The Unz Review: An Alternative Media Selection
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Genomics

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The Eurogenes blog is running a fundraiser. I chipped in mostly to support his continued blogging. I don't agree with everything he posts, but the site is a good and valuable resource. "Genome blogging" hasn't gotten as far as I'd have thought it would have in 2010, mostly because the initial burst of enthusiasm wasn't... Read More
Listened to an interesting interview this morning with the author of a new book, The Latinos of Asia: How Filipino Americans Break the Rules of Race. There was a lot to agree with and disagree with, but it rang true in many ways for me because I have had a fair number of students with... Read More
Would You Want To Know The Secrets Hidden In Your Baby's Genes? Turns out most people don't. The article profiles the BabySeq Project, and the offer of whole exome sequencing (exomes are the parts of the genome which code for proteins). In some ways, the results were discouraging: So that leaves 6 percent. That's not... Read More
There are several reports in the media about a third hominin group besides Denisovans and Neanderthals, and how they contributed to Melanesians. Science News has a sober summary of it all. Several people have asked me on email and Twitter about this, and I told them to ignore it. The reason I say this is... Read More
For various sociocultural reasons ancient Egyptians are a big deal. The pyramids of Giza are about as distant from the time of Augustus as Classical Rome is from us. When the pyramids were rising the world was mostly prehistory. Africa was dominated by hunter-gatherers, as was much of Southeast Asia. The genetic cluster which we... Read More
I really admire what 23andMe has done. To a great extent they are the "Uber" of DTC personal genomics. FamilyTree DNA really pioneered the sector in the early 2000s, while The Genographic Project scaled things up massively in the middle 2000s. But in the late 2000s 23andMe brought Silicon Valley "disruption" to the game, pushing... Read More
One of the most incredible journeys that the human species has undergone is the Austronesian expansion of the past 4,000 years. These maritime peoples seem to have emerged from the islands of Taiwan, and pushed forward south, west, and east, so that their expansion pushed to East Africa, and the fringes of South America. There... Read More
A friend asked me about population structure, and methods to ferret it out and classify it. So here is a quick survey on the major methods I'm familiar with/utilize now and then. I'll go roughly in chronological order. First, you have trees. These are pretty popular from macroevolutionary relationships, but on the population genetic scale... Read More
In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the archaeologist David Anthony outlines the thesis that migrations from the west Eurasian steppe during the Bronze Age reshaped the culture of Northern Europe. When Anthony published the book, which you should really read if you are... Read More
There was a time, five years ago or so, when we knew all the humans who had been sequenced. Or at least most of them. But now we're coming into the period when the first sequenced animals of any given species are starting to die. Above is Cinnamon, the first sequenced cat is no longer... Read More
The Estonian Biocentre has been one of the best resources in human population genomics, because their policy under Mait Metspalu seems to be to release the data once it's published. Today I went and checked the site, and noticed a vlog accompanying their Nature paper, Genomic analyses inform on migration events during the peopling of... Read More
The above results are from Ancestry. You can see here 4% Melanesian. This is common in South Asians. And it's not an error in the method. Rather, it is a natural outcome of the methods uses to generate admixture profiles. Basically what's going on is this: 1) You have data. In this case, the data... Read More
A new paper in PNAS, Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne, weighs in the question of whether the Châtelperronian culture were Neandertals, with an answer in the affirmative in this case: The details about stratigraphy are beyond me. But the protein and mtDNA
We live in an age when we have a lot of SNP data on a lot of populations. This allows for a very fine level of granularity in terms of analysis. To illustrate, Genetics recently published Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity, which analyzes hundreds of Danes with hundreds of thousands of... Read More
Ewen Callaway reports from a conference in England, Elephant history rewritten by ancient genomes: Modern elephants are classified into three species: the Asian elephant (Elephas maximus) and two African elephants — the forest-dwellers (Loxodonta cyclotis) and those that live in the savannah (Loxodonta africana). The division of the African elephants, originally considered a single species,... Read More
Jonathan Novembre and Benjamin Peter have posted a preprint of a review, Recent advances in the study of fine-scale population structure in humans, which readers will find useful. In particular, the citations are a gold-mine for anyone attempting to navigate this literature. The figure above from their preprint illustrates the number of markers needed to... Read More
About thirteen years ago I expressed the opinion that an understanding of population structure will become a matter of intellectual curiosity once we have a better understanding of the genetic basis of characteristics. A friend, who was a statistical geneticist, told me that this was unlikely. We were unlikely to capture the ability to predict... Read More
In 2011 I was having dinner with an old friend who was an engineer at Intel. He also has a Ph.D. from MIT. Smart guy. But when I mentioned casually offhand that we were all a few percent Neanderthal (outside of Africa), he was surprised. I was a bit shocked, as I explained that this... Read More
Joe Pickrell and Yaniv Erlich did an AMA on Reddit yesterday. I recommend you check it out. They promote their new project, seeq. It looks pretty slick, and I'm excited to be part of the batch of beta testers.
