Where the wild clines aren’t
In the recent ‘do human races’ exist controversy Nick Matzke’s post Continuous geographic structure is real, “discrete races” aren’t has become something of a touchstone (perhaps a post like Cosma Shalizi’s on I.Q. and heritability).* In the post Matzke emphasized the idea of clines, roughly a continuous gradient of genetic change over space. Fair enough. […]
Beyond trees and European trees
Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there’s a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow […]
Extraordinary claims require a lot of evidence
Several people have emailed me about the Solutrean hypothesis. The trigger is the publication of Across Atlantic Ice: The Origin of America’s Clovis Culture. To my surprise this has received a lot of media attention. The Washington Post, io9, and The New Scientist. Granted, the coverage has been appropriately skeptical. But it still gets to […]
Race: maybe it’s agriculture
I’m too busy to really blog today, but I thought of putting up a post, the gist of which was actually expressed in Ian’s comment below: When I was younger, I thought of human races as archetypes, and the variation between them a product of mixing. I blame it on the fact that I read […]
Are Sardinians like Iberians?
Dienekes asks: In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if […]
Ötzi the Iceman and the Sardinians
Well, the paper is finally out, New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. In case you don’t know, Ötzi the Iceman died 5,300 years ago in the alpine region bordering Austria and Italy. His seems to have been killed. And due to various coincidences his body was also […]
Men on the move and women in place?
After posting on Basque mtDNA I wanted to make something more explicit that I alluded to below, that uniparental lineages are highly informative, but they may not be representative of total genome content. This is plainly true in the case of mestizos from Latin America, but we don’t need genetics to point us in the […]
The data sets in the dark
Recently I was tipped off to the appearance of a new paper, Genome-Wide Association Study Identifies Chromosome 10q24.32 Variants Associated with Arsenic Metabolism and Toxicity Phenotypes in Bangladesh. This is the section which caught my eye: “Using data on urinary arsenic metabolite concentrations and approximately 300,000 genome-wide single nucleotide polymorphisms (SNPs) for 1,313 arsenic-exposed Bangladeshi […]
Adam’s end was never in the cards
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 […]
The race question: are bonobos human?
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. […]
Loss-of-function & variation in load
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 […]
Europe’s special northeast
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 […]
Extraordinary mutations require extraordinary evidence
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 […]
Kalash haplotype sharing
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 […]
Kalash on the human tree
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 […]
The Kalash in perspective
When Zack ran ChromoPainter/fineStructure on South Asians the results naturally yielded a blueish hue along the diagonal. This is expected because the diagonal represents the population’s own relationship with itself. The bluer the diagonal, the more inbred and isolated the population is likely to be. To the top left you see various Austro-Asiatic tribes, […]
Clusters where they “shouldn’t be”….
Uyghur girls A few people have pointed me to the paper, Implications for health and disease in the genetic signature of the Ashkenazi Jewish population. You should check it out if you don’t have academic access to papers, it’s not gated. Rather, I want to focus on a methodological issue. In the genetics reader survey […]
American medicine & American red-tape
I just attended a presentation where a researcher outlined how epigenomics could help patients with various grave illnesses. Normally I don’t focus on human medical genetics too much because it always depresses me. I don’t understand how medical geneticists don’t start wondering what hidden disease everyone around them has. In any case the researcher outlined […]
ChromoPainter & fineSTRUCTURE on a South Asian data set
Over at Harappa DNA Zack ran ChromoPainter/fineStructure on his South Asian data set and posted the results. The new method immediately makes a few things clear: 1) The “South Asians” in the HGDP data set that’s been used for so long are rather on the inbred side, and relatively genetically distinct as far as South Asian populations […]
Out of who knows where
In The New York Times, DNA Turning Human Story Into a Tell-All: The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins. The new view is fast supplanting the traditional idea […]