Maybe We Were . . . Wrong?
Principal component analysis of genetic data
By David Reich, Alkes L Price and Nick Patterson
Nature Genetics 40/5 (2008) 491-2
Principal component analysis (PCA) has been a useful tool for analysis of genetic data, particularly in studies of human migration. A new study finds evidence that the observed geographic gradients, traditionally thought to represent major historical migrations, may in fact have other interpretations.
Senate Protects Confidentiality
of Personal Genetic Data
Measure would bar use of information by insurers, employers
Baltimore Sun
April 25, 2008
By Jonathan D. Rockoff
WASHINGTON - Coming to grips with the growing role of genetic testing in American life, Congress acted yesterday to outlaw the use of genetic information in employment or insurance decisions.
The Senate approved a measure, which the House of Representatives is expected to ratify and President Bush to sign, that would become the first federal law dealing with the growing role of genetics in the prediction, diagnosis and individualized treatment of disease.
Many patients who could benefit have refused genetic testing out of fear of discrimination, experts say . . . Read article.
New directions in the anthropology of migration and multiculturalism
Steven Vertovec
Ethnic and Racial Studies, Volume 30, Number 6, November 2007, pp. 961-978(18)
Abstract
It is a kind of boom time for the anthropology of migration. Anthropologists are currently studying a wide range of migration-related topics. Many of them, of course, are not entirely new: anthropologists have been researching migration dynamics and impacts since at least the 1930s (most notably within the Manchester School of anthropology). Since the 1970s the discipline's burgeoning interst in ethnicity has largely entailed research on post-migration communities. Since the 1990s, migrant transnationalism has become one of the most fashionable topics. There is still much to do in research and theory around migration, not least with regard to public debates around multiculturalism. This introduction suggests a number of possible new directions for anthropological inquiry into migration and multiculturalism, and summarizes the special issue's contributing articles in light of their contributions toward moving the discipline in these directions.
Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England?
John E. Pattison
Proceedings of the Royal Society of the Biological Sciences
Published online April 22, 2008
Abstract
It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population.
Read article.
Scientists reshape Y chromosome haplogroup tree gaining new insights into human ancestry
Wednesday, April 2, 2008 – The Y chromosome retains a remarkable record of human ancestry, since it is passed directly from father to son. In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.
Human cells contain 23 pairs of chromosomes: 22 pairs of autosomes, and one pair of sex chromosomes. Females carry a pair of X chromosomes that can swap, or recombine, similar regions of DNA during meiosis. However, males harbor one X chromosome and one Y chromosome, and significant recombination between these dissimilar sex chromosomes does not occur. Therefore, the non-recombining region of the Y chromosome (NRY) remains largely unchanged over many generations, directly passed from father to son, son to grandson, and so on, along with genetic variations in the NRY that may be present. Scientists can use genetic variations, such as single nucleotide polymorphisms (SNPs), on the Y chromosome as markers of human ancestry and migration.
In 2002, the Y Chromosome Consortium (YCC) constructed a tree of 153 haplogroups based upon 243 unique genetic markers. In this report, researchers led by Dr. Michael Hammer of the University of Arizona recognized the need to revisit the Y chromosome haplogroup tree and incorporate the latest data. “The YCC effort in 2002 was a landmark in mapping the then known 300 or so Y-linked SNPs on a single tree, and getting the community to use the same nomenclature system,” explains Hammer. “The rate of SNP discovery has continued to increase over the last several years, as are publications on Y chromosome origins and affinities. While this new information is useful, ironically it also brings with it the danger of introducing more chaos into the field.”
Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando Mendez, a co-author of the study.
In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”
Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”
“More SNPs are being discovered, and we anticipate the rate to increase with the 1000 Genomes Project,” says Hammer, referring to the wealth of human genetic variation data that will soon be available. While this report represents a significant advance in mapping ancestry by Y chromosome polymorphisms, it is certain that future discoveries will necessitate continual revisions to the Y chromosome haplogroup tree, helping to further elucidate the mystery of our origins.
Scientists from the University of Arizona (Tuscon, AZ) and Stanford University (Stanford, CA) contributed to this study.
This work was supported by the Salus Mundi Foundation.
Media contacts:
Michael Hammer, Ph.D., has agreed to be contacted by email for more information (mfh@u.arizona.edu).
About the article:
The manuscript will be published online ahead of print on April 2, 2008. Its full citation is as follows:
Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F.
New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree.
Where Did European Men Come From?
