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:

China spying on deCODE?

Wikileaks: US Says Chinese Spies Operate in Iceland

Chinese authorities are believed to be spying on companies involved in genealogy and medical research in Iceland, as stated in documents sent by the US Embassy in Reykjavík to the US Foreign Service in Washington, leaked by Wikileaks.

This is stated in a report from February 26, 2009, which is marked as “confidential”. Copies of it were sent to the CIA, FBI and DIA, Fréttabladid reports.

In another report from December 24, 2009, also marked as “confidential”, an annual meeting of the US Embassy’s counter-spying group directed by the ambassador’s substitute Sam Watson is covered.

The report states that US authorities believe that their Chinese counterparts have continued with their intellectual spying in Iceland, by means of human intelligence and with technical equipment, such as bugging telephone lines and breaking into databases on the internet.

deCODE employs a Chinese national as "Vice President of Statistics", but Kari Steffanson is unconcerned on that front since the employee "has lived here for 14 years and considers Iceland his home".

Ethnic origins of Quebec regional populations estimated from genealogy

Tables from Admixed Ancestry and Stratification of Quebec Regional Populations:

New England self-perception circa 1810

Some fairly random excerpts from Timothy Dwight's Travels in New England and New York (4 vols., 1821–1822).

Miscellaneous links

Polako: Locating and visualizing minority non-European admixtures across our genomes

Dienekes: Clusters galore: extremely fine-scale ancestry inference

Rienzi fumes about Dienekes' description of his own efforts as "cutting edge" and explains:

In my opinion, Dienekes and Doug McDonald and Polako should be commended for attempting to further our understanding of human genetic diversity. They are trying to broaden our understanding. Hopefully, all three gentlemen are self-aware enough to know that their "findings" are at best tentative, should be interpreted cautiously, and await confirmation in the literature.

This is not how science works. Anyone can download the software and reference data Dienekes is playing with and attempt to verify or impugn his results. Certainly some amateurs make ridiculous claims based on faulty analyses. So do some commercial entities and published academics. If you're not able to assess Dienekes' work on it's own merits, you're not in a better position to do so with comparable research merely because it has passed "peer review". One can certainly choose to ignore results generated by amateurs if one pleases, but choosing to do so has no bearing on the validity of the results.

Hail: The Blackest Surnames in the USA; The Hated Richard Nixon’s Ancestry

Another theory on the origin of blond hair:

Many traits have been investigated for their role in attractiveness, but one question has repeatedly captured the attention of researchers down the years – why do many men prefer blondes? Over time, many explanations have been put forward. It has been suggested that men prefer rounder faces and that blonde hair is kinder to the outline of the face, or that natural blondes have softer skin, which men find attractive. Another suggestion is that blondes were a genetic mutation which men evolved to value as a status symbol because of the original scarcity.

But according to research out of the University of California, the answer is that blonde hair, like the peacock's tail or the rooster's bright-red plumage, is a sign of fitness. The evolutionary reason why men are attracted to blondes is that the hair and skin colour make it easier to spot problems. Anaemia, jaundice, skin infections, cyanosis (a sign of heart disease) and some other conditions, are, these researchers say, much easier to detect in fair-skinned individuals than in brunettes.

Genetic Evidence for Multiple Biological Mechanisms Underlying In-Group Favoritism

The best-fitting model revealed that a biological mechanism facilitates affiliation with arbitrary groups and exists alongside essentialist systems that evolved to process salient cues, such as shared beliefs and ancestry.

7 Ways the Mafia Made the U.S. a Better Place

TGGP drops a link to an article (republished by the ever-daring LewRockwell.com) by a HuffingtonPost contributor who fancies himself a purveyor of "Renegade History". Thaddeus Russell says America has Jewish and Italian gangsters to thank for:

• Jazz music
  
• Las Vegas
  
• Hollywood
  
• Racial mixing
  
• "Gay liberation"
  

I especially enjoyed Russell's retelling of how plucky Jewish gangsters and movie makers warded off attempts by Thomas Edison's thugs to defend Edison's intellectual and physical property:

23andMe sale today (24 November)

For those who are interested, according to someone on twitter:

DIYgenomics: @23andMe $99 discount returns; code B84YAG to be live 10 AM Wednesday for the new v3 chip

The updated chip is said to be the Illumina OmniExpress Plus:

The original press release described a chip with coverage of 733,202 markers, while the enhanced "Plus" version appears to cover greater than 900,000 markers. Either way, it is a significant upgrade from the previous 580,000 SNPs.

