Category: Population Genetics

Out of Africa's end?

By Razib Khan | September 17, 2011 12:54 pm

The BBC has a news report up gathering reactions to a new PLoS ONE paper, The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology. This paper reports on remains found in Nigeria which date to ~13,000 years B.P. that exhibit a very archaic morphology. In other words, they may not be anatomically modern humans. A few years ago this would have been laughed out of the room, but science moves. Here is Chris Stringer in the BBC piece:

“[The skull] has got a much more primitive appearance, even though it is only 13,000 years old,” said Chris Stringer, from London’s Natural History Museum, who was part of the team of researchers.

“This suggests that human evolution in Africa was more complex… the transition to modern humans was not a straight transition and then a cut off.”

Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.

They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought.

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Tutsi probably differ genetically from the Hutu

By Razib Khan | August 29, 2011 11:04 pm

Paul Kagame with Barack and Michelle Obama

I first heard about Rwanda in the 1980s in relation to Dian Fossey’s work with mountain gorillas. The details around this were tragic enough, but obviously what happened in 1994 washed away the events dramatized in Gorillas in the Mist in terms of their scale and magnitude. That period was a time when the idea of “ancient hatreds” leading to internecine conflict was in the air. It was highlighted by the series of wars in the former Yugoslavia, and the TutsiHutu civil wars in Rwanda, Burundi, and Congo. Of the latter the events in 1994 in Rwanda were only the most prominent and well known.

After having read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa I am relatively conscious of the broader canvas of what occurred in Central and East Africa in the 1990s. Not only was there a conflict between Tutsi and Hutu in Rwanda, but a similar dynamic also flared up in Burundi. The tensions are more complex in Congo and Uganda, in large part because there are many ethnic players, and the Hutu role as the antagonists with the Tutsi is divided among many different populations. In trying to distill the complex ethnography of this region in setting the structural parameters of the landscape into which the violence of the late 20th century emerged many pundits have pointed to the role of the Belgian colonial authorities in crystallizing, sharpening, and perhaps even originating the distinction between Tutsis and Hutus. This is not totally unreasonable if you don’t know much. A quick “look up” will confirm that there is no linguistic or religious distinction between the two groups; they share a common culture in many ways. Rather, the differences seem more of class and ecology. The Tutsi minority had a much stronger pastoral element to their economy. The Hutus were conventional farmers, clear legacies of the Bantu expansion which swept from West-Central Africa east and south, all the way to the Cape of Good Hope and the Indian Ocean. As is not uncommon in the history of humankind the pastoral Tutsi tended to dominate the Hutu peasant. This is where the class dimensions are clearest, as the modest Hutu were traditionally ruled by the wealthier Tutsi aristocracy.

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The geography of genes tells us only so much about history

By Razib Khan | August 24, 2011 11:29 pm

L. L. Cavalli-Sforza’s The History and Geography of Human Genes is a book I reference a great deal. Cavalli-Sforza is the godfather of the field of historical population genetics, the phylogeography of humankind. Though his work was on classical autosomal markers, the huge literature which drew inferences from Y chromosomal and mtDNA variation followed in the wake of the The History and Geography of Human Genes. Spencer Wells, the director of the Genographic Project, alluded to Cavalli-Sforza’s influence in The Journey of Man. But at this point I think we have to be very careful of making inferences about the past from present patterns of genetic variation. This is made most stark by the fact that ancient DNA, which is a snapshot of the past, as opposed to an inference of it, sometimes diverges from our expectations based on present patterns of variation in surprising ways.

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The point mutation which made humanity

By Razib Khan | August 16, 2011 1:30 am

Steve Hsu points me to a piece in The New Yorker on the science and personality of Svante Pääbo. The personality part includes references to Pääbo’s bisexuality, which to me seemed to be literally dropped into the prose to spice it up. Of course it was the science which I found interesting. There are many more bisexuals than there are heterodox scientists. And yet like many researchers of yore it seems that Pääbo is out to find the genes which make humanity distinctive as we understand it (if the reporting is accurate, which I don’t take as a given). There are some interesting tantalizing clues littered about; some genes implicated in autism seem to exhibit Neandertal vs. modern human differences (with the Neandertals carrying the autism-implicated variants).

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DIY admixture analysis

By Razib Khan | July 27, 2011 11:24 am

Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to work fine. It is somewhat limited in that you start out with the parameters which Dienekes has set for you, but if you don’t want to write your own scripts and get familiar with all the scientific programs out there, I think this is a very good option. Additionally, it seems to run rather fast, so you won’t spend days experimenting with different parameters.