Kalevi Wiik
Journal of Genetic Genealogy 4 (2008) 35-85
Ten Y chromosome haplogroups are studied with 17 maps showing spread and frequencies, including R1a, R1b, N, G, I, J, E3b.
Read or download.
The Dawn of Human Matrilineal Diversity
Doron M. Behar et al.
The American Journal of Human Genetics, April 2008
Abstract
The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,00070,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.
The success of the genome-wide association approach: a brief story of a long struggle
By Ku Chee Seng and Chia Kee Seng
European Journal of Human Genetics (2008) 16, 554–564, published online 20 February 2008
The genome-wide association approach has been the most powerful and efficient study design thus far in identifying genetic variants that are associated with complex human diseases. This approach became feasible as the result of several key advancements in genetic knowledge, genotyping technologies, statistical analysis algorithms and the availability of large collections of cases and controls. With all these necessary tools in hand, many genome-wide association studies were recently completed, and many more studies which will explore the genetic basis of various complex diseases and quantitative traits are soon to come. This approach has started to reap the fruits of its labor over the past several months. Publications of genome-wide association studies in several complex diseases such as inflammatory bowel disease, type-2 diabetes, breast cancer and prostate cancer have been abundant in the first half of this year. The aims of this review are firstly, to provide a timely summary for most of the genome-wide association studies that have been published until June/July 2007 and secondly, to evaluate to what extent these results have been validated in subsequent replication studies.
Second Generation DNA Tests
Reveal More Than Just Identity
Washington Post
Sunday, April 20, 2008; Page A01
A report in the Washington Post by Rick Weiss suggests that "second generation" forensic DNA tests, just like second generation ancestry tests, can do much more than just identify a person. They can yield information on someone's health and even their emotions.
Read DNA Tests Offer Deeper Examination Of Accused
Editorial in Nature Cautions
Against Too Much Regulation
In Genetic Testing Industry
Nature 452, 666 (10 April 2008) |
Ready or not
Transparency and honesty are essential if the genetic-testing industry is to live up to its potential.
Navigenics, a California start-up company with solid backing, launched its flagship product this week. The Health Compass, a US$2,500 genetic test, is being offered to consumers directly, over the Internet. It will scan DNA from a customer's saliva sample for a host of tiny variations and pronounce on the person's risk of developing 18 common medical conditions, including heart attack, prostate cancer and type 2 diabetes.
Why now? Because, as the company says in its corporate literature, "the science is ready. Genetic testing is ready to enter into common health-care practice."
Certainly genetic testing is here, ready or not. In the past year, genome-wide association studies have begun to pour out of labs, linking the blips in our genetic make-up to risks of developing particular medical conditions. Whether people would or could change their behaviour to ameliorate these risks remains unclear. But the ink on the research papers is barely dry before companies unveil commercial versions of the tests. Navigenics is simply the most recent; others include high-profile players such as 23andMe in Mountain View California (see Nature 450, 11; 2007) and the Icelandic genomics company deCODE Genetics. They also encompass smaller operations such as Philadelphia-based Smart Genetics, which last month offered a genetic assessment of the risk of Alzheimer's disease. Rarely have basic discoveries morphed into a commercial product quite so swiftly.
Following almost as quickly are the concerns being raised about the use of such tests. Many of these worries have been around for some time, but now that the tests are here, these discussions have taken on a new urgency. If consumers are to reap the benefits that genetic testing can offer, they need understandable information about the basis, validity and limitations of the tests. One proposed structure for providing this information is a publicly accessible registry into which test-makers would be required to upload data about their tests and the studies that back them. This information should be updated as genetic risks are changed or refined, as inevitably they will be.
Such a registry should be international, harmonizing information in what will doubtless be an industry without borders. This approach seems preferable to stepped-up regulation by agencies such as the Food and Drug Administration (FDA), which — in addition to travelling at the snail's pace of bureaucracy rather than the lightning speed of burgeoning markets — could easily have the effect of driving less-than-desirable players underground, where sub-standard tests will remain as easy to buy as black-market DVDs.
Many critics would say that a hands-off approach by the FDA is irresponsible. But on what basis should genetic tests be treated any differently from others done in government-certified clinical labs? Many of these tests — including almost all of those done by labs in-house, rather than sent out to patients and doctors as kits — are not required to demonstrate clinical utility on a test-by-test basis. For that matter, why should genetic tests be treated differently from medical devices such as MRI scanners, which were left by the FDA to prove their utility and clinical validity to physicians and providers in the marketplace, rather than in pre-market assessments?