A follow up on the Ancient Archaic Admixture Into the Andamanese story, No evidence for unknown archaic ancestry in South Asia: Last I heard they hadn't released the bam files. Mistakes are made, that's how science is done, and other people help in the process of correction. But, it is starting to get worrisome to... Read More
A new paper in Nature Genetics, Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery, is both interesting and important. But, as with the paper on the Andaman Islander genomes it starts out with a naive and misleading utilization of model -based clustering to frame the later results. Here's a major offending... Read More
Update: If Pontus Skoglund fails to replicate your results it is not an optimal outcome.... @razibkhan I tried to replicate the archaic admixture signal (using 4 other data sets with similar power) but failed — Pontus Skoglund (@pontus_skoglund) July 26, 2016 end update A new paper on on archaic admixture in Andaman Islanders has come... Read More
The Time and Place of European Admixture in the Ashkenazi Jewish History: The Ashkenazi Jewish (AJ) population is important in medical genetics due to its high rate of Mendelian disorders and other unique genetic characteristics. Ashkenazi Jews have appeared in Europe in the 10th century, and their ancestry is thought to involve an admixture of... Read More
One can appreciate a work of art on two levels. When one beholds the sculpted renderings of the Classical Greeks, across the distance of more than 2,000 years we can feel viscerally that they have touched something beautiful, and made it stone. To reduce this to biology, our perception maps onto to deep grooves in... Read More
The chart is from an article in Nature. But the source is NHGRI. It illustrates that between 2008 and 2012 genomics as a field crushed Moore's law. Then there was a leveling off between 2012 and the middle of 2015. Illumina had a quasi-monopoly for that period and sequencing costs did not decrease too much.... Read More
Years ago I had a long phone conversation with a journalist about the origins and natural history of the red wolf. The reason was that I had casually mentioned that there was genetic evidence suggesting that the red wolf is a stabilized hybrid between gray wolfs and coyotes. That was 2007, if I recall correctly.... Read More
Years ago when I was noticing specific population genomic estimates I asked a friend about the confidence intervals, and how much to trust the values therein. One thing he mentioned offhand is that linkage disequilibrium based estimates of time since admixture often seem to give a relatively low figure in terms of generations. When it... Read More
When I wrote the Pleistocene was humanity's Hyborian age, I meant humanity. For contingent reasons the new genetic sciences of ancient DNA have elucidated the history of northwest Eurasia first. But prior to the Great Divergence Europe was not quite so exceptional. In fact the historian Victor Lieberman wrote Strange Parallels, his macrohistory of Eurasia,... Read More
No time to comment. Yes, the hits with SNPs are cool. But look at all the functional associations and analysis in this paper! Some serious biology in this. The figure from the paper to the left which shows how the genes associated with this SNP hits are expressed in different tissue/types and organs. These are... Read More
Behold, Summer Institute in Social Science Genomics: The future is not the future anymore.
