Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

Full text is free:

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.

Jean M comments:

Their results are remarkably neat, showing two clearly distinct lineages, with comparatively little inter-mixture, confirming the picture from the archaeology of the LBK, for example, which seems to indicate that farmers and foragers kept to their own zones.

This helps to explain why the presumed Neolithic Y-DNA haplogroups G, E and J do not dominate Europe today, and decline in frequency the further one moves from the Mediterranean. The farming pioneers in Europe, though initially successful, eventually encountered problems which led to population crashes. Then after the Neolithic, Europe had two great bursts of migration, both from fringe regions where farming had been adopted by foragers. One came from the European steppe in the Copper and Bronze Ages. The other was the spread of their Germanic and Slavic descendants in the Migration Period.

Most bizarre rationale for creating racial hybrids I've yet come across

On the second-to-last page of The $1,000 Genome, Kevin Davies recounts noticing two small children running around at the GET (Genomes, Environments, Traits) Conference:

They turned out to be [. . .] the children of Jong Bhak, the director of the Personal Genomics Institute in Korea, and his American (Caucasian) wife. They were also the youngest members of the genome sequencing club. "We wanted to know how different two siblings can be," said Bhak. "Our hybrid kids can give us some easy confirmation on that. They are brothers, but their genetic makeup will be much more different from each other than any two random people in the same population."

Nothing says "family" like "more different from each other than any two random people in the same population." In fairness, I'm not sure if Bhak is attempting to celebrate this fact, or merely acknowledging a reality that the vast majority of multiracialists no doubt fail to grasp.

Further update on People of the British Isles project

From their most recent newsletter (pdf):

We are pleased to tell you that we have just submitted our first scientific paper about the project. The main function of this paper is to announce PoBI to the scientific world and in it we show that, even with a relatively small number of samples and a few genetic markers, the samples we collected should be sufficient to detect genetic differences across the UK. [. . .]

One aspect that is of particular interest is the surnames we collected and we have spent some time with our collaborators at UCL (Professor Paul Longley and his group) dividing them into local and non-local surnames. The figure on the left shows a couple of examples. The idea is that individuals whose surname is local to an area are more likely to have family in that area for many generations than individuals whose surnames are found all over the country. This is obviously a generalisation, but it does seem that there are some genetic differences between sets of volunteers with local surnames and sets with non-local surnames and we are really looking forward to analysing all the data rather than just the small subset we have been studying so far. [. . .]

Our next priority is to analyse the 1.3 million genetic markers that have been typed on 3,000 of our volunteers [. . .] The data we analyse from these samples should shed light on the genetic impact of the different historical incursions into Britain. It is an extremely large data set and so it will take a while to analyse and write up. As mentioned in our last newsletter, 100 of our samples are having their complete DNA sequenced by the 1,000 Genomes Project (www.1000genomes.org) and it should not be too long before that very valuable information becomes available to us. [. . .]

As you will know from the last newsletter, the Wellcome Trust has given us funding for a further five years to look for genes involved in normal traits. The main focus is on facial features, but other traits include handedness, taste perception and skin colour. We have been going back to our volunteers to collect these data. We take 3D photographs of each volunteer’s face in order to identify genes involved in the control of particular facial features. Over the last 18 months, we have collected 475 such photographs and are beginning to analyse them with our collaborators in Surrey (Professor Josef Kittler and his group).

Last newsletter (pdf):

There is a great deal of interest in the genetics of facial features and, in addition, the frequency of genetic variants for facial features may well differ significantly between different parts of the UK. We will also be collecting data on a variety of other normal features including height, hair and skin colour, handedness, milk tolerance, musical preferences and perfect pitch, taste and smell preferences and features of the hand.

Victor Mair talk on Tarim Basin Mummies

Part of a series of lectures related to the "Secrets of the Silk Road" exhibition at the University of Pennsylvania Museum of Archaeology and Anthropology. The mummy and artifacts abruptly pulled from the exhibition by the Chinese government before it opened are back for now.

1000 Genomes Pilot Data Suggests Recent Selective Sweeps Rare in Human Lineage

Via GenomeWeb Daily News:

"Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome," co-senior author Mary Przeworski, a human genetics, ecology, and evolution researcher at the University of Chicago, said in a statement. "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture."