It would be naive to suggest that transparency will solve all problems, or to assume that the marketplace will separate the wheat from the chaff with unfailing accuracy and efficiency. But to advocate relatively light regulation does not mean turning a blind eye to the risks of such a strategy. It means taking seriously the presumption that people should be free to inform themselves and make their own choices, and that by doing so they may benefit not just themselves but also the overall pace of innovation. Should it become clear that the system is allowing harm, then enhanced regulation will be appropriate.
It is also worth noting that the scientists who have driven this revolution need to assume a prominent role in ensuring that its benefits are not mishandled. Those who start companies, or advise them, can and must lead the way in ensuring that their enterprises are transparent and valid. In the meantime, online shoppers who buy genetic tests would do well to keep asking themselves whether the science is, indeed, ready.
DNA from Human Coprolites in Oregon
Strongest Proof Yet of Pre-Clovis Date
For Human Presence in North America
M. Thomas et al.
Published Online April 3, 2008, in
Science DOI: 10.1126/science.1154116
ABSTRACT
The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America ca. 11-10.8 thousand radiocarbon years before present (14C ka B.P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, south-central Oregon, by 12,300 14C yr. B.P., through recovery of human mtDNA from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are>1000 14C years earlier than currently accepted dates for the Clovis-complex.
"This . . . is the best evidence that humans were living in North America 14,000 years ago, a millennium before the Clovis people, long thought to be the first Americans," said one commentator on the Web.
Recreational genomics? Dreams and fears on genetic susceptibility screening
European Journal of Human Genetics (2008) 16, 403–404
GertJan B van Ommen and Martina C Cornel
With the advent of direct-to-the-consumer genetic screening and personalized genomics, a host of health care policy questions arise. "Genomic health care has the potential to reduce aggregate cost of health care by enabling better preventive strategies, but calls for a health-care system that is not fragmented. The emergence of individualized medicine is a compelling reason to deliver universal health care."
Read editorial.
Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs
Malyarchuk BA, Derenko M, Perkova M, Grzybowski T, Vanecek T, Lazur J.
European Journal of Human Genetics advance online publication 9 April 2008
Abstract
To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.
Ed. Note: African mitochondrial lineages in Eastern European populations could help explain Sub-Saharan African matches for Ashkenazi Jews in OmniPop. Another factor may be male haplogroup E3b, a common Jewish paternal lineage. Both incursions are so ancient as to be virtually meaningless for ethnotyping, however.
DNA Consulting Renamed
DNA Testing Systems
Inks Agreement with DNAPrint Genomics, Moves Offices to Scottsdale, Arizona
SCOTTSDALE, Ariz. – (March 11, 2008) – DNA Testing Systems, previously of Santa Fe, N.M., and formerly named DNA Consulting, has signed an agreement to sell DNAPrint Genomics’ line of biogeographical ancestry tests and has moved its offices to Scottsdale, Ariz.
DNAPrint Genomics was one of the first DNA testing companies to be formed in an industry now estimated to be worth over $150 million in consumer sales. It was launched in Sarasota, Florida, in 1997 to commercialize the biogeographical, and proprietary, genetic markers developed from the work of Mark Shriver, a biogenetics professor at Pennsylvania State University.
DNA Testing was a spin-off from the research of founder Donald N. Yates into the Jewish and American Indian genetics of a rare Appalachian ethnic group called Melungeons, a family background to which he belongs. “I had to start my own company to understand my own unusual DNA test results,” Yates said. “And then I was doing so many consultations for Melungeon cousins that I decided to commercialize my sideline and get paid for what I was doing.”
Donald Yates of DNA Testing
Yates moved his business from Savannah, Ga., where he was a professor, to Santa Fe, N.M., in 2004 and has now settled in Scottsdale, where he hopes one day to retire. The company uses genomics laboratories in Salt Lake City, Utah; Richmond, Calif., and Sarasota, Fla.
DNA Testing sells DNAPrint® tests through a large web presence, marketing them as Whole DNA, a test that estimates percentages of American Indian and other admixture; EurasianDNA, which divides a customer’s DNA into four regions of Eurasia, and EuroDNA 2.0, the newest ancestry test from DNAPrint. EuroDNA 2.0 uses discoveries in genetic markers and human migration to determine an individual’s proportion of ancestry in five parts of Europe, including the Iberian Peninsula.