Selection is one of the major parameters which population geneticists investigate. The easiest way to investigate selection is to have omniscience as to the change in allele frequencies over time. If you are a Drosophila geneticist this is feasible, as you control the reproduction of your model organism in the lab. It is obviously much... Read More
The above is what I have flippantly referred to as "standard PSMC plot you always see" from the origin paper which debuted the method. Basically PSMC uses the pattern of variation over a good quality whole genome to infer the population history of that individual's genealogy. All of use unique snowflakes do after all reflect... Read More
Dienekes argues: I'm not sure that this is the main piece, though it was a major reason. Here are two other reasons: 1) Anatomically modern humans show up in Africa first. 2) The deepest divergences in the mtDNA, Y chromosomes, and autosomes, are all found within Africa (in particular, between hunter-gatherer African populations and everyone... Read More
The figure in Ewen Callaway's piece in Nature, Evidence mounts for interbreeding bonanza in ancient human species, does a good job at relaying what we know about admixture between different human lineages informed by ancient DNA. But is that all there is? Before ancient DNA in large quantities came online there were attempts to infer... Read More
About ten years ago a standard model of the understanding of the peopling of the world by modern humans was that ~50,000 years ago a massive demographic swell out of eastern Africa overwhelmed, to elimination, all other human populations. With a few exceptions, such as the New World, these modern Africans quickly settled down, and... Read More
Last fall while at ASHG this paper came out, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent: Turns out that there was a bioinformatics error which negates the magnitude of these results. Erratum to Gallego Llorente et al. 2015: The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture... Read More
I am wont to say that the genomics of human pigmentation are solved. Arguably this has been one of the major successes of the early GWAS era. In 2005 the postscript to Mutants: On Genetic Variety and the Human Body alluded to the fact that the genetic architecture of pigmentation in humans was relatively mysterious.... Read More
Several years ago I read a book, The Origins of the Irish, by the famed archaeologist J. P. Mallory. Unfortunately, I remember very little of this work, and recall thinking that it was published just a bit too early, as archaeogenetics was clearly going to revolutionize our understanding of the prehistory of Northern Europe, though... Read More
The human genome is littered with many genes from diverged lineages. That is, any given human has segments from lineages which are deeply diverged from the dominant demographic element in our ancestry, which diverged from an African population which flourished on ~200,000 years ago, and among non-Africans a population derived from Northeast Africa ~50,000 years... Read More
A friend sent me a link to this long piece in The New Republic, What's a species anyways?. Its subtitle is "The search for the red wolf's origins have led scientists a new theory about how evolution actually works." This is wrong. In fact, the article itself admits that there's nothing revolutionary here. You just... Read More
The question of Italy population genetic structure comes up rather often for various reasons. I haven't visited this topic in much detail since reading Consanguinity, Inbreeding, and Genetic Drift in Italy, a very old book using classical genetic techniques. L. L. Cavalli-Sforza did not find much structure in Italy at the time, but it turns... Read More
How fast can evolution occur? More precisely, how fast can adaptation occur? The rough answer is pretty fast. For humans that's clear when you read a book like 10,000 year explosion, or see the results from ancient DNA in papers, that selection (~1% coefficient) on variation can drive allele frequency changes rapidly (~0% to ~100%).... Read More
Over the past few years we have seen ancient DNA researchers "carve nature at its joints" when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren't at the end of the road, but I do think that the terminus is within... Read More
This year at ASHG one of the most fascinating talks was Po-Ru Loh's, where he reviewed the BOLT-REML method. It's introduced in the paper, Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. As you likely know many diseases such as schizophrenia manifest as complex trait; that is, they're basically quantitative... Read More
Nathan Taylor points out that sequencing costs are crashing again. Not very surprising from what I've been hearing about the direction that firms like Illumina are moving. The cost of sequencing isn't going to be the rate limiting step in the near future. Here's some raw data for the past year: Cost per genome Jul-14... Read More
- Rig Veda Five years ago I found out that my friend Daniel MacArthur and I are members of the same Y chromosomal haplogroup, R1a. Both of us thought it was rather cool, that ~5,000 years ago there lived a man who was ancestral to us both on the direct paternal line. Five years on,... Read More
Iain Matheison, first author of Eight thousand years of natural selection in Europe, has a short note up at his website, Selection on height in Europe. He concludes: North Chinese are also taller than South Chinese. And there are many quantitative traits in humans. We're living in a golden age of phylogenomic analysis of humans... Read More
For several years there has been a nerdy debate in some labs about sequencing vs. genotyping (more precisely, doing genotyping-by-sequencing vs. going with an array). There are many pros and cons. If you are working on non-model organisms there may not be a good SNP array for you, so the decision is done. If you... Read More
If you're not sleeping under a rock, you know that today 23andMe has rolled out its plan to provide government (FDA) approved medical results. In the generality I knew this was in the offing. I asked contacts within the company, and they pretty much signaled this was imminent, though they didn't detail the specifics. This... Read More
The media is blowing up with a new story about the phylogeography and phylogenetics of the domestic dog.* The New York Times has a good write up, and I like its title: Central Asia Could Be Birthplace of the Modern Dog (the headline was changed to "15,000 Years Ago, Probably in Asia, the Dog Was... Read More
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"