French Canadians are genetically special (not that that’s a good thing)

By Razib Khan | September 30, 2013 2:40 am

Jack Kerouac, credit: Tom Palumbo

The Pith: Higher Mendelian disease rates among French Canadians may be due to their demographic history.

As I have noted before, demographic bottlenecks with extremely strong effects on the character of population genetic variation need to be very radical in their nature to be of any significance. The population pinhole has to be on the order of hundreds, rather than thousands, of individuals. But that does not preclude more modest bottlenecks generating subtle shifts in the genetic site frequency spectrum. Strong bottlenecks may be needed to drive wholesale extinction of once common alleles (or the fixation of those at moderate frequencies), but mild bottlenecks may nevertheless perturb the allele frequency distribution. In particular, the number of alleles which are present at very low frequencies can be strongly impacted by demographic variation and natural selection. This is the logical rationale which serves as the basis for nucleotide sequence based tests for detecting natural selection, such as Tajima’s D. An excess of low frequency variants suggest a bottleneck and subsequent population expansion, or positive and/or purifying selection. In contrast, balanced polymorphism frequencies point to a shrinking population or balancing selection.

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CATEGORIZED UNDER: Population Genetics

Open Thread, 9/29/2013

By Razib Khan | September 29, 2013 10:14 pm

Back from Canine Feline Genomics Conference. Turns out most variation between dog breeds may be due to correlated allele frequency differences, not fixed ones (i.e., Lewontin’s Fallacy applies to dogs too!).

MORE ABOUT: Open Thread

The Emperor Gladwell is naked

By Razib Khan | September 27, 2013 10:03 pm

The food equivalent of a Malcolm Gladwell book, credit, Larry A. Moore

Several years ago I had an email exchange with Christopher Chabris, the author of The Invisible Gorilla. I half-joked that it should have been retitled “Why Malcolm Gladwell Is Wrong.” Chabris replied with a “no comment.” That was probably politic; Chabris is a serious academic, while Gladwell runs a vast pop-social science empire of sorts. But in a new piece in The Wall Street Journal reviewing Gladwell’s new book, David and Goliath: Underdogs, Misfits, and the Art of Battling Giants, Chabris pretty much goes for it in terms of saying what many academics think privately.

You can get an ungated version if you go through Google News.

MORE ABOUT: Social Science

Open Thread, 9/22/2013

By Razib Khan | September 22, 2013 4:46 am

I found this broadside against intellectual ignorance by Christoper Beckwith rather amazing and enjoyable. Long time readers will be aware that I am a fan of his Empires of the Silk Road. In any case, I have noticed that many of my friends and acquaintances use the term ‘ignorance’ to connote a set of views which they find normatively offensive. That is not my preferred usage of the term. Rather, I take it rather at its face value as denoting those who are lacking in the basic facts from which to even attempt audacious inference. The latter I appreciate. The former I detest.

MORE ABOUT: Open Thread

Older fathers and the IQ of their children

By Razib Khan | September 20, 2013 2:53 am

From what people tell me IQ is a social construct which is totally controlled by environmental variables, and so is not of much interest. But curiously the other day when I looked at the hits on this website over the past 3+ years a huge number of highly accessed posts had to do with intelligence and IQ. In any case, seeing as how many readers of this weblog are having, or going to have, children at a relatively advanced age (in an evolutionary sense) I thought this post would be a good public service announcement. Below is a figure from a preprint posted on arXiv, The effect of paternal age on offspring intelligence and personality when controlling for paternal trait level (via Haldane’s Sieve):

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CATEGORIZED UNDER: Behavior Genetics, Psychology

Admixture mapping in Northern Europeans?

By Razib Khan | September 19, 2013 7:46 pm

Dienekes has a post up highlighting a preprint out of Pontus Skoglund’s group. It is titled Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe. It doesn’t seem to be online (fingers crossed that it shows up linked at Haldane’s Sieve soon). In any case I am not surprised by the broad outlines of the thesis. And, it is not as if Skoglund’s group is the only one working in this area, I have suspicions that others are finding something very similar. These results out of Europe are probably reflective of the fact that much of the model in Peter Bellwood’s First Farmers is generally correct, the emergence of an agriculture revolution in a few select world societies produced a cultural and demographic revolution.

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CATEGORIZED UNDER: Agriculture, History, Human Genetics

Tiger, tiger! (genome of the day edition)

By Razib Khan | September 17, 2013 5:09 pm

Credit: Derek Ramsey

Getting a paper published with a newly sequenced genome is considered somewhat passé and so aughts at this point, but there are cases which are exceptions to this rule. Tigers are a charismatic and rare (<10,000 in the wild) super-predator, so when you see that they, along with a few other Panthera species, have been sequenced you take some note. The paper in question is open access, so you can read it yourself: The tiger genome and comparative analysis with lion and snow leopard genomes (not to spoil it, but there’s a Venn diagram!).

