There has been a lot of talk in the media about a new paper which reports that the Y chromosome is not deteriorating, as had been previously inferred from the data. In the 2004 Bryan Sykes wrote Adam’s Curse: A Future Without Men which used this model as a framing device (and naturally elicited great general interest). You can read some earlier critiques at Gene Expression Classic. I never paid attention to this debate in the details because it seemed ludicrous on the face of it. Bryan Sykes’ was predicting the extinction of males in ~100,000 years. Right, we just happen to be living right before the genomic Götterdämmerung. I don’t think so. Sometimes absurd results which fly in the face of plain history and robust theory are profoundly insightful. But most of the time they’re just false leads.

We Are All Panamanians:

When the Isthmus of Panama rose from the sea, it may have changed the climate of Africa–and encouraged the evolution of humans.

The emergence of the Isthmus of Panama has been credited with many milestones in Earth’s history. When it rose from the sea some 3 million years ago, the isthmus provided a bridge for the migration of animals between North and South America, forever changing the fauna of both continents. It also blocked a current that once flowed west from Africa to Asia, diverting it northward to strengthen the Gulf Stream. Now Steven Stanley, a paleobiologist at Johns Hopkins, says that that change in currents may be behind yet another major event: the evolution of humans. When the isthmus rearranged the ocean, he says, it triggered a series of ice ages that in turn had a crucial impact on the evolution of hominids in Africa.

Question: do we have enough nukes to re-open the isthmus?

Recently Jason Antrosio began a dialogue with readers of this weblog on the “race question.” More specifically, he asked that we peruse a 2009 review of the race question in the American Journal of Physical Anthropology. Additionally, he also pointed me to another 2009 paper in Genome Research, Non-Darwinian estimation: My ancestors, my genes’ ancestors. Normally I don’t react well to interactions anthropologists who are not Henry Harpending or John Hawks. But Dr. Antrosio engaged civilly, so I shall return the favor.

I did read all the papers in the American Journal of Physical Anthropology special issue, as well the Genome Research paper. My real interest here are specific questions of science, not history or social science. But I will address the latter areas rather quickly. I am not someone who comes to this totally naked of the history or social science of the race question. I’ve read many books on the topic. And as a colored person who has moderate experience with racism I get rather bored and irritated with excessively patronizing explanations of how racism afflicts us coloreds from white academics (non-white academics who focus on this subject are usually careerists or activists who don’t have to make much pretense toward scholarly substance and can be duly ignored, at least in my experience). The main point which I think we can all agree upon is that colloquial understanding of race has only a partial correlation with any genetic understanding of race. I myself have ranted against the confusions which have ensued because of the conflation of the two classes, and it is certainly a legitimate area of study, but it is not my primary concern. And importantly, I have no great primary interest in battling racism.

Read More

Greg Cochran pointed out something that I’d been considering about the MacArthur et al. paper: if the average human (OK, non-African human) has ~100 loss-of-function variants, then the standard deviation should be ~10. That’s because the distribution is presumably poisson, and variance = mean, and the square root of the of the variance (~100) is the standard deviation (~10). In plainer English there should be a substantial variation in the number of loss-of-function variants within a population, and across siblings. Though by definition these loss-of-function variants don’t kill you, in general there is the assumption that this class of mutants does exhibit some fitness drag (e.g., the fitness of a heterozygote for a variant which is lethal as a homozygote genotype may be ~0.90). A quick back of the envelope calculation implies to me that there is a 1 out of several hundreds of thousands probability that two siblings may exhibit a range of 60 loss-function-variants. But a 40 unit gap is more like a 1 out of one thousand chance.

This variance in mutational load has been the hobby-horse of intellectuals for a while now. Armand Leroi suggested that it correlated with beauty. Geoffrey Miller with intelligence. In the near future presumably we’ll get to see if there’s anything real in this. And obviously we don’t need to leave it to scientists. We’ll all know the summary statistics about own genomes, and probably be able to intuit rough patterns…if they exist.