Przeworski et al. Classic Selective Sweeps Were Rare in Recent Human Evolution. Science 18 February 2011: vol. 331 no. 6019 pp. 920-924. DOI: 10.1126/science.1198878

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of “classic selective sweeps” (in which a beneficial mutation arises and rapidly fixes in the population).Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast to expectation, however, the trough in diversity around human-specific amino acid substitutions is no more pronounced than around synonymous substitutions. Moreover, relative to the genome background, amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations. These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.

[. . .]

This conclusion does not imply that humans have experienced few phenotypic adaptations, or that adaptations have not shaped genomic patterns of diversity. Comparisons of diversity and divergence levels at putatively functional versus neutral sites, for example, suggest that 10 to 15% [and possibly as many as 40% (29)] of amino acid differences between humans and chimpanzees were adaptive [e.g., (30)], as were 5% of substitutions in conserved noncoding regions (22, 29) and ~20% in UTRs (22). Given the paucity of classic sweeps revealed by our findings, an excess of functional divergence would point to the importance of other modes of adaptation. One way to categorize modes of adaptation is in terms of their effect on the allele frequencies at sites that affect the beneficial phenotype. In this view, classic sweeps bring new alleles to fixation; selection on standing variation or on multiple beneficial alleles brings rare or intermediate frequency alleles to fixation; and other forms of adaptation, such as selection on polygenic traits, increase or decrease allele frequencies to a lesser extent. Such changes in allele frequencies can decrease variation at closely linked sites—to a lesser extent than in a full sweep—and might therefore contribute to a reduction in diversity near functional elements (31) as well as to excess divergence. Alternatives to classic sweeps are likely for parameters applicable to human populations (7, 32); in particular, many phenotypes of interest are quantitative and plausibly result from selection at many loci of small effect (8).

An important implication is that in the search for targets of human adaptation, a change in focus is warranted. To date, selection scans have relied almost entirely on the sweep model, either explicitly (by considering strict neutrality as the null hypothesis and a classic sweep as the alternative) or implicitly (by ranking regions by a statistic thought to be sensitive to classic sweeps and focusing on the tails of the empirical distribution). It appears that few adaptations in humans took the form that these approaches are designed to detect, such that low-hanging fruits accessible by existing approaches may be largely depleted. Conversely, the more common modes of adaptation likely remain undetected. Thus, to dissect the genetic basis of human adaptations and assess what fraction of the genome was affected by positive selection, we need new tests to detect other modes of selection, such as comparisons between closely related populations that have adapted to drastically different environments [e.g., (33)] or methods that consider loci that contribute to the same phenotype jointly [e.g., (34)]. Moreover, if alleles that contribute to recent adaptations are often polymorphic within a population, genome-wide association studies should be highly informative.

DNA USA: A Genetic Biography of America

Apparently not due out for another year, but here's what Bryan Sykes has been working on:

The best-selling author of The Seven Daughters of Eve now turns his sights on the United States, one of the most genetically variegated countries in the world. From the blue-blooded pockets of old-WASP New England to the vast tribal lands of the Navajo, Bryan Sykes takes us on a historical genetic tour, interviewing genealogists, geneticists, anthropologists, and everyday Americans with compelling ancestral stories. His findings suggest: Of Americans whose ancestors came as slaves, virtually all have some European DNA. Racial intermixing appears least common among descendants of early New England colonists. There is clear evidence of Jewish genes among descendants of southwestern Spanish Catholics. Among white Americans, evidence of African DNA is most common in the South. European genes appeared among Native Americans as early as ten thousand years ago. An unprecedented look into America's genetic mosaic and an impressive contribution to how we perceive race, this is a fascinating book about what it means to be American.

Also of possible interest: Viking DNA: The Wirral and West Lancashire Project (Stephen Harding, Mark Jobling, Turi King); Surnames, DNA, and Family History (George Redmonds, Turi King, David Hey).

