

Science 25 January 2008:
Vol. 319. no. 5862

Female choice is thought to drive evolution through sexual selection. It has been assumed that females over time would show consistent preferences for the same male traits. However, Chaine and Lyon (p. 459; cover) found in a long-term study of sexual selection in lark buntings that females have flexible patterns of choice for male traits over several years. This finding explains both the stability of traits under sexual selection and the evolution of multiple male sexual signals. Analyses of phenotypic selection with short time frames can lead to incorrect predictions about the trajectory of sexual selection, which might explain earlier contradictory findings.

DNA SEQUENCING:
A Plan to Capture Human Diversity in 1000 Genomes

Jocelyn Kaiser

Science 25 January 2008:
Vol. 319. no. 5862, p. 395

Over the next 3 years, an international team plans to create a massive new catalog containing the complete genome sequences of 1000 individuals. It will help fill out the list of new genetic markers for common diseases that came out in 2007.


BREAKTHROUGH OF THE YEAR:
Human Genetic Variation

Elizabeth Pennisi

Science 318/5858 (21 December 2007) 1842-43.

Equipped with faster, cheaper technologies for sequencing DNA and assessing variation in genomes on scales ranging from one to millions of bases, researchers are finding out how truly different we are from one another. Read article .


Genetics News Highlight of 2007
According to the Editors of Nature

First whole human genome decoded

James Watson, co-discoverer of the structure of DNA, and genomics pioneer Craig Venter announced that their full genomes had been sequenced. The achievements were the first in an anticipated wave of personal-genome sequencing and crucial steps towards personalized medicines tailored to an individual's genetic makeup. Watson's genome, announced in June, was analysed by Connecticut company 454 Life Sciences' new rapid-sequencing technique. Venter's, published in September, was the first fully sequenced diploid genome — detailing DNA inherited from both parents — and revealed that human genetic variation is greater than previously thought.

In November, Google-backed Californian biotech firm 23andMe launched a $1,000 personal genome service; the same month that Icelandic deCODE genetics offered DNA testing for disease-linked genes for the same price. And 2007 saw a splurge of research papers from genome-wide disease-association studies, including diabetes and cancer.

New Evolution Textbook Receives Good Review

A textbook covering all aspects of evolution puts the spotlight on the molecular motor that drives it.

Evolution, by Nicholas H. Barton, Derek E. G. Briggs, Jonathan A. Eisen, David B. Goldstein & Nipam H. Patel

Cold Spring Harbor Laboratory Press: 2007. 833 pp. $100

Keeping pace with change

A review by Daniel Hart

Textbooks in evolutionary biology have generally kept pace with [recent] changes and several excellent books are available. This new one by Barton and colleagues is among the best. The production quality is superb in layout, composition, typesetting, colour palette, illustrations and gorgeous half-tones; and the writing is excellent, as one might expect from such a stellar cast of experts in population genetics, palaeontology, human genetics, bacterial genomics and developmental biology (respectively).

The book is in four parts. The first is a history of evolutionary thinking and evidence for the evolutionary process, which clarifies common misconceptions about evolution and rebuts 'intelligent design'. The latter is unfortunately necessary in the United States, where people who think that space aliens have landed on Earth outnumber those who believe in the darwinian theory of human evolution by about 3:1.

Part I also includes an excellent introduction to molecular biology, although I suspect that much of this duplicates what most students already know. Part II, on the origin and diversification of life, is up to date with discussions on the last universal common ancestor, as well as being an outstanding introduction to evo-devo. Part III comprises about half the book and deals with the genetic mechanisms of evolution, including speciation, in a treatment that is fresh, thorough and professional. Subtle concepts, including Fisher's geometrical theory of adaptation and the coalescent, are clearly described with minimal mathematics. The final section is devoted to human diversity and evolution, and includes an engaging discussion of human nature.

This book may not fit every instructor's needs. Some may prefer a different balance of origin, diversity, molecular evolution, population genetics and human evolution, or they may need a textbook written at a different level. But every instructor should examine this book and make an individual decision.

Turkish Population Not as Asian as You May Think

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans

Ceren Caner Berkman et al.