According to Yates, “We are finding that many people who think they are exclusively English, Irish and Scottish have a large element of Spanish and Portuguese ancestry they did not suspect.” One reason, he said, was that the British Isles were settled chiefly by a people very much like the Basques after the last Ice Age.
Of the handful of DNA testing companies in the United States, DNA Testing is the only one that specializes in customized and personalized reports. “We’re rather boutique-like in our approach,” said Yates, “and probably want to keep it that way.” In addition to biogeographical DNA tests, the company also sells traditional paternity, Y chromosome (male) and mitochondrial (female-passed DNA) tests.
For more information, visit DNA Testing at www.dnaconsultants.com or call toll free 1-877-473-5155.
The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies
By A. Achilli et al.
PLoS ONE. 2008 Mar 12;3(3):e1764
ABSTRACT
Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.
Dwarf Race of Humans Discovered on Pacific Island
PLoS One 10.1371/journal.pone.0001780 (2008)
As reported by Brooks Hanson, diminutive fossils of Homo sapiens, perhaps representing several tens of individuals, have been found in two caves in Palau. The fossils, described by Berger et al., range in age from about 3000 to 1500 years; humans are thought to have arrived on the island from the Philippines (700 km to the west) about 1000 years earlier. The fossils include several complete, small crania still encased in flowstone. Preliminary measurements suggest a brain size near the low end of extant Homo sapiens and close to that of Homo erectus. Measurements of multiple postcranial bones imply a corresponding body size comparable to those of the smallest known H. sapiens and the early hominin Lucy. Although many traits are consistent with H. sapiens, some fossils also exhibit more primitive traits, including minimal chins and an enlarged brow ridge. These traits and some aspects of the teeth and the small body size are similar to those seen in the older, enigmatic diminutive fossils found recently on the nearby island of Flores, which in turn have been ascribed to a relict population of an earlier Homo species. Although any relation between these fossils is not clear, the sample on Palau is further evidence of the extremes in size and characteristics that may develop in isolated island human populations.
These fossils could correspond to widespread legends around the Pacific of a pygmy race of humans that retreated into the mountains as the first Polynesians arrived.
According to critics, however, the skeletons may be those of children in a mass grave.
The Late Pleistocene Dispersal of Modern Humans in the Americas
Ted Goebel et al.
When did humans colonize the Americas? From where did they come and what routes did they take? These questions have gripped scientists for decades, but until recently answers have proven difficult to find. Current genetic evidence implies dispersal from a single Siberian population toward the Bering Land Bridge no earlier than about 30,000 years ago (and possibly after 22,000 years ago), then migration from Beringia to the Americas sometime after 16,500 years ago. The archaeological records of Siberia and Beringia generally support these findings, as do archaeological sites in North and South America dating to as early as 15,000 years ago. If this is the time of colonization, geological data from western Canada suggest that humans dispersed along the recently deglaciated Pacific coastline. There was another dispersal several thousand years later responsible, perhaps, for the Clovis Culture.
(Ed. Note: While this theory can account for the majority of lineages studied today among American Indians, it cannot explain the high incidence of mitochondrial haplogroups B or X, which are not found in Mongolia or Siberia in significant amounts.)
Beyond Out of Africa
Jun Z. Li et al.
Science 22 February 2008:
Vol. 319. no. 5866, pp. 1100 - 1104
Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.
Read extensive discussion on Dienekes' Anthropology Blog.
Y-chromosome diversity characterizes the Gulf of Oman
Alicia M Cadenas et al.
European Journal of Human Genetics (February 2008) 16, 374–386
Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.
Check Out Heredity's Free Podcast Series
Each month Elli Leadbeater and Steve Le Comber present a free audio show. The podcast features interviews with the people behind the science and a digest of breaking news from Heredity editor Richard Nichols at Queen Mary University of London.
Fly in the Ointment of Evolutionary Theory?
Featured in January's episode is H.-J. Bandelt of the University of Hamburg, a leading statistician in the area of population genetics. His commentary on mutation rates, "Clock debate: when times are a-changin': Time dependency of molecular rate estimates: tempest in a teacup," appeared in Heredity, vol. 100, in February 2008. According to Bandelt, many current studies on the molecular clock use outmoded data and confused models to arrive at their conclusions regarding human evolution and ancient migrations. Experts do not always distinguish between hot spots in DNA sequences and an average rate of mutation. They may base their suppositions about changes in coding regions (genes) on variation in non-coding regions such as the control loop in mitochondrial DNA. For these reasons, many of our theories about time to coalescence of genetic types may be essentially flawed. Bandelt mentions the model of Amerind migration as an example.