Some links

Ahnenkult: Miscellaneous musings on the Ainu; race quotes

Hail: USA’s Total Fertility Rates by Race, 1980-2008; The Decline of Abortion

Genetic Future: On sharing genes with friends

Forward: Newer DNA Tests Uncover Hidden Jewish Bloodlines

JASON: The $100 Genome: Implication for the DoD (US Department of Defense) (pdf)

Genome Res.: Adaptive selection of an incretin gene in Eurasian populations

Haplotype structure analysis suggests that the derived allele at rs2291725 arose to dominance in East Asians ~8100 yr ago due to positive selection. The combined results suggested that rs2291725 represents a functional mutation and may contribute to the population genetics observation. Given that GIP signaling plays a critical role in homeostasis regulation at both the enteroinsular and enteroadipocyte axes, our study highlights the importance of understanding adaptations in energy-balance regulation in the face of the emerging diabetes and obesity epidemics.

PLoS ONE: Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas

MBE: The Genetic Structure of Domestic Rabbits

Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries.

Am J Hum Biol.: Substantial variation in qPCR measured mean blood telomere lengths in young men from eleven European countries

Controlling for age and case-control status, telomere lengths averaged 10.20 kilobases (interpolated from qPCR measures) across study centers and ranged from 5.10 kilobases in Naples, Italy to 18.64 kilobases in Ghent, Belgium-a greater than threefold difference across populations.

La antropología física y los «zoológicos humanos»: exhibiciones de indígenas como práctica de popularización científica en el umbral del siglo XX

All along the nineteenth century different anthropological exhibitions were held in many countries, in which people from a number of indigenous communities, especially transported from their homeland for the occasion, were exhibited publicly, both for citizenship's instruction and for specialists's "in vivo" studies on human biology. This paper presents a brief description of some of these scientific shows, and tries to relate them to contemporary human biology theories.

NYT: Heavy Doses of DNA Data, With Few Side Effects

John Hawks: Genomes too cheap to meter

J Pers Soc Psychol.: To be liked versus respected: Divergent goals in interracial interactions

Pervasive representations of Blacks and Latinos as unintelligent and of Whites as racist may give rise to divergent impression management goals in interracial interactions. We present studies showing that in interracial interactions racial minorities seek to be respected and seen as competent more than Whites do, whereas Whites seek to be liked and seen as moral more than racial minorities do.

Norwegian foundation plans ancient DNA analysis of Rollo descendants

The Explico Historical Research Foundation:

will attempt to find out if Rollo the Viking [male line ancestor of William the Conqueror] was Danish or Norwegian to settle a dispute that has been going on for centuries in Scandinavia. This we will do by retrieving DNA from corpses of his descendants.

They say they "hope to be able to perform our analysis by Easter 2011." The foundation's other projects include searching for remnants of the Celts in Turkey and Goths north of the Black Sea. More:

- Successfully conducted research on the Easter Island, proving South American origin for parts of the Easter Island population through genomic HLA typing. This research indicates strongly that some of the original Easter Island inhabitants some how migrated to the island from the east, from South America, and not only from Polynesia in the west, which has been the official story of Easter Island immigration. The research report by professor Erik Thorsby can be read here.

- On the Canary Islands contributed to the understanding of how the Canary Islands were originally settled and by whom (Pereira et al: Population expansion in the North African Late Pleistoscene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 2010 10:390). Also, DNA from a Royal Native lineage on the Canary Island La Gomera proves a connection most likely with the Basque, North Portugal or a British 'Celtic' connection.

- In Normandy, in our search for famous historical figures, closed in the lead on the patriach of William the Conqueror, the great Viking giant Rollo, in order to solve a close to thousand year old riddle about his origin. To be continued..

- In the Ukraine on Crimea and the Black Sea coast of Azov our successful 2006 expedition work is now continued in the labs, hopefully providing us with new vital knowledge on the ancient Greeks, who they were and whom today are most closely related to them.

- In the Caribbean we have worked hard on finding the DNA and especially the Y-chromosome lineage of Christopher Columbus' heritage. This work now seems to have paid off, giving us the opportunity to make new revelations about one of the worlds greatest explorers.

- Established good contact and made all preparations ready for field work in Northern Africa. We are awaiting the neccesary permissions to continue our scientific work in the Atlas Mountains.

