Category: Genetics
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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…
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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.…
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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…
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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…
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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…
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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…
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Population structure using haplotype data
The Pith: New software which gives you a more fine-grained understanding of relationships between populations and individuals. According to the reader survey >50 percent of you don’t know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of…
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When Eve met Creb
The excellent site io9 has a piece up today which is a fascinating indicator of the nature of popular science publications as a lagging indicator. It is a re-post of a piece published last April, How Mitochondrial Eve connected all humanity and rewrote human evolution. In it you have an encapsulation of a particular period…
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Personal genomics and adoption
With DNA Testing, Suddenly They Are Family: Several companies provide tests that can confirm whether adoptees are related to individuals they already know. Others cast a wider net by plugging DNA results into databases that contain tens of thousands of genetic samples, provided mostly by people searching for their ancestral roots. The tests detect genetic…
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Genetic profiling: CSI edition
Apparently the national media is reporting that scientific genealogy may result in leads to a cold case. The principle is simple: apparently Y chromosomal material was matched to public genealogy databases. From this the researcher concluded that the perpetrator is probably a male line descendant of Robert Fuller of Salem, Massachusetts. Contrary to the urban…
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How the Amhara breathe differently
I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the…
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The quest for an Afrikaner genotype
Update: If interested, please email me at contactgnxp -at- gmail -dot- com. Also, I am getting some feedback via 23andMe that people with white South African matches noticed Africa segments in many of the ancestry paintings. This has definitely increased by probability that the admixture proportion is ~5 percent. There will probably be a few…
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The phylogeography of the trans-Caucasus
Randy McDonald points me to this fascinating post, Genetic clues to the Ossetian past. In the post author outlines phylogeographic inferences one can make from uniparental lineages; maternal and paternal lines of descent. Specifically, they are in interested in the origins and relationships of the Ossete people. I assume that one reason Randy pointed me…
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Genes and Rex Wandalorum et Alanorum
The idea of a “folk wandering” was once a well accepted idea in history, in particular for the phase of the Late Roman Empire, and the subsequent fall of the Western Empire. It’s a rather simple concept: the collapse of the Pax Romana occurred simultaneous with a mass ethnic reordering of Europe, primarily via the…
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Mendelism is not magic
Michelle points me to this article in The Lost Angeles Times, The Colors of the Family: I was holding my 1-year-old, ambling about downtown with some friends. White friends. She must have thought my boy belonged to one of them. There’s a simple explanation: I’m black but my son, Ashe, is white. At least he…
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Reconstructing a generation unsampled
In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue…
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Between the desert and the sea
Zinedine Zidane, a Kabyle There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with…
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More on the “missing heritability” and epistasis
Please see Luke Jostins’ posts at Genetic Inference and Genomes Unzipped. Update: Steve Hsu weighs in. He read the supplements! Mad props.
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James F. Crow, 1916-2012
Sad news. John Hawks passes along that James F. Crow has died. Further mention from the National Center For Science Education. A little over 5 years ago I sent Crow an email with only minimal expectation of response, asking about an interview. He responded in less than 24 hours! I think it says a lot…
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Are genes the key to the Yankee Empire?
That’s the question a commenter poses, albeit with skepticism. First, the background here. New England was a peculiar society for various demographic reasons. In the early 17th century there was a mass migration of Puritan Protestants from England to the colonies which later became New England because of their religious dissent from the manner in…