genetics
razib | February 17, 2006A few days ago I saw that Dienekes commented on a recent paper published in The American Journal of Human Genetics where the authors used 10 markers, specifically single nucleotide polymorphisms (SNPs), to discern continental level population differentiation. Dienekes has generated a map which shows the extent of clustering. The authors selected specific SNPs that they assumed would be extremely informative, and so obviated the need to extend their sample of assayed loci into hundreds. They express their results with some caution, and highlight that the inferences need to be judged in…
razib | February 16, 2006With all the hoopla over Darwin Day (justified in my opinion) I thought I'd point you to this article, Gregor Mendel: The father of genetics. The contemporaneous insights of Charles Darwin and Gregor Mendel illustrate the beauty of science, nature's gift to us in its underlying unity of form. Darwin looked at the big picture and saw the compelling connection between biological variation across space and time and natural selection. Mendel's experiments elucidated the most atomic and elementary reactions which buttressed the grand arcs of natural history and the flow of selection. Though…
evolgen | February 13, 2006One of the most important developments in evolutionary biology in the past few decades has come without much fanfare outside of a small circle of population geneticists. The early models of population genetics were limited when it came to analyzing the nucleotide sequence polymorphism data that began to appear in the 1980s. New statistical techniques were developed to analyze this data, and they all fell under the umbrella of coalescent theory. If you want to understand the evolution of populations, you're missing a lot if you do not understand the coalescent.
When I wrote about the best…
evolgen | February 11, 2006There's lots of cool stuff coming out in the speciation literature. The Questionable Authority has posted on two recent studies on sympatric speciation (see here and here). Nature, which published the two sympatric speciation papers, has a summary available here. I am of the opinion that most examples of sympatric speciation are actually allopatry with reinforcement (for more on this, see here). That is not to say that sympatric speciation is impossible, just extremely rare. In the end, some reproductive isolation is a requirement for speciation in sexually reproducing organisms (whether…
razib | February 11, 2006I've commented on the African American Lives series a few times. One thing I've said in other threads is that these massively more data rich ancestry analysis tests aren't going to tell you anything you don't already know in 99% of the cases. That doesn't mean that it's not worth it to get tested, but if the kit costs you hundreds or thousands of dollars, most people are really better off passing I think. When these tests get down to the $10-20 range then I'll be sanguine if a friend of mine starts mooting the possibility of purchasing a kit. By analogy, I wouldn't get worked up over a $…
razib | February 10, 2006Yesterday in my conversation with David Miller I told him I didn't think that the new autosomal "ancestry" tests really delivered the extent of separability of ancestral quanta that most people really expect. Well, look at this principal component chart that Dienekes put up from a paper published by Dr. Mark Shriver. Granted, these tests are good at differentiating continental races...but many people want to know if they are "pure Hakka" or "pure German," as opposed to Cantonese whose ancestors picked up the Hakka dialect or Slavic Sorbs who were Germanized. In terms of the autosomal tests…
razib | February 9, 2006About 1/4 of the way into the Radio Open Source The Al-Jazeera Effect episode Brendan mentions my comments regarding the science of genealogy (he notes that I'm "producing" their show for them). I just talked to David, the staffer that started that thread, this afternoon, and we bounced some ideas off each other. So, the moral is that blogging gets results!
In related news, Dienekes has a review of some of the findings in African American Lives.
razib | February 8, 2006As I have said before, sometimes you actually have to play the game. An interesting thing that surprised me years ago was that the time until fixation of a highly deleterious allele was lower than a neutral allele. In other words, if you had an allele with negative fitness implications the time it takes to traverse 0% to 100% on the frequency chart for the population will be shorter than for one with no fitness implication (neutral fixation in generations is 4 * effective population size). Why? Because for a highly deleterious allele to fix it has to do it quickly, selection works…
pharyngula | February 8, 2006Here's some very cool news: scientists have directly observed the evolution of a complex, polygenic, polyphenic trait by genetic assimilation and accommodation in the laboratory. This is important, because it is simultaneously yet another demonstration of the fact of evolution, and an exploration of mechanisms of evolution—showing that evolution is more sophisticated than changes in the coding sequences of individual genes spreading through a population, but is also a consequence of the accumulation of masked variation, synergistic interactions between different alleles and the environment,…
razib | February 7, 2006Radio Open Source is going to do a show on The Genetics of Genealogy. I've recently expressed some skepticism about many of the tests peddled by corporations and their scientist promoters, so I'm primed to jump into this discussion. I have already offered a few comments, and will probably post more as the show comes up. Until then, I also highly recommend John Hawks' comment on this topic.
