genetics
razib | November 16, 2006A post on my other blog from p-ter on the second Neandertal genomics paper. Here is the important conclusion:
...expect some big papers on "sexy" genes like ASPM, microcephalin, and FOXP2 in the coming years.
Remember "Netscape time." Feels like genetics is approaching that in the Post-genomic era....
razib | November 16, 2006From here: "Cronin et al. (1991) then discovered that mtDNA of brown bears is paraphyletic with respect to polar bears. That is, the mtDNA of brown bears of the Alexander Archipelago in southeastern Alaska is more closely related to the mtDNA of polar bears than it is to the mtDNA of other brown bears. Cronin et al. (1991) reported that mtDNA sequence divergence between Alexander Archipelago brown bears and polar bears is only about 1%, whereas a divergence of about 2.6% separates polar bears from brown bears occurring elsewhere...Following the discovery of Cronin et al. (1991), others…
razib | November 15, 2006This comment made me aware that I should probably be more precise about how I view the "new model," which I will provisionally label "Ecotype Persistence" (EP), as being different from Multi-regionalism in the old school. Consider two variables:
Full genome content
Phenotypically salient characters (controlled by a few selected loci)
Full genome content is the whole shebang, and it can be thought of as a proxy for ancestry. Phenotypically salient characters on the other hand are simply a reflection of adaptation's power in a local time and space, sans phylogenetic constraint they can be…
razib | November 15, 2006My next post on Gillespie's chapter in Evolutionary Genetics: Concepts & Case Studies is going to cover "genetic draft." I don't know when I'll get to it, so I'll point to Robert Skipper's post on the topic from six months ago. Yes, selection is proximately stochastic. Like this.
razib | November 15, 2006I have spoken of the probability of extinction and the rate of substitution once past extinction, but now to something more prosaic, genetic drift. My post is based on John Gillespie's treatment in Evolutionary Genetics: Concepts & Case Studies. Like R.A. Fisher he does not think much of this process in evolutionary dynamics, and deemphasizes its salience. The easiest way to think of drift is simply as sample variance over generations, the expected deviation from the mean as one moves through time. In a diallelic model the deviation between generation n and generation n + 1 is:
σ…
razib | November 14, 2006Over at my other weblog there is a post up, Genomics and socialized health care, which asks if the new DNA era might not explode the acturial edifice that is modern health insurance in the United States. I suspect in this case many will welcome a "broken" system which needs to be replaced by a universal single-payer system, at least on the basal level. But, with privilege comes responsibilities. I suspect that the overturning the old system of health insurance, which was predicated on imperfect knowledge, will be correlated with the rise of a new system where particular values common…
razib | November 14, 2006This is more for google, but if you missed anything, you should check it out. Here is a replay of the introgression & Neandertal related posts....
Preview:
Neandertal & H. sapiens sapiens interbreeding
Neandertal-"modern" mixing
Introgression related posts over the past 6 months
Main course:
Did Modern Humans Get a Brain Gene from Neandertals? (link to Lahn. et. al.)
Neandertal & humans - introgression (this has the nice graphic that people seem to think illustrates the concept pretty well)
The Neandertal child (a face to it all)
Introgression vs. gene flow (illustration of…
razib | November 13, 2006Scientific American has a nice link round up on l'affaire Lahn & Neandertals.
pharyngula | November 13, 2006
Oh happy day, the Sea Urchin Genome Project has reached fruition with the publication of the full sequence in last week's issue of Science. This news has been all over the web, I know, so I'm late in getting my two cents in, but hey, I had a busy weekend, and and I had to spend a fair amount of time actually reading the papers. They didn't just publish one mega-paper, but they had a whole section on Strongylocentrotus purpuratus, with a genomics mega-paper and articles on ecology and paleogenomics and the immune system and the transcriptome, and even a big poster of highlights of sea urchin…
purepedantry | November 13, 2006I see that Simon Baron-Cohen has a piece in Seed about his theory of autism. I am really skeptical of many of his arguments related to autism, so I thought I would discuss a couple of them. Here is his core argument:
So what has all of this got to do with autism? We know that autism runs in families, and that if a child with autism is a twin, the chances of the other twin also having autism is much higher if the twins are identical. This tells us that genes are likely to be an important part of the explanation, and that one should look at the parents of children with autism for clues.…
razib | November 11, 2006John Hawks has a long post on introgression in the context of the Species Concept problem.