Before today only Felis silvetris catus had a reference sequence within the mammalian family Felidae. This fact should make you reconsider the idea that a new genome sequence is always boring and not noteworthy, as most lineages of mammals are represented by only one representative individual from one representative species. In ~5 years it is true that we’ll be beyond this stage of data scarcity in the sense of phylogenetic coverage, but we’re not there yet.

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MORE ABOUT: Genomics, Tiger genome

The Central Dogma goes YouTube

By Razib Khan | September 17, 2013 3:36 pm

You have probably seen these animations at some point, but if not, I encourage you to check them out. They certainly make abstractions such as DNA → RNA → Protein “come to life.” Below you have transcription, and then translation.

Though the DNA replication visualization is probably the most impressive to me:

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Evolution has a simple genetic skeleton

By Razib Khan | September 17, 2013 3:39 am

Citation: Keinan, Alon, and Andrew G. Clark. “Recent explosive human population growth has resulted in an excess of rare genetic variants.” science 336.6082 (2012): 740-743.

Some of the topics that I discuss in this space may seem abstruse, but really they’re often elaborations upon rather elementary basic models of the world. When it comes to a subject like evolutionary genetics deep thinking extending from a few simple conceptual anchors yields great insight. Those anchors trace back to the foundations of Mendelian genetics. For diploid organisms the law of equal segregation states that of the two gene copies organisms have there is an equal probability of contribution of either to their offspring. This explains the simple power of Punnett squares and the inheritance patterns of recessive traits. The law of independent assortment states that genes (and therefore implicitly Mendelian traits) are passed independently from each other from parents to offspring. These abstractions are concretized on the cytological and molecular genetic scale during meiosis, as homlogous chromosomes which are composed of packed sequences of genes partition themselves into separate haploid gametes (sperm and egg*). Early in meiosis, during prophase 1, crossing-over between homologs results in genetic recombination, which preserves the law of independent assortment even when genes are on the same chromosome by breaking apart associations between specific physical genetic regions which might exhibit co-inherited distinctiveness (if the genes are very close they are linked).

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MORE ABOUT: Genetics

What is your American dialect?

By Razib Khan | September 16, 2013 2:14 am

Razib’s Dialect Similarity

Language dialect is something that we often pick up unconsciously, so I find it an interesting if narcissistic project to query my own dialect affinities. The above was generated using a 140 question test (warning: server often slow). In case you were curious, my most ‘similar’ city (to my dialect) is Sunnyvale, California. Though most of my life has been spent on the West coast of the United States, I did spend my elementary age years in upstate New York. You can see evidence of that in the heat-map. There are particular words I use and pronunciations that I have which I know are probably relics of my formative years, but it was a little surprising that this survey picked up on that, as I thought most of them had disappeared.


Open Thread, 9/15/2013

By Razib Khan | September 15, 2013 4:39 pm

How do people manage to keep track of the scientific literature in their area?

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Against informed pragmatism in the Middle East

By Razib Khan | September 15, 2013 4:38 pm

A little editorializing by me….

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CATEGORIZED UNDER: International Affairs
MORE ABOUT: Middle East

Writing about science on the internet

By Razib Khan | September 14, 2013 2:30 am

Don’t be shy

A few weeks ago I was asked on Twitter by someone for advice on how to write a science blog/do science communication. Since I was studying up for my qualifying exam I said I’d get back to him later. I passed, and now this is later.

First, you should probably read Sabine and Chad. Second, I’ll be up front and admit that I don’t give much thought in the details to this sort of thing (though I follow with interest the opinions of others, such as Bora Zivkovic, on this topic). I really only have one qualification: I’ve been doing this for a long time. Since spring of 2002. To my knowledge only Derek Lowe has been blogging continually and without interruption about science longer than I have (Chad Orzel of Uncertain Principles also started in the spring of 2002).

So in no special order, my “advice”….

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MORE ABOUT: Blogging

Selection without adjective and bound

By Razib Khan | September 13, 2013 4:03 pm

A “space colony”

In my post below where I take a stand against the tired, but inevitable, assumption that a post demographic transition society necessarily entails a cessation of biology evolution, a reader brings up a trite but specious observation:

But you’re missing the point really. We’ve slowed (not stopped because it can’t be stopped) because we now control our environment. Evolution is moving from individual biological expression to cultural and technological evolution.

This isn’t novel or exceptional in its wrongheadedness. The same idea comes up when I engage in discussion with the types of intellectuals in sociology or anthropology unencumbered by the constraints of “Western linear thinking.” The presumption is that natural selection operates through exogenous environmental pressures, and as we attenuate those pressures we diminish the rate of evolutionary change. The stylized model being:

Rate of evolution ∝ natural selection ∝ 1/(control of environment)

As the magnitude of human control of the environment increases, the magnitude of natural selection decreases, and so does the rate of evolutionary change. This impression was already cursorily dispatched in my prior post. But as there hasn’t been strong selection in the human past for reading and comprehending something before commenting on it, this issue might require a little teasing out, as the stylized model above is so ubiquitous as to be a background assumption of many.