Update: On Point with Tom Ashbrook interviewed Henry Louis Gates Jr. on his new series African American Lives, which leverages genetic science in exploring the genealogy of many prominent black Americans…
evolgen | February 3, 2006Free Association (the Nature Genetics blog) has published a commentary from Laura Ranum, the senior author on the recent Abraham Lincoln ataxia paper. It begins:
In 1992 I received a phone call from a neurologist with an ataxia patient that had a strong family history of the disease. Impressed upon hearing there were at least eight affected family members, I asked if I could contact the patient directly. After talking to this woman about her family history she paused and said "but you know, you really ought to talk to my mother...I think she knows of some more cousins"; the SCA5 odyssey…
evolgen | February 2, 2006There are quite a few articles sitting around on my desktop waiting for me to write about them. It's gotten to the point where I just need to unload them on the blogosphere. Click through below the fold for some cool stuff from the scientific literature.
More on Neutrality from Laurence Hurst and Colleagues -- I just wrote about the nearly neutral theory, and here is an analysis of selection on silent sites in the human genome. Is this a coincidence or was this article subconsciously on my mind? From the abstract:
"At least in species with large populations, even synonymous mutations in…
razib | February 2, 2006Instead of an update, I want to specifically point readers to Evolgen's extended post on the nearly neutral theory. He takes my 10 yard pass on genetic drift and jukes and jives all the way to the end zone (with a good block from John Hawks). The take home message is that science is about successively more accurate approximations of nature, with the caveat that in probabilistic field like much of genetics the "answer" is the most likely explanation (expectation), around which there will be exceptions to the rule galore (variance). Chad's initial post seems to have been a little epidemic in…
razib | February 1, 2006Chad Orzel is asking about misconceptions in science that irritate. Evolgen and Afarensis have chimed in. My problem is not an misconception, it is a pet peeve. As I've noted before, random genetic drift is a catchall explanation for everything.
I am not saying drift is not powerful, it is the basis for the neutral theory of molecular evolution. This theory states that the rate of substitution on a neutral locus is proportional to the rate of mutation. Substitution would be when you have allele X at 99% frequency at time 1 and allele Y at 99% frequency at time 2 on a particular locus…
razib | January 31, 2006I've been getting queries about the ear wax paper...below the fold I've copied table 1, which shows the frequencies of the haplotypes in various populations.
First, note the sample sizes.
Keep these sample sizes in mind as you try to get an understanding of the clines the authors were talking about.
Greg Cochran points out that since dry ear wax is a recessive trait it seems plausible that the phenotype being selected is different. It might be dominant or additive so that a total approach toward fixation of the allele would not be necessary for the fitness to be maximized. Consider the…
evolgen | January 31, 2006This blog doesn't seem to want to write itself. I've got a few posts in the pipeline (including the next on detecting natural selection), but I can't seem to finish them. I'm in this writing funk where I start to lay some words onto paper (well, text editor, actually), and then I can't organize all my thoughts or just can't finish writing the post (do I have an undiagnosed case of ADD?).
Luckily for me, I have Chad at Uncertain Principles to inspire me, as he's already done once before. This time he's asking people about their least favorite misconception in their field. One commentor…
razib | January 30, 2006Life can be really funny. When I was in college I was incorrigibly curious and I asked a Korean American friend if his ear wax was dry (I'd read that East Asians had dry ear wax once) and his response was, "Isn't everybody's?" When it comes to interpersonal differences there are many things we take for granted and extrapolate to others that aren't necessarily true.1 Nick Wade in The New York Times has an interesting write up about the genetics of the ear wax phenotype. While the populations of Europe and Africa have wet ear wax, those of East Asia have dry ear wax. Other populations are…
razib | January 29, 2006Newsweek has an entertaining story which highlights the recent penetration of science into the venerable enterprise of genealogy. The good:
...Adopted at birth, Royer knew nothing about her biological parents. But certain physical traits-wide nose, dark skin-led people to guess that she was Iranian or even Cambodian. "I always wondered," she says. Two hundred dollars and a swab of her cheek gave her an answer: Royer's maternal ancestors were most likely Native American. The knowledge, she says, "makes you feel more of a person."
The dumb:
DNA testing is forcing some people to rethink…
razib | January 27, 2006Science isn't perfect, it often misses obvious truths. Consider the 2005 Nobel in medicine, awarded for the work of Barry Marshall and J. Robin Warren in establishing the connection between Helicobacter pylori and ulcers. After the fact you hear many stories of doctors who had stumbled onto the solution, antibiotics, long before the scientific consensus. Many others now understood why they always saw these pathogens in samples taken from patients with ulcers. Now it all makes sense, but these sort of screw ups make you wonder how far we've gone past Galen! Falsification is a decent…
razib | January 21, 2006The Harvard Crimson reports on George Church's attempt to develop super-cheap genomic sequencing, though this time he's giving a $10-20,000 price point quote instead of $1,000. Scientific American has a subscription only piece.