From OpenSNP:

At the end of last year we announced that we’ve got some funding from the German WikiMedia foundation to get more people – who are willing to share their results – genotyped. We have now settled on a process that should allow us to perform the project without too many problems.Starting today, you can apply for one of the free genotypings. The deadline for applications is Sunday, 03/25/12 23:59 o’clock, so you still have some time to think about an application. In the two weeks following the deadline, we will select as many participants as we can afford to get genotyped using the 5000 Euros we received from Wikimedia. We’ll get in contact with everybody who has sent an application to let all applicants know whether their application was successful or not.

The genotyping will be done through 23andMe. We will order you a gift kit which will be delivered to your address. These gift kits include prepaid access to the 23andMe website for 12 months, so you can check up on the latest findings about your genetic variation as well. After this 12 month period, those features will expire automatically, you don’t have to cancel any subscriptions.

Our application form contains some standard questions (Where do you live? Does 23andMe deliver to your country? etc.) but also some details about your motivation, why you want to make your dataset available to the public and why your data might be of great interest (For example: Do you have a rare disease where research is lacking?). Additionally, we will also try to get people genotyped who are currently under-represented in publicly available data sets. Most data up to now is from WEIRDs: Western, Educated, Industrialized, Rich and Democratic people (most are probably male, too).

Bastian already contacted me about getting Afrikaners typed this way. I haven’t had time to get back to him, but this might be a viable option if you live in a country where 23andMe ships.

The Fennoscandia Project has now gone through chromosomes 1 to 6 with Chromopainter/fineSTRUCTURE. The conclusion:

If we looker at the bigger picture we see that most of continental Europe is tied to each other more trough mutations than others making them harder to seperate even at this level (6 chromosomes). We see that Lithuanians seem to have stronger affiliation to the large continental European cluster including Scandinavians but this affiliation is weaker for Vologda Russians. This connection is even weaker for Finns and almost non-existing for Saamis. This is in accordance with the MDS plot.

Here is the relevant plot (I have added some labels):

Read More

Over at Genomes Unzipped Dr. Daniel MacArthur has a review up of a paper in Science where he is first author (note for grad students and aspiring post-docs, Dr. MacArthur is starting a new lab, where he posted an ungated version of the paper). He hits all the salient points, so I will cover two issues, a general and a specific.

Read More

Prompted by my posts, Dienekes, A teaser on the Kalash:

I am in the middle of a ChromoPainter/fineSTRUCTURE analysis of a broad dataset designed to explore certain mysteries that have often come up in my previous experiments. Barring the unexpected, the analysis should be completed sometime next week.

Below you can see the normalized number of “chunks” donated by various populations to the Kalash….

Here is the bar plot which Dienekes generated (left to right indicates extent of “donation” to the Kalash):

I highlighted the most significant non-South Asian donor. Dienekes states:

Read More

A recent paper on Turkish genetics has a tree which illustrates a summary of how the Kalash shake out:

I say summary because this tree takes a lot of information and tries to generate the best fit representation. It does hide some information by the nature of its aggregation of patterns. For example, the position of the Burusho, or Turks, has to do with the fact that both of these have low, but noticeable, levels of East Asian admixture on top of a different base. If you removed this eastern element both groups would come much closer to similar groups. The extreme long branches leading to the Kalash and Mozabites are almost certainly a function of endogamy and inbreeding. Their allele frequencies diverged from nearby populations because of isolation.

But notice the nearby populations of the Kalash. They’re northwest South Asian. In many ways if you removed the drift and endogamy from the Kalash I suspect you’d been left with a group very similar to their Pathan neighbors.

Finally, as many of you know I put a substantial number of comments into ‘spam’ on this weblog. Here’s one related to the Kalash which you didn’t see:

Read More

The New York Times and Nature both have favorable reviews of Oxford Nanopore’s showy claims at Advances in Genome Biology and Technology. If you don’t know what I’m talking about, please see the twitter stream, or the post at Genomes Unzipped.

Read More