Category: Genomics
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A genetic map of Italy
Since the Ralph & Coop paper on IBD patterns across Europe I’ve been keen to see what gets uncovered about Italy. Recall, if you will, that in that paper the authors noted that Italy in particular of European nations exhibits a lot of deep po…
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Genes, a gene, genes….
I spend some time thinking about genetic architecture. If you read media accounts of genetics you wouldn’t know there was such a thing. Why not? Because it makes a narrative rather messy and complex. Rather, a better story is one where you have a…
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On ENCODE
There’s a reason that people say that the 21st century is the century of biology, whereas the 20th was the century of physics. See Brendan Maher, Ed Yong, and Dr. Daniel MacArthur’s coverage. I haven’t read the papers, so I can’…
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Deep dive into the Denisovans
By now you have probably seen the new Denisovan paper in the media. John Hawks has an excellent overview, as you’d expect. The only thing I will add is to reiterate that I think population movements in near and far prehistory significantly obscur…
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Not all genes are created the same
The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It’s for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for a…
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A note on open genomics
A few months ago I purchased a decent desktop just to crunch ADMIXTURE and other packages to analyze genomic data. More recently I set up a ~100 GB Dropbox account, and have started to “push” all of my output files from ADMIXTURE, PLINK, et…
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Consent and genomics
Interesting story in The New York Times, Genes Now Tell Doctors Secrets They Can’t Utter: One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer…
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Genes & geography – the great correlation
A paper is out in PLoS Genetics which attempts to formalize the relationship between genes and geography, A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations. They found a reasonable correlation, but …
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Inter-population difference in European height
A quick mea culpa. Yesterday I put up a post on the difference in height between northern and southern Europe, following the lead of the heading of the paper which I blogged. But, in the text they do note that their sample is skewed toward northern Eur…
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On phylogenetic instrumentalism
ADMIXTURE and STRUCTURE tests aren’t formal mixture tests. Yes! In fact, in the “open science” community this issue is repeated over and over and over, because people routinely get confused (our audience does not consist of population gen…
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Cultures & genes: Paleolithic to the Neolithic
Spatial linguistic variation Spatial genetic variation Temporal linguistic variation Temporal genetic variation Paleolithic Very high High Moderate-to-high Moderate-to-low Neolithic Moderate Moderate-to-low Moderate High Bronze Age Mod…
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Not all homozygosity is created the same (way)
Browsing the most recent issue of The American Journal of Human Genetics I stumbled upon a paper with some neat figures, Genomic Patterns of Homozygosity in Worldwide Human Populations. More specifically they focused on patterns of “runs of homo…
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Ötzi – more Neandertal than the average bear
Neandertal ancestry “Iced”: Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human po…
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The Jewish Diaspora: not an empire of the mind
Berber queen? In light of the previous post you know that I was going to post on the new paper in PNAS, North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Additionally, the press people at Albert Einstein did reach …
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An exegesis of Robert Pollack?
I was going to review North African Jewish and non-Jewish populations form distinctive, orthogonal clusters at some point soon, but I’m going to have to move that up. Someone on Twitter pointed me to this really weird article, Being Jewish Is Mor…
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Humanity 2.0
Dienekes points to a David Reich video where he shows his hand as to future possible results to come out of his lab. The short of it is that it seems likely that most agricultural populations exhibit the same dynamic outlined in Reconstructing Indian H…
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Azores to Atlantis: Africa through the shadows
In many ways the image of Africa in the minds of Westerners has become a trope. The “Dark Continent,” eternal, and primal. Like many tropes the realized existence of this Africa is only within the imagination. The real Africa is far differ…
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The Genographic Project: on to the autosome!
The Genographic Project is now moving beyond uniparental lineages with Geno 2.0. Spencer Wells kindly invited me to a conference call last month where he outlined a lot of the details, so I’ll hit the salient points for readers of this weblog: *…
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On the effects of effective population
Nathaniel Pearson has an eminently readable post up on human effective population sizes. If you don’t know the importance of harmonic means in this domain, worth a read. He finishes though with an issue of practical importance, the proliferation …
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Ashkenazi Jews are not inbred – 2
I know I excoriate readers of this weblog for being stupid, ignorant, or lazy. But this constant badgering does result in genuinely insightful and important comments precisely and carefully stated on occasion. I put up my previous post in haste, and wh…