Dienekes has already run me, but I put my parents’ genotype files through the system. Here are the results:

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Why the human X chromosome is less diverse

By Razib Khan | July 25, 2011 12:37 am

The Pith: The human X chromosome is subject to more pressure from natural selection, resulting in less genetic diversity. But, the differences in diversity of X chromosomes across human populations seem to be more a function of population history than differences in the power of natural selection across those populations.

In the past few years there has been a finding that the human X chromosome exhibits less genetic diversity than the non-sex regions of the genome, the autosome. Why? On the face of it this might seem inexplicable, but a few basic structural factors derived from the architecture of the human genome present themselves.

First, in males the X chromosome is hemizygous, rendering it more exposed to selection. This is rather straightforward once you move beyond the jargon. Human males have only one copy of genes which express on the X chromosome, because they have only one X chromosome. In contrast, females have two X chromosomes. This is the reason why sex linked traits in humans are disproportionately male. For genes on the X chromosome women can be carriers of many diseases because they have two copies of a gene, and one copy may be functional. In contrast, a male has only a functional or nonfunctional version of the gene, because he has one copy on the X chromosome. This is different from the case on the autosome, where both males and females have two copies of every gene.

This structural divergence matters for the selective dynamics operative upon the X chromosome vs. the autosome. On the autosome recessive traits pay far less of a cost in terms of fitness than they do on the X chromosome, because in the case of the latter they’re much more often exposed to natural selection via males. In the rest of the genome recessive traits only pay the cost of their shortcomings when they’re present as two copies in an individual, homozygotes. A simple quasi-formal example illustrates the process.

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Reify my genes!

By Razib Khan | June 28, 2011 1:04 am


In the comments below Antonio pointed me to this working paper, What Do DNA Ancestry Tests Reveal About Americans’ Identity? Examining Public Opinion on Race and Genomics. I am perhaps being a bit dull but I can’t figure where its latest version is found online (I stumbled upon what looks like another working paper version on one of the authors’ websites). Here’s the abstract:

Genomics research will soon have a deep impact on many aspects of our lives, but its political implications and associations remain undeveloped. Our broad goal in this research project is to analyze what Americans are learning about genomic science, and how they are responding to this new and potentially fraught technology.

We pursue that goal here by focusing on one arena of the genomics revolution — its relationship to racial and ethnic identity. Genomic ancestry testing may either blur racial boundaries by showing them to be indistinct or mixed, or reify racial boundaries by revealing ancestral homogeneity or pointing toward a particular geographic area or group as likely forebears. Some tests, or some contexts, may permit both outcomes. In parallel fashion, genomic information about race can emphasize its malleability and social constructedness or its possible biological bases. We posit that what information individuals choose to obtain, and how they respond to genomic information about racial ancestry will depend in part on their own racial or ethnic identity.

We evaluate these hypotheses in three ways. The first is a public opinion survey including vignettes about hypothetical individuals who received contrasting DNA test results. Second is an automated content analysis of about 5,500 newspaper articles that focused on race-related genomics research. Finally, we perform a finer-grained, hand-coded, content analysis of about 700 articles profiling people who took DNA ancestry tests.

Three major findings parallel the three empirical analyses. First, most respondents find the results of DNA ancestry tests persuasive, but blacks and whites have very different emotional responses and effects on their racial identity. Asians and Hispanics range between those two poles, while multiracials show a distinct pattern of reaction. Second, newspaper articles do more to teach the American reading public that race has a genetic component than that race is a purely social construction. Third, African Americans are disproportionately likely to react with displeasure to tests that imply a blurring of racial classifications. The paper concludes with a discussion, outline of next steps, and observations about the significance of genomics for political science and politics.

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John Gillespie, "the evil scientist from America"

By Razib Khan | April 20, 2011 1:35 am

I own a book of Motoo Kimura’s collected papers, and of course I have a copy of John Gillespie’s Population Genetics: A Concise Guide. But I’d forgotten the acrimony between the two men. Gillespie has been retired for half a decade now, while Kimura died in in 1994. I randomly stumbled onto an old newspaper story from 1992 covering the feud between these two eminent population geneticsts, Scientists in Open War over “Neutral Theory” of Genetics. It was in the Sacramento Bee, which is based near Gillespie’s university. The background is that both were principals in the “neutralist–selectionist” debate of the 1970s and 1980s. Kimura was one of the main theoretical architects of the neutral theory of molecular evolution, which eventually spread its influence to the point where old-line adaptationists such as Richard Dawkins had to offer up a counter-argument.

Some choice bits:

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CATEGORIZED UNDER: Genetics, Population Genetics

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