American Journal of Physical Anthropology (online early) 10.1002

From Dieneke's Anthropology Blog: "In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. . . . Together with the data compiled from other databases, the similarity of the Anatolian population to that of the Balkans and Central Asia has been visualized by multidimensional scaling method. Analysis suggested that, genetically, Anatolia is more closely related with the Balkan populations than to the Central Asian populations. . . . In the present study, the Central Asian contribution to Anatolia was estimated as 13%. This was the lowest value among the populations analyzed."

Other genetic surveys have estimated the incidence of Central Asian genes in Eastern Europe as only 3%.


Is Evolution Itself Evolving?

Not the notion of evolution, which of course is always changing, but the reality of evolution and the genetic mutations underpinning it. Are mutations in humans increasing?

Yes, according to John Hawks et al. in "Recent Acceleration of Human Adaptive Evolution" published online December 17 in PNAS 10/1073.

Want to know more? Read an explanation by Razib in the blog Gene Expression.

Genomics sizes up

China launches large-scale human sequencing initiative

Jane Qiu & Erika Check Hayden

Published online 16 January 2008 in Nature 451, 234

Next-generation human genomics has arrived. The first large-scale whole-genome sequencing project has now begun in China, and an international multi-genome sequencing programme is hot on its heels.

The Yanhuang Project, which will sequence the entire genomes of 100 Chinese individuals over 3 years was announced by the Beijing Genomics Institute (BGI) on 8 January. Ye Jia, a spokeswoman for the project, said that once it is completed, the BGI aims to sequence the genomes of thousands more people, including ethnic groups from other Asian countries.

And a large international project, which aims to sequence the genomes of close to 1,000 individuals, is expected to be formally unveiled by the US National Institutes of Health in Bethesda, Maryland, and the Wellcome Trust Sanger Institute in Cambridge, UK, later this week. As yet it doesn't have a name, but is informally called the '1,000 genomes' project and the 'Multigenome project'. It will probably include the hundreds of individuals who participated in the International HapMap Project — an ongoing study of genetic diversity — as well as hundreds of other individuals.

The BGI will also participate in the 1,000 genomes project, says director Yang Huanming. However, only participants who meet the ethics and consent rules decided on by the international collaboration will be able to join that study, he says.

The projects usher in what many scientists think will be a new era of large-scale genomics — made possible with rapid-sequencing technologies — that will lead to more powerful comparisons between and within populations. Last year, scientists Craig Venter and James Watson became the first to release their complete individual DNA sequences. And a team led by George Church at Harvard University in Cambridge, Massachusetts, has begun the 'Personal Genome Project' that will examine portions of DNA from ten individuals who have agreed to share their information with the rest of the world.

But the Yanhuang Project — named after two emperors thought to be the ancestors of China's largest ethnic group — is the first to examine the entire genomes of private individuals. The first individual sequenced in the Yanhuang Project was a researcher; the second paid 10 million yuan (about US$1.4 million) to have his genome sequenced, Yang says. It is unclear whether such people will qualify for the international project, whose rules on confidentiality of data and the informed consent of participants may differ from China's.

Whole-genome sequencing studies are expected to deepen our scientific understanding of populations such as the Chinese, whose genetics have not been studied in great detail. The findings will inform medical research specific to those populations, and improve our understanding of human history, says Rasmus Nielsen of the University of California, Berkeley. “One of the exciting things about having so many sequences from Chinese individuals is that we will be able to say how much genetic exchange there has been between continents since [early humans migrated] out of Africa. That's been very hotly debated.”

The sequencing will allow scientists to add more detail to their maps of human diversity. The last large study of diversity, the HapMap, analysed only single-nucleotide polymorphisms, or SNPs — places in which DNA differs between two individuals by just one letter of the genetic code. This approach allows scientists to hunt for relatively common genetic variants. But the evidence linking disease to rare variants is growing, says Richard Myers, director of the Stanford Human Genome Center in Palo Alto, California. Whole-genome sequencing will improve detection of these rare variants, and offer a more complete understanding of the genetics of many human traits, he predicts.

"It's going to be very useful to sequence genomes from all populations and have large enough numbers so you can do comparisons between populations,” Myers says. “Even if you don't care about disease, it's going to help us look at human population history and phenotypes not relevant to disease, such as craniofacial structure, eye colour, hair colour and other fascinating things."