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MORE ABOUT: Rate of Evolution

The fox and Stonehenge

By Razib Khan | September 13, 2013 2:04 am

Unless you are under a rock you are aware of the controversy around the sound that the fox makes. But did you know about Stonehenge?

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Soft sweeps in the Ethiopian highlands

By Razib Khan | September 13, 2013 2:01 am

Soft serve

The trait of lactase persistence (lactose tolerance) is probably one of the better schoolbook examples of natural selection in human populations. The reasons for this are probably two-fold. There is a very strong signature of selection within a specific gene known to associate with the trait in question in many populations. And, there is a very compelling historical narrative which explains rather neatly how this particular functional change could have undergone such strong selection within the past ~5,000 years across these populations. But the elucidation of the origin and spread of this genetic adaptation is also interesting because it looks as if it was not a singular event. Populations as disparate as Arabians, Danes, and Masai seem to carry different alleles around the locus of interest which confer the ability to digest milk. This illustrates the fact when selection pressures have a viable target, there is a rapid response on the genomic level. At some point during the maturation of a mammal the regulatory pathway which produces lactase enzyme shuts down. Yet within numerous human populations this gradual shutdown process has been short-circuited.

The variety of response in relation to this adaptation was brought home to me as I read Diversity of Lactase Persistence Alleles in Ethiopia – Signature of a Soft Selective Sweep, in the latest issue of The American Journal of Human Genetics:

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Ancient people were not static

By Razib Khan | September 12, 2013 9:53 pm

Citation: Witas HW, Tomczyk J, Jędrychowska-Dańska K, Chaubey G, Płoszaj T (2013) mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization. PLoS ONE 8(9): e73682. doi:10.1371/journal.pone.0073682

Today Dienekes points to a PLoS ONE paper, mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization. The title is pretty self-explanatory, though above I’ve posted a figure which shows the mtDNA haplogroup affiliations of the four individuals dated to between 2500 BC and 500 AD. If you are a even moderately familiar with the human mtDNA phylogeographic literature then you know that haplogroup M is not West Eurasian, and these lineages are often South Asian. The existence of people of South Asian origin in West Asia during the Roman period is rather unsurprising, the Persian (and Hellenistic) polities spanned West and South Asia (albeit, in a liminal sense in the latter case). But what about extremely ancient finds? This too has an explanation. From Brotherhood of Kings: How International Relations Shaped the Ancient Near East:

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Man still evolves

By Razib Khan | September 12, 2013 8:02 pm

Still a great book!

Sir David Attenborough is the latest public intellectual who should know better than to opine that evolution has ended for human beings. Here are the quotes from The Telgraph: “Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection. We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

John Hawks does a good job hitting back the balls hanging just over the plate. There are still many parts of the world where 95-99 percent of babies being born do not reach adult. Second, there is still a great deal of variation in fertility. Some people choose not to have any children, while others are quite prolific. For adaptation by natural selection to occur what you need is heritable variation of some sort to correlate with this fertility variation. It seems highly plausible that indeed heritable variation does correlate with fertility variation. As John notes the advancement of genome sequencing over the population will probably answer these questions definitively within the next 10 years (e.g., I am willing to bet that siblings who score higher on impulsiveness and lower on IQ tests will be more reproductively fit than their less impulsive and more intelligent brothers and sisters).

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CATEGORIZED UNDER: Evolution, Genetics

We have been “consumed” for ~100,000 years

By Razib Khan | September 11, 2013 2:27 am

Citation: Comas, Iñaki, et al. “Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.” Nature Genetics (2013).

The two phylogenies above represent Mycobacterium tuberculosis, to the left, and human mitochondrial DNA (passed from mother to daughter) on the right. It was pulled from the paper, Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, which just came out recently, and has naturally been making a splash. As the title implies the paper concludes that humans and tuberculosis have been each other’s “partners,” after a fashion, for the whole existence of modern humanity. The main method here is somewhat brute force and straightforward, by sequencing 259 tuberculosis strains from all across the world they managed to make relatively robust phylogeographic inferences. Throwing data at a question usually resolves something. The correspondence between human and pathogen strains is qualitatively uncanny, and there is plenty enough statistical footwork to confirm it more rigorously within the body of the text.

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CATEGORIZED UNDER: Evolutionary Genetics

Bay Area Population Genomics (BAPG) IX Conference

By Razib Khan | September 11, 2013 12:54 am

Registration is free. It will be hosted by the Nielsen Group in Berkeley on October 5th. As I am not going to be at the methods-orgy (OK, my own peculiar perspective) that is going to be ASHG 2013 I am definitely going to BAPG to get a preview of anything that might be unveiled in Cambridge a few months later (and to be frank I registered last June when it was announced).

MORE ABOUT: Genomics

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