- Continued our work in the different fields of expertise involving new technologies and our constant search for new discoveries. We are currently involved in projects in the Caribbean, the Ukraine, in Peru, Russia, Spain, France, Turkey, on Greenland and in Scandinavia. The new technologies we continue to make use of are foremost DNA and the mapping of Human Migrations and Georadar instruments for discovering treasures underground.

(Via the GENEALOGY-DNA list.)

Open thread (5)

For links, comments, suggestions, etc. Previous open threads: 1 2 3 4

Not skin deep

Basque communist Maju thinks this study indicates "patterns of inter-population differentiation are stronger in the genes of appearance mostly" and "the actual underlying differences between populations [. . .] are invariably much smaller than it looks".

But this is not what the paper shows at all. The single most highly population-differentiated gene group in the authors's analysis relates to pituitary gland development. Next comes dorsoventral neural tube patterning. Then some low-level cellular functions, more brain development, sperm motility and development, and thyroid gland development. Pigmentation comes about halfway down the list and hair follicle development below that.

The placement of pituitary- and thyroid-related genes near the head of the list brought to mind Carleton Coon's comments on endocrines and racial differences in temperament.

Why a dominant China could spark tribal warfare

A commenter links to an article in Foreign Policy which argues:

With China's new prominence in global affairs, the Han race, which constitutes 90 percent of the Chinese population, is suddenly the most dominant cohesive ethnic group in the world -- and it is seeking to remain that way through strategic alliances, aggressive trade policy, and attacks on racial minorities within the country's boundaries. The less tribally cohesive, more fragmented West is, meanwhile, losing out. [. . .]

Such primitive racial instincts were supposed to be long ago passé: We're supposed to be living in Thomas Friedman's "flat" world or Kenichi Ohmae's "borderless world." By now, supposedly, everyone is increasingly interconnected and undifferentiated. Affairs should be managed neatly by deracinated professionals, working on their iPads from Brussels, Washington, or any of the other "global" capitals.

But most people do not really see themselves as members of a large multinational unit, global citizens, or "mass consumers." Instead the drivers of history remain the essentials: the desire to feed one's family, support the health of the tribe, and shape the immediate community. The particularistic continues to trump the universalistic.

On differences within Europe:

The wigger mindset

A reader forwards a reference to this passage by Hebrew wigger / wigger expert William Upski Wimsatt. In line with my own perception of what motivates these types, Wimsatt acknowledges "romanticization of blacks was also a way to elevate myself":

Why does head form change in children of immigrants? A reappraisal.

More from Jantz on Boas:

CONCLUSIONS: The results support the two hypotheses tested. Change in Hebrew cranial indices resulted from abandoning the practice of cradling infants in America. U.S.-born Sicilian children experienced an environment worse than the one in Europe, and consequently experienced impaired growth. We conclude that the changes Boas observed resulted from specific behavioral and economic conditions unique to each group, rather than a homogeneous American environment.

Greater population differences for some functional genes

Different level of population differentiation among human genes:

Background
During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations.

Results
Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.

Conclusion
Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

Provisional pdf.

Blonde women earn more, have husbands who earn more

David W. Johnston. Physical Appearance and Wages: Do Blondes Have More Fun? (Economic Letters 108, s. 10-12):

Our data source is the 1979 cohort of the National Longitudinal Survey of Youth (NLSY79). [. . .] We limit our sample to Caucasian women aged 25 and over. [. . .] Regression results indicate that blonde women receive a wage premium equivalent in size to the return for an extra year of schooling. A significant blondeness effect is also evident in the marriage market. Blonde women are no more or less likely to be married; but, their spouse's wages are around 6% higher than the wages of other spouse's.

Twenty-eleven

I'll skip the predictions (you're welcome to post your own), and just post a bit more information on a few projects that should be announcing results this year:

(1) Otzi genome. Here's a 9 minute podcast from Life Technologies containing a few more details:
- "above 5X coverage"
- "looking at potentially medically-relevant SNPs"
- "this individual living over 5000 years ago would represent an ancestor for, we think, a significant proportion of the European population."
- "looking at his ancestry and indeed trying to determine exactly where is he from"

(2) People of the British Isles Project. A movie from the Wellcome Trust:



Most interestingly, the project is now collecting phenotypic data, including skin color, and taking 3-d facial photographs. Bodmer: "The next stage of our study, we're now taking pictures of people's faces so we can analyze components statistically [. . .] and then look for the genetic features behind that. What are the genes, what are the variations that determine facial features. Will it be possible to reconstruct from a piece of DNA what a person really looked like."