You can subscribe to the service and receive the latest episode in your email or browse the archives. Listen to the podcast now.
Iceland's deCODE Sharpens Image
"Backed by years of experience deCODE has created the most complete genetic map of the human genome and has an unrivalled track record in mapping and validating disease genes for common and complex diseases." Such is the hype in genomics giant deCODE's new advertising campaign. How much is science and how much is marketing? Judge for yourself by going to their website. Here's more: "deCODE is also leveraging its expertise in human genetics and integrated drug discovery and development capabilities to offer innovative products and services in DNA-based diagnostics, bioinformatics, genotyping, structural biology, drug discovery and clinical development."
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.
Scientists show that mitochondrial DNA variants are directly linked to risk factors for type 2 diabetes
Ed. Note: In retrospect, this may have been the biggest breakthrough in disease association research last year.
Monday, August 13, 2007 – Today, researchers report for the first time that genetic variants in mitochondria—energy-producing structures harboring DNA that are inherited only from the mother—are directly linked to metabolic markers for type 2 diabetes. The study, which highlights the role of mitochondrial genome variation in the pathogenesis of common diseases, is published online in Genome Research (www.genome.org).
According to the Centers for Disease Control, 7% of the U.S. population has diabetes, and 90-95% of those cases are classified as type 2 diabetes. Type 2 diabetes is caused by external factors such as diet and exercise, and is influenced by several genes. While most of the genes known to be involved in diabetes susceptibility are located in the nuclear genome, a recent study estimated that more than 20% of type 2 diabetes cases may involve mutations in the mitochondrial genome.
In the study published today, the scientists compared two different rat strains; the strains possessed virtually identical nuclear genomes but different mitochondrial genomes. This eliminated any complicating effects due to environmental factors or variation in the nuclear genome. Any differences observed between the two rat strains could be attributed to variation in the mitochondria.
When comparing the two rat strains, the researchers found that the two strains exhibited significant differences related to energy metabolism and storage. One rat strain exhibited impaired glucose tolerance, reduced muscle glycogen synthesis, decreased skeletal muscle ATP (energy) levels, and decreased activity of an energy-producing enzyme called cytochrome c oxidase, when compared to the second rat strain. These metabolic characteristics are typical of diabetic individuals.
The researchers then obtained DNA sequences from mitochondria of both rat strains, and found DNA variants in genes that encode for proteins involved in energy production. Thus, for the first time, they were able to directly link inherited variation in the mitochondrial genome to metabolic markers for type 2 diabetes.
“Our study highlights the role of mitochondrial DNA variation in common genetic diseases,” says Dr. Theodore Kurtz, the lead investigator on the project. “In addition, the animal models developed in this study will open the door for future studies in which the effects of mitochondrial genome variation can be investigated on fixed nuclear genetic backgrounds.”
Scientists contributing to the study were from the Academy of Sciences of the Czech Republic (Prague); the Institute for Clinical and Experimental Medicine (Prague); the Osaka University Graduate School of Medicine (Japan); the Sapporo Medical University (Japan); the University of California, San Francisco; and the University of Michigan Medical School.
The work was supported by grants from the National Institutes of Health; the Ministry of Education, Youth, and Sports, the Ministry of Health, and the Grant Agency of the Czech Republic; Charles University (Prague); and the EURATools project (which is funded through the European Union’s Sixth Framework Program).
Media contacts:
Theodore Kurtz, MD., principal investigator on the project, has agreed to be contacted (KurtzT@Labmed2.ucsf.edu; phone +1-415-353-1979) for additional information.
About the article:
The manuscript will be published online ahead of print on Monday, August 13, 2007. Its full citation is as follows:
Pravenec, M., Hyakukoku, M., Houstek, J., Zidek V., Landa, V., Mlejnek, P., Miksik, I., Dudová-Mothejzikova, K., Pecina, P., Vrbacký, M., Drahota, Z., Vojtiskova, A., Mracek, T., Kazdova, L., Oliyarnyk, L., Wang, J., Ho, C., Qi, N., Sugimoto, K., and Kurtz, T. 2007. Direct linkage of mitochondrial genome variation to risk factors for type 2 diabetes in conplastic strains. Genome Res. doi:10.1101/gr.6548207.
Read the article.
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.