The era of genetic transparency is almost here

Matter has a very long feature by my friend Virginia Hughes, Uprooted, on how personal genomics is changing, and sometimes disrupting, family relationships. I sat in on one session at the Consumer Genetics Conference last week, and an audience member expressed worry about how genetic results might cause family disruption. This individual was actually a faculty member who wanted to introduce personal genomics into the classroom as a way to educate, but was wary of these sorts of side effects. Even neglecting the reality that paternity uncertainty is likely far less pervasive among the sorts whose parents would be enrolling their offspring at universities in the Boston area, these worries always have to be predicated by the fact that even dodging this ethical gray zone in the specific case only delays the near-future inevitable. Unless medical authorities ubiquitously and invariably selectively shield this sort of information from the relevant parties the widespread adoption of genetic analysis as a consumer product will result in exposure of this sort of information. Though it may seem crazy preemptive testing of all offspring to ascertain biological relatedness of putative parents may simply be the best way to head off this issue, which will be like a ticking time bomb.

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

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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The Emperor Gladwell is naked

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.

Open Thread, 9/22/2013

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.

Older fathers and the IQ of their children

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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Admixture mapping in Northern Europeans?

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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Tiger, tiger! (genome of the day edition)

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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Evolution has a simple genetic skeleton

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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