Discerning the ancestry of European Americans in genetic association studies

Alkes Price et al.

European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false positive or negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.

Get the whole article here.

mtDNA haplogroups of indigenous Mexican populations

Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

Hum Biol. 79/3 (Jun 2007)313-20

R. I. Peñaloza-Espinosa et al.

ABSTRACT: In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca-Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua-Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua-Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua-Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.

Population structure in Sweden - A Y-chromosomal and mitochondrial DNA analysis

T. Lappalainen et al.

From Dienekes Anthropology Blog

ABSTRACT: A population sample representing the current Swedish population was analyzed for both maternally and paternally inherited markers with the aim of characterizing the genetic variation and structure of a modern North European population. We genotyped 12 Y-chromosomal and 27 mitochondrial DNA SNPs from DNA extracted and amplified from Guthrie cards of all the children born in Sweden during one week in 2003. The sample set consisted of 1914 samples (960 males) grouped according to place of birth. The ancient migration patterns are reflected in the clear north-south gradients in several palaeolithic and neolithic haplogroups in the mtDNA (U5, I, K, T, X) and the Y chromosome (R1b, N3). The haplogroup frequencies of the counties closest to Finland and Norway showed clear associations to the neighboring populations, resulting from the formation of the nations during the past millennium. Moreover, the recent immigration waves of the 20th century are visible both maternally and paternally, and have led to increased diversity and divergence from the main population in the major cities. Unfavorable population development in the ancient or recent past can be detected in several remote counties with low diversities and other signs of low population size and/or population crises. In conclusion, our study yielded valuable information about the various factors affecting the structure of the modern Swedish population that is vital for the use of the population in large population-based studies. Our sampling strategy, nonselective on the current population rather than stratified according to ancestry, represents the future of genetic studies in the increasingly panmictic populations of the world.

Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations

By P.A. Underhill and T. Kivisild

Annu Rev Genet. 41 (Dec. 2007) 539-564.

ABSTRACT: Well-resolved molecular gene trees illustrate the concept of descent with modification and exhibit the opposing processes of drift and migration, both of which influence population structure. Phylogenies of the maternally inherited mtDNA genome and the paternally inherited portion of the nonrecombining Y chromosome retain sequential records of the accumulation of genetic diversity. Although knowledge regarding the diversity of the entire human genome will be needed to completely characterize human genetic evolution, these uniparentally inherited loci are unique indicators of gender in modulating the extant population structure. We compare and contrast these loci for patterns of continuity and discreteness and discuss how their phylogenetic diversity and progression provide means to disentangle ancient colonization events by pioneering migrants from subsequent overlying migrations. We introduce new results concerning Y chromosome founder haplogroups C, DE, and F that resolve their previous trifurcation and improve the harmony with the mtDNA recapitulation of the out-of-Africa migration.

According to Dienekes Anthropology Blog, "this is a very important review paper which is a must-read for anyone interested in human population history. The new results allued in the abstract involve the discovery of the CF and DE clades, which the authors propose were involved in separate Out-of-Africa founder events. Previously, with the exception of the Paleoafrican Y-chromosome clades A and B, all other human Y chromosomes fell into three separate clades C, DE (also known as YAP), and F. Now, C and F are shown to be united by a common ancestory into a new clade CF."


DNA does NOT Support Bering Land Bridge Sole Source

Here we go again. A small number of Siberians crossed the Bering Strait when it was dry land 12,000 years ago and populated the entire New World.

I refer to the article in PLoS (Public Library of Science) Genetics, titled "Genetic Variation and Population Structure in Native Americans," by S. Wang et al. So far from vindicating a decrepit theory that had nearly drawn its last breath in anthropology circles in the late 1990s, the "new evidence" does nothing but perpetuate geneticists' circular reductionist logic again. Set up a survey the right way and you will get the results you want.

First, the 678 markers the scientists investigated are those they have determined are associated with Native Americans in the first place. Surprise! They were found in high frequencies in the 29 Native American populations of the study -- the very populations that have been studied to death since the 1980s. One much-cited study of alleged Siberian origins of Native Americans used only 9 North American Indians, all from the tiny Papago tribe in Arizona. Most of the Indians were from South America. No study will touch an Indian with admixture, although it is likely all Indians have some degree of admixture, at least in North America, even the reservation-born and bred Navajos, considered the "purest" (as much as 20% by one measure).