Update: Discount code works. New chip tests 1,000,000+ SNPs.

Conferences

PDF slides of some presentations from Family Tree DNA's "6th International Conference on Genetic Genealogy", which took place at the end of October: Family Finder: Looking Under the Hood; Family Finder & Population Finder; "Inferring Genetic Ancestry: Oppourtunities, Challenges, and Implications"; IT Roadmap 2010; Predicting Individual Ancestry Using Genome-wide Genetic Data; Summarizing and Anticipating the Next Decade with NRY, mtDNA, and Autosomal DNA; Walk Through the Y Project.

Michael Hammer (according to an attendee): "village of origin can and will be done in the future as the database grows".

The 60th Annual ASHG meeting was held November 2-6 in Washington, D.C. A 23andMe employee comments and links to other coverage (see end of post) here. Video and slides from a 1000 Genomes Project tutorial here.

According to Luke Jostins:

at Biology of Genomes conference in May of next year; we’ll be putting out a large (~1100) sample dataset from around a dozen populations. These will be based on low-coverage whole-genome and high-coverage exome data on every sample, along with >2M genotypes from the Omni2.5 chip, to create a very high-quality set of data. Lots of work is going into putting together combined SNP, indel and CNV calls as nicely phased haplotypes. This dataset should be a massive boon to association studies

This should also provide an additional public source of data for people undertaking projects like Polako's and Dienekes'.

CF mutant heterozygote advantage in heavy metal exposure

Teeth and leg bones from Iron Age people are showing a 21st century scientific-research team that there might be an evolutionary silver lining to the gene defects that cause cystic fibrosis (CF)

DNA analysis of ancient archeological finds is revealing that some CF gene defects may protect those who carry them from lead and other metal poisoning, or perhaps tuberculosis. [. . .]

Since the protective CF gene mutation is so common among people living in or coming originally from central and Western Europe, Farrell suspects that the mutation first arose in that part of the world, very likely in early Celtic populations. [. . .]

To understand what in the environment could cause the mutated CF gene to occur in the first place, Farrell turned to ancient burial remains. Evidence from his earlier studies already showed that transgenic mice carrying the gene might be resistant to lead toxicity. He wanted to see if there were links to people living in Europe during the Iron and Bronze Ages.

“This was an era in which people were exposed to toxic heavy metals for the first time in history,” he says. [. . .]

The first analyses are showing that specimens containing CF gene defects were not affected by lead or other metal poisoning, hinting at the mutation’s protective advantage. The specimens also contained very little tuberculosis. The scientists can’t pinpoint exactly where the first CF carrier may have lived, but they think current day Austria is a good candidate.

Via Jean M. The manuscript is freely available at Nature Precedings: Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans

Icelandic C1 distinct from Amerindian and Asian subclades

A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out. Am J Phys Anthropol, 2010.

The logic and evidence behind the authors' assertion that "a Native American origin seems most likely" is wanting; I find it much more likely C1 entered Iceland via Europe. Scientists will need to look elsewhere to explain Björk.

The 11 mutations that differentiate the Icelandic C1 sequences from the C1 root are in the upper range of mutation counts that differentiate the other C1 sequences from the root. [. . .]

A simple [polite way of saying retarded] argument in favor of a Native American origin of C1e is the fact that three of the four previously characterized C1 subclades are associated with these groups and the vast majority of C1 sequences in the literature have been sampled from individuals of Native American ancestry. [. . .]