(3) 1000 Genomes Project. Another short film by the Wellcome Trust:



Chris Tyler-Smith: "[The project has] told us that natural selection has influenced virtually every part of our genome [. . .] we've now got a catalog of some thousands of genes that we think have been specifically positively selected in our fairly recent history."

Evidence for Homo erectus genes in Papuans (and Chinese)?

Steve Sailer says he's "been alerted that there should be science news soon of a caliber comparable to the recent human-neanderthal inter-mating story." At Gene Expression, Greg Cochran calls attention to a comparison in the supplementary material of the Neanderthal genome paper showing "San closer to Han+French than to" Papuans. The San are also shown to be closer to the French than to the Chinese (and the Papuan closer to Han than French), though to a lesser degree. In addition, the San are shown to be closer to Han+French than to Yorubans, perhaps reflecting archaic admixture among West Africans; on the other hand, Yorubans are closer to non-Africans than to San.

Incidentally, this last point is in keeping with Kalinowski's assertion based on autosomal STR data. But as before I'm inclined to attribute any increased similarity between Negroids (as opposed to Bushmen) and non-Africans to back-migration from Eurasia to Africa, given that Y chromosomes likely of ultimate Eurasian origin (namely, E, and to a much lesser extent R1b, lineages) predominate among Negroids, while among Bushmen older clades predominate.

Update: A commenter passes on a link to a Google translation of a Spanish newspaper article reporting that Paabo and friends have sequenced the genome of the Denisova hominin, evidently a Homo erectus, and found evidence that genes related to the specimen persist in Melanesians. Update 2: Links are now dead (I assume the story is still supposed to be under embargo); see below for Google translation. Update 3: Much more information on this story is now available elsewhere, of course.

The computer program STRUCTURE does not reliably identify the main genetic clusters within species

Says this guy. While the author seems to be motivated by race-denialism, I think he's probably right that "forcing STRUCTURE to place individuals into too few clusters" can lead to non-optimal results (which would be consistent with what Dienekes appears to be finding). Certainly, contra Rienzi's railing against "incompetent amateurs, with their K=15 ADMIXTURE plots and clustering with up to 124 components", there's no reason to assume that in general runs with lower K will give more meaningful or accurate results than runs with higher K using programs like STRUCTURE and admixture.

I'm not terribly interested in Kalinowski's specific attempt to prove that African farmers are genetically closer to Europeans than to African hunter gatherers, but two things: (1) if this is true, I'd say it's much more likely to be attributable to back-migrations from Eurasia than to Europeans being descended from "African farmers"; (2) I enjoyed the section of the article in which the author promotes neighbor-joining trees as a superior method for visualizing relationships between populations, only to go on to explain that "even a tree with a R2 of 0.98 does not accurately depict all of the relationships between populations" since it still "depicts all sub-Saharan African populations as being more similar to each other than to European populations."

Reference: KALINOWSKI ST (2010) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity (Published online). pdf

Google ngrams

"dumb blonde"

"fair and handsome" vs. "dark and handsome"

"melting pot"

"immigrant stock"

"nation of immigrants"

Use ngrams tool here or see Science paper here.

The Denisova hominin need not be an out of Africa story

I had a similar reaction when the original article was published, but this piece in the Journal of Human Evolution makes a much more extensive and better-argued case:

The recent retrieval of a complete mitochondrial (mt) DNA sequence from a 48–30 ka human bone from Denisova (Siberia) (Krause et al., 2010) is a remarkable achievement fully deserving international acclaim. Without wishing to detract from this feat, however, we wish to challenge their conclusion that the Denisova hominin “derives from a hominin migration out of Africa [ca. 1.0 Ma] distinct from that of the ancestors of Neanderthals and of modern humans” (Krause et al., 2010: 894). In addition, we challenge their assumption that the ancestors of the Neanderthals left Africa between 500–300 ka. In our view, alternative interpretations of the evidence are available and should be considered.

Longer excerpts below: