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."

Cranial differentiation of eastern and western pygmies

Diversity among African Pygmies (PLoS One):

Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. [. . .] Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.

Middle-eastern milk drinkers?

A Der Spiegel article makes a case for the role of mass migration in shaping the European gene pool, while failing to mention the evidence for large-scale post-Neolithic population replacement. Jean M is unclear on whether the attempt to link lactase persistence to the LBK rests on unpublished aDNA results or questionable computer models. Greg Cochran on the latter eventuality:

Judging from the comment about lactose tolerance in Austria/Slovakia/Hungary, they may be relying on a paper that came out of Mark Thomas's lab last year: "The Origins of Lactase Persistence in Europe".
The authors of that paper tried to estimate the region of origin using simulations - but one of the inputs was the current distribution of that allele. Which is reasonable, except that they did not use the actual distribution of that allele, but rather a truncated distribution - their map is centered on central Europe and stops halfway through the Ukraine. That ensured that they would find an origin in somewhere in middleuropa.

The allele doesn't stop there, though: it has a second region of fairly high frequency in northern India. Before Mongols and Turks took over the Eurasian steppe, the frequency of that allele may have been high in those steppe regions. Scythians are described as milk-drinkers quite a while ago - in the Iliad. And my sources claim that the royal guard of the Hittites also 'drank sweet milk'...

Checking out ancient DNA from Kurgan burials in that region might clarify this.

I think it is difficult to imagine a historical process that moves a lot of people from Bavaria to the Punjab: it is easier to imagine one that expands to both regions from somewhere in-between.
Which would explain the distribution of the Indo-European languages, also.

When you think about it, it may not be easy for German researchers to talk about this hypothesis. I think they have trouble saying "Aryan" nowadays.

John Hawks agrees:

Problem is: from the standpoint of ancient DNA samples, the lactase persistence mutation was also absent within the early Neolithic! The article is full of details that are wrong or misleading. [. . .]

The [mtDNA] differences between early Neolithic and later Europeans suggests that post-Neolithic migrations -- real Völkerwandurung -- actually had a major impact on the European gene pool. What we see today is not a pattern established 6000 years ago, but a palimpsest richly painted with strokes from successive migrations.

One aspect of this scenario: There's no reason to link the early Neolithic with Indo-European languages. There were many later widespread population movements that might have carried this language family, and we know that these later movements were genetically decisive -- at least, as concerns the maternal genealogy. The relation of Y chromosome haplogroups with mtDNA haplogroups is a critical question, but even more necessary is the development of an effective means of testing these hypotheses with nuclear genotype data.

Miscellaneous links

Bio-IT World road to $1,000 genome issue (via Genomes Unzipped)

Distinct clones of Yersinia pestis Caused the Black Death (via Jean M)

Inference of Unexpected Genetic Relatedness among Individuals in HapMap Phase III

"non-western children don’t do so well on the old mirror-recognition test"

"Lost" Francis Crick correspondence found

Wilkins [. . .] complained to Crick and Watson in a rediscovered letter: "To think that Rosie had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ."

A rare variant of the mtDNA HVS1 sequence in the hairs of Napoleon's family

Darwin's Family Tree Re-Discovered

The horse, the wheel, and language

It appears someone took the liberty of uploading David Anthony's book on Indo-European origins to scribd. Read and discuss if you wish.

Genetic deterioration of modern populations?

A post by Notus Wind brought this paper to my attention:

Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. [. . .] a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.

I know Hamilton expressed similar concerns, but to the extent accelerated accumulation of deleterious mutations under modern conditions is a real/serious problem this author's suggestion of "multigenerational cryogenic storage and utilization of gametes and/or embryos" seems preferable to some of Hamilton's goofier "solutions" (such as marrying HIV- Nairobi prostitutes to protect one's offspring from impending AIDS epidemic). I'm not too worried about imminent mutational meltdown (some modern "problems" like antibiotics may be in the process of solving themselves), but from a strictly conservationist or even historical standpoint, large-scale, long-term storage of human genetic and/or gametic material makes sense. If we can see the need for plants and animals, why not for ourselves?

Ptolemy map of ancient Germania deciphered

Berlin Researchers Crack the Ptolemy Code

All this offers up rather exciting prospects, since it makes half the cities in Germany suddenly 1,000 years older than previously believed. "Our atlas is a treasure map," team member Andreas Kleineberg says proudly, "and the coordinates lead to lost places in our past."

Archaeological interest in the map will likely be correspondingly large. Archaeologists' opinions on the Germanic tribes have varied over the years. In the 19th century, Germany's early inhabitants were considered brave, wild-bearded savages. The Nazis then transformed them into great heroes, and in the process of coming to terms with its Nazi past, postwar Germany quickly demoted the early Germanic peoples to proto-fascist hicks. [. . .] More recent research proves this view to be complete invention.