The German sequence (Pfeiffer et al., 2001) represents a perfect match to the Icelandic C1e for the short HVS1 fragment spanning sites 16024–16365. This raises the intriguing, but perhaps unlikely, hypothesis that C1e is a European-specific subclade of C1, following the precedent of the European and Native American subclades of mtDNA haplogroup X2 (Brown et al., 1998; Reidla et al., 2003). However, given the dense sampling of mtDNA variation in European populations, it is clear that C1e is exceedingly rare, a fact that weighs against a hypothesis of antiquity in Europe.

The frequency of C1 in a sample of 1538 Icelandic mtDNA sequences was 0.26%. Coincidentally, another abstract that recently appeared in PubMed is that of a Russian publication reporting:

The role of natural selection in the evolution of human populations from Northeastern Eurasia was studied. Selection for the regions-specific haplogroup C was demonstrated.

Update on People of the British Isles project

A reader forwarded me this message, posted to a mailing list by a third party:

One of my project members wrote to one of the organisers of the People of the British Isles Project to find out a few more details. He was told the following:

"The data will be made publicly available after we have done some analyses, and so anyone should be able to get hold of it when it is!

As for SNPs, we have had 3,000 samples typed on a large scale (about 1.2M SNPs, of which something like 2,000 are on the Y-chromosome). There are about 150 or so that are on the y-chromosome consortium tree, so hopefully we should get quite a lot of information out of the analyses!"

That should make a big difference to Population Finder and all the other admixture tests. Perhaps those of us who already know that we are of 100% British origin might then actually get some meaningful results. The Orkney Islands are not exactly a good proxy for the entire British Isles!

The website is showing a total of 4214 samples collected.

Amerindian admixture in Gaspesia (Franch Canadia)

When Genetics and Genealogies Tell Different Stories-Maternal Lineages in Gaspesia

Data from uniparentally inherited genetic systems were used to trace evolution of human populations. Reconstruction of the past primarily relies on variation in present-day populations, limiting historical inference to lineages that are found among living subjects. Our analysis of four population groups in the Gaspé Peninsula, demonstrates how this may occasionally lead to erroneous interpretations. Mitochondrial DNA analysis of Gaspesians revealed an important admixture with Native Americans. The most likely scenario links this admixture to French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century. However, in contrast to genetic data, analysis of genealogical record shows that Native American maternal lineages were brought to Gaspesia in the 18th century by Acadians who settled on the south-western coast of the peninsula. Intriguingly, within three generations, virtually all Métis Acadian families separated from their nonadmixed relatives and moved eastward mixing in with other Gaspesian groups, in which Native American maternal lines are present in relatively high frequencies. Over time, the carriers of these lines eventually lost memory of their mixed Amerindian-Acadian origin. Our results show that a reliable reconstruction of population history requires cross-verification of different data sources for consistency, thus favouring multidisciplinary approaches.

I haven't read the article, so I have no idea on what basis the authors assert DNA results specifically pointed to "French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century" as the most likely source of the admixture; but I'm all in favor of integrating DNA results with genealogical records in studies of this sort.

Ancestry analysis method

Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010 Oct 15;11(1):94.

BACKGROUND: The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations in space and time. However, the size of the datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as the STRUCTURE or BAPS software may not be able to cope with this unprecedented amount of data. Thus, there is a need for less computer-intensive approaches. Multivariate analyses seem particularly appealing as they are specifically devoted to extracting information from large datasets. Unfortunately, currently available multivariate methods still lack some essential features needed to study the genetic structure of natural populations.

RESULTS: We introduce the Discriminant Analysis of Principal Components (DAPC), a multivariate method designed to identify and describe clusters of genetically related individuals. When group priors are lacking, DAPC uses sequential K-means and model selection to infer genetic clusters. Our approach allows extracting rich information from genetic data, providing assignment of individuals to groups, a visual assessment of between-population differentiation, and contribution of individual alleles to population structuring. We evaluate the performance of our method using simulated data, which were also analyzed using STRUCTURE as a benchmark. Additionally, we illustrate the method by analyzing microsatellite polymorphism in worldwide human populations and hemagglutinin gene sequence variation in seasonal influenza.

CONCLUSIONS: Analysis of simulated data revealed that our approach performs generally better than STRUCTURE at characterizing population subdivision. The tools implemented in DAPC for the identification of clusters and graphical representation of between-group structures allow to unravel complex population structures. Our approach is also faster than Bayesian clustering algorithms by several orders of magnitude, and may be applicable to a wider range of datasets.

Website: http://adegenet.r-forge.r-project.org/

Demographic simulation framework

Ray N, Currat M, Foll M, Excoffier L. SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics. 2010 Oct 17.

SUMMARY: SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially-explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs, or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework. Availability and Implementation: SPLATCHE2 is a C++ program compiled for Windows and Linux platforms. It is freely available at www.splatche.com, together with its related documentation and example data. CONTACT: mathias.currat@unige.ch.

Masculinity, skin color, and male facial attractiveness

Does Masculinity Matter? The Contribution of Masculine Face Shape to Male Attractiveness in Humans (PLoS ONE):

The proposal [. . .] that masculine men are immunocompetent and attractive – underpins a large literature on facial masculinity preferences. Recently, theoretical models have suggested that current condition may be a better index of mate value than past immunocompetence. This is particularly likely in populations where pathogenic fluctuation is fast relative to host life history. As life history is slow in humans, there is reason to expect that, among humans, condition-dependent traits might contribute more to attractiveness than relatively stable traits such as masculinity. [. . .]

The relationship between masculinity and attractiveness was assessed in two samples of male faces. Most previous research has assessed masculinity either with subjective ratings or with simple anatomical measures. Here, we used geometric morphometric techniques to assess facial masculinity, generating a morphological masculinity measure based on a discriminant function that correctly classified >96% faces as male or female. When assessed using this measure, there was no relationship between morphological masculinity and rated attractiveness. In contrast, skin colour – a fluctuating, condition-dependent cue – was a significant predictor of attractiveness.

The authors point out problems with attempts to assess the affect of masculinity on facial attractiveness that rely on human ratings of perceived masculinity or digital manipulation of photographs: (1) for rated masculinity, "subjective judgments of masculinity are based on factors other than just morphological masculinity"; (2) with morphing techniques, factors potentially more important than masculinity in determining real world attractiveness are not allowed to vary, and a preference for averageness might result in participants systematically preferring more or less masculine morphs even if women are completely indifferent to masculinity. As for the effects of skin color, in this sample:

The regression retained only skin yellowness as a predictor of attractiveness, and the effect of skin yellowness was positive and highly significant (F(1,71) = 10.806, Beta = .366, t = 3.287, p<.002). Skin lightness, redness and morphological masculinity did not significantly predict attractiveness (all p>.114, see Table 1).

Other studies have also found increased skin lightness and redness associated with perceived health and attractiveness. The association of yellowness with attractiveness "may be attributable to dietary carotenoid deposition in the skin. This suggests that carotenoids, which are involved in health signaling (Massaro et al. 2003; Saks et al. 2003) and sexual selection (Eley 1991; MacDougall and Montgomerie 2003; Massaro et al. 2003) in many species of birds and fish, may also affect the appearance of health in humans."

Race and physical attraction

A commenter links to a 2007 neuropolitics.org post ("Who Are The Caucasians Attracted To? Politics, Religion, and Physical Attraction") that reports the following survey results. As expected, "white females were more attracted to whites than are white males".

Miscellaneous links

Mangan on Transparency International's World Corruption Index

A One-Way Human Mission to Mars:

There are many reasons why a human colony on Mars is a desirable goal, scientifically and politically. The strategy of one-way missions brings this goal within technological and financial feasibility. Nevertheless, to attain it would require [. . .] a return to the exploration spirit and risk-taking ethos of the great period of Earth exploration, from Columbus to Amundsen, but which has nowadays being replaced with a culture of safety and political correctness.

The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms.

The Lost Tribes of Europe ("As national borders blur, the Continent's original minorities are fighting to reclaim their ancient cultures and identities")

Steve Sailer mentions: "a video of part of the amazing 1983 documentary First Contact with footage of the arrival of Australian explorers in the highlands of New Guinea around 1930."