In every other population of the world except those in the New World, greater diversity equals source. Thus, geneticists established the "out of Africa" theory because Africa has the most genetic diversity.

But does it? Actually, the Americas have more. Rather than pointing to the source of migrations, the gradual increase in frequency of the 678 markers as we get closer to the Bering Strait could reflect a decrease in diversity as a result of genetic drift the farther removed populations became from a center situated, say, in Central America. The same phenomenon occurs on the fringes of the Atlantic, where one particular genetic type, the male lineage known as the Atlantic Modal Haplotype, reaches frequencies of over 80% in Connaught, Ireland. It did not originate in Ireland, though, but rather in Basque lands, which have a high amount of diversity, like Africa.

Geneticists set great store by a concept known as time to coalescence. This is a backtracking calculation of the age of a population according to how many mutations it has accumulated, usually in its mitochondrial DNA. Wind back the mitochondrial clock and you get to zero hour. Nothing is wrong with this approach, but the geneticists go further and set the time together with theoretical migrations to arrive at a source -- say Lake Baikhal in central Siberia. So they use theoretical migrations to prove theoretical migrations. For Native Americans, supposing even that they had one central origin, it could just as well have been in Panama. But for geneticists, it must be in Siberia or Mongolia because that is the only place it is allowed to be.

The search for one single source is illusory and reductionist anyway. Who would suggest that all Europeans came, say, from Tajikistan, 40,000 years ago.

Rather than keep attempting to reiterate Native Americans' lack of diversity, a colonial attitude with blinkers to begin with, geneticists should study how and why Native American diversity far exceeds that of the Europeans, Africans, Asians and all other world populations.

--Donald N. Yates
Principal Investigator
DNA Consulting

New Book Explores DNA Profiling

In Genetic Witness: Science, Law, and Controversy in the Making of DNA Profiling, author Jay D. Aronson uncovers some of the dirty little secrets of forensics. When DNA profiling was first introduced into the American legal system in 1987, it was heralded as a technology that would revolutionize law enforcement. As an investigative tool, it has lived up to much of this hype—it is regularly used to track down unknown criminals, put murderers and rapists behind bars, and exonerate the innocent.

Yet, this promise took ten turbulent years to be fulfilled. Aronson uncovers the dramatic early history of DNA profiling that has been obscured by the technique’s recent success. He demonstrates that robust quality control and quality assurance measures were initially nonexistent, interpretation of test results was based more on assumption than empirical evidence, and the technique was susceptible to error at every stage. Most of these issues came to light only through defense challenges to what prosecutors claimed to be an infallible technology. Although this process was fraught with controversy, inefficiency, and personal antagonism, the quality of DNA evidence improved dramatically as a result. Aronson argues, however, that the dream of a perfect identification technology remains unrealized.

Praise for Genetic Witness

“Thorough and detailed, Aronson’s work will be the definitive treatment of the recent history of DNA typing.”—Simon Cole, author of Suspect Identities: A History of Fingerprinting and Criminal Identification

About the Author

Jay D. Aronson is an assistant professor of history at Carnegie Mellon University in Pittsburgh, Pennsylvania.

Buy from Rutgers University Press.

Was Your Grandmother Named Persis?

According to the blog Gene Expression, there was a strong tendency for new Persian converts and their offspring to use very Arabic names during the first centuries, specifically ones associated with early Muslims. While Arab Muslims themselves might on occasion have had names which might also have been used by Jews or Christians (e.g., Arabic forms of David), Persian converts were underrepresented in these "ambiguous" variants, rather their names signified that they had to be Muslim. But as the proportion of Iran's population which was Muslim increased (going from minority to majority sometime in the 10th century), there was a modest bounce back of pre-Islamic Persian names among the elites. The argument goes that only with the indigenization of Islam within Persian culture were Iranian forms and elements allowed to make an explicit come back, since they no longer posed any threat as an alternative . . . . This of course neglects the elephant in the room that the early Caliphs seem to have transplanted Sassanian court motifs in toto to generate the aura around their monarchy. . . .


Some reviews of Nicholas Wade’s Before the Dawn: Recovering the Lost History of Our Ancestors

By far the best book I have ever read on humanity's deep history.
--E. O. Wilson

Tracing the history and the evolution of the human race from our common ancestor with chimpanzees 5 million years ago in a 300 page book was an ambitious undertaking, but Wade was clearly up to the task. If you are interested in human evolution and the history of mankind, this book is required reading.
--Searching for the Truth

....brings together a selection of early results [from genetics] to tell the story of modern man, homo sapiens sapiens. We have known a good deal about this topic for decades, from investigations in archeology, anthropology, and comparative linguistics. However, our new, detailed knowledge of the human genome has clarified our understanding dramatically. A good analogy would be the results sent back by the first interplanetary probes, resolving what for centuries had been mere points of light or fuzzy blobs in our telescopes into actual landscapes of craters, volcanoes, and dunes, while at the same time demolishing wishful-thinking fantasies [like those about Martian canals].
--National Review Online

More informative than Nature via Nurture, more readable than The Blank Slate, and proves (contra The Emperor's New Clothes) that popularizations of population genetics don't have to be deceitful and revolting.
--Bookosphere

Wade's coverage includes the ancient near extinction of humanity (DNA analysis shows at one point there were only 5000 humans left after a mass die off), human migration, and intra-human relations between Neanderthals and Homo sapiens. He also talks about the idea of race and the violent warmaking nature of human society.
--World History Blog

While 'race' is often a dirty word in science, one of the book's best chapters shows how racial differences can be marked genetically and why this is important, not least for the treatment of diseases.
--Publishers Weekly

And finally, a big slam from Wade’s former employer Nature magazine!

Wade's explanations commit various well-known errors, such as equating correlation with causation and extrapolating from individual traits to group characteristics.... Most of the scenarios he reports have not been rigorously tested, nor is it clear how they could be. The book has many internal inconsistencies, and one can easily find contrary evidence or readily construct alternative 'just so' stories that invoke the same genetic scenario and the same kind of reasoning.... Wade claims example after example of 'genes for' traits.

Read original review in Nature.

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

European Journal of Human Genetics (2008) 16, 124–134

By Mark G Thomas et al.

The Alps are one of the most significant geographical barriers in Europe and several isolated Swiss and Italian valleys retain the distinctive Ladin and Romansch languages, alongside the modern majority of Italian and German languages. Linguistically, Ladin belongs to the Romance languages, but some studies on mitochondrial DNA (mtDNA) variation have suggested a major Middle Eastern component to their genealogical origin. Furthermore, an observed high degree of within-population diversity has been interpreted as reflecting long-standing differentiation from other European populations and the absence of a major bottleneck in Ladin population history. To explore these issues further, we examined Y chromosome and mtDNA variation in two samples of Ladin speakers, two samples of German speakers and one sample of metropolitan Italian speakers. Our results (1) indicate reduced diversity in the Ladin-speaking and isolated German-speaking populations when compared to a sample of metropolitan Italian speakers, (2) fail to identify haplotypes that are rare in other European populations that other researchers have identified, and (3) indicate different Middle Eastern components to Ladin ancestry in different localities. These new results, in combination with Bayesian estimation of demographic parameters of interest (population size, population growth rate, and Palaeolithic/Neolithic admixture proportions) and phylogeographic analysis, suggest that the Ladin groups under study are small genetically isolated populations (subject to strong genetic drift), having a predominantly European ancestry, and in one locality, may have a greater Palaeolithic component to that ancestry than their neighbours.

The impact of genetics and genomics on public health

By Angela Brand et al.

European Journal of Human Genetics (2008) 16, 5–13

Public health practice has to date concerned itself with environmental or social determinants of health and disease and has paid scant attention to genomic variations within the population. The advances brought about by genomics are changing these perceptions. In the long run, this knowledge will enable health promotion messages and disease prevention programmes to be specifically directed at susceptible individuals and families, or at subgroups of the population, based on their genomic risk profile. As the controversial discourse in science and health politics shows, the integration of genomics into public health research, policy and practice is one of the major challenges that our health-care system is currently facing.

Hominid Harems: Big Males, Small Females and Bodybuilding

By Ann Gibbons
From Science magazine

A study on page 1443 of the November 30 (2007) issue of Science finds that the males of an extinct species of hominid in South Africa took longer to grow up than females and got much larger, suggesting that top males of this australopithecine species invested energy in bodybuilding in order to possess a harem of females, much like silverback gorillas do today.

Genetic Determinants of Hair, Eye and Skin Pigmentation in Europeans

Patrick Sulem et al.
Nature Genetics 39:1443-1452
Published 21 Oct. 2007

From a review by OBBeC
Scientists at deCODE genetics and colleagues in Iceland and Holland have reported the discovery of variations in the human genome that influence pigmentation of hair, eyes and skin. By studying more than 300,000 SNPs (single-letter variants in the human genome) across the whole genome in close to seven thousand individuals of European origin, the deCODE team discovered several novel SNPs influencing hair, eye, and skin pigmentation, at the same time refining earlier findings influencing these traits.

The findings help in the understanding of the molecular basis for and evolution of these most visible of characteristics, and may be useful for teasing out the biology of skin and eye disease as well as for forensic DNA analysis....

It is known that pigmentation characteristics such as freckles and hair and eye colour run in families. However, only few genes have been strongly linked to normal variation of these characteristics. Skin pigmentation in human populations tends to be darkest near the equator and to lighten with increasing latitude. This variation has a generally accepted dual biological function: heavier pigmentation affords protection against ultraviolet radiation in sunlight, protecting against sunburn and skin cancer but also reduces the body’s capacity to synthesize vitamin D. By contrast, there is no clear functional role for hair and eye color. The vast majority of variations in these two traits is confined to populations of European origin, with most populations around the globe with only dark hair and brown eyes....

The multitude of genes affecting pigmentation and their varied effects are reflected in the great degree of diversity of pigmentation seen in Europeans.

Mitochondrial Haplogroup H1 Protective for Stroke

Dienekes Anthropology Blog has this and other abstracts from the recent American Society of Human Genetics meeting.

DNA Tests Find Branches but Few Roots

New York Times
By RON NIXON
Published: November 25, 2007

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.

An estimated 460,000 people have taken genetic tests to determine their ancestry or to expand their known family trees, according to Science magazine. Census records, birth and death certificates, ship manifests, slave narratives and other documents have become easier to find through the Internet, making the hunt for family history less daunting than in years past.

Yet for many, the paper or digital trail eventually ends. And for those who have reached that point, genetic DNA tests may help to provide the final piece of the puzzle.

The expectations and reasons for taking the test vary. For some, the test allows them to reconnect with African ancestors after centuries of slavery wiped out links between African-Americans and their forebears. Others want to see if they have links to historical figures like Genghis Khan or Marie Antoinette. For still others, it’s an attempt to fill gaps in family histories and find distant cousins they might not otherwise have known.

The demand has spawned an industry. Almost two dozen companies now offer such services, up from just two or three only six years ago. The field is so hot that private equity investors have moved in: Spectrum Equity Investors recently bought Ancestry.com, an online genealogy site, for about $300 million shortly after the site added genetic testing as a service.

But as the number of test takers and companies has grown, so has the number of scientists or scholars like Mr. Gates who have questioned assertions that companies make about their tests. One of the most controversial issues is the ability of the tests to determine the country or the ethnic group of origin for African-Americans or Native Americans.

Mr. Gates, director of the W.E.B. Du Bois Institute for African and African American Research at Harvard, said his experience and similar stories from others have prompted him to enter the field.

Mr. Gates recently teamed up with Family Tree DNA, a DNA testing and genealogy firm in Houston, to provide genetic testing and genealogy work for African-Americans. The new venture is called AfricanDNA.

“What we hope to do is combine this with genealogical and other records to try to help people discover their roots,” he said. “The limitations of current genetic DNA tests mean you can’t rely on this alone to tell you anything. We hope to bring a little order to the field.”

In an editorial in Science magazine in October, a number of scientists and scholars said companies might not be fully explaining the limitations of genetic testing, or what results actually mean.

The authors said that limited information in the databases used to compare DNA results might lead people to draw the wrong conclusions or to misinterpret results. The tests trace only a few of a customer’s ancestors and cannot tell exactly where ancestors might have lived, or the specific ethnic group to which they might have belonged. And the databases of many companies are not only small — they’re also proprietary, making it hard to verify results.