razib | November 10, 2006Yesterday Michael Blowhard enthusiastically linked to the recent Neandertal introgression story, and a reader commented:
Don't bet on it, Michael. Paleoarchaeology postdoc. and regular Querencia reader Laura wrote to me off- blog:
"Saw your blog and the mention of the neanderthal interbreeding article last week...it's all fluff, published by one of the two main proponents of the PC theory that neanderthals were just like us, blah blah blah....I don't exclude the possibility that they did interbreed, but so far there isn't any convincing evidence. And if they did, it would have been on such a…
razib | November 9, 2006SEED hits the major points, and Paabo confirms:
At last, anthropology and genetics have a point of agreement in terms of the fate of Neanderthals. Henry Harpending, an anthropologist at the University of Utah who edited Lahn's paper, described the analysis supporting its conclusions as "quite bulletproof."Pääbo, made famous for his mtDNA evidence against interbreeding, hailed it as "the most compelling case to date showing a genetic contribution of Neanderthals to modern humans," and said he plans to to seek confirmation of Lahn's findings in his own work on the Neanderthal genome.
razib | November 9, 2006From John Hawks:
I heard from a long-time correspondent this morning concerning introgression of microcephalin from archaic humans. I'm not sharing the whole message, but I thought it would be worth paraphrasing a key point for some thought.
The basic point is this: Why are we talking about "introgression"? Why isn't this just gene flow?
He answers lucidly, but I would like to offer something that I think is important, and is behind why I do not use the term "gene flow," and prefer "introgression" even though it is more jargonistic. Gene flow is a generic term, and can correctly…
razib | November 9, 2006Since I will be writing a great deal about Neandertals, please keep this image in your mind. I know that most readers of this blog don't view Neandertals as chimps, but I check google news for evolution and genetics related topics and the recent spate of articles on archaic genomics did spawn a few "Neandertals closer to chimpanzees" pieces. Those of you versed in cladistics, or any sort of taxonomy, are likely outraged, but that's just how it is. The photo to the left is of a child, and perhaps "humanized" a bit too much, but Neandertals were clearly humans. The child has light skin, hair…
razib | November 8, 2006Two articles, here and here ($) on the Paabo group's sequencing attempt. Seems rather well timed. I strongly suspect that all the morphological papers that came out in the last few months anticipated Lahn's work, it isn't like stuff doesn't float around as pre-prints.
razib | November 8, 2006Slashdot now has a post on Neandertal introgression:
While modern day eugenicists might all too eagerly read into these findings to draw their own politically biased conclusions, people such as myself, who happen to be of northern European ancestry, may find it fascinating that somewhere in our lineage ancient humans and Neanderthals decided to make love and not war on the ancient plains of Eurasia."
There's a problem with this: sex is not always a gentle act, and can occur via force. Neandertals were a robust people, powerfully built. Am I the only one who has watched or read The Clan of…
razib | November 8, 2006The paper of record reports on introgression. Here is a tantalizing tidbit:
Two other reports of DNA studies of possible mixing of human and related genes are expected to be published in the next few weeks.
...I have suspicions, but I'm in the dark, so I'll be checking in on John Hawks regularly via my rss feed just like you. I am a little disappointed that Nick Wade didn't tackle this, but perhaps he is busy writing copy for the other "Big Idea" that Hawks and Cochran have brewing....
Related: I'm starting to be convinced by readers that the "Living Neandertals" that Hawks and Cochran have…
razib | November 8, 2006John Hawks says:
UPDATE (11/8/2006): My colleague, Greg Cochran, has a post at GNXP discussing introgression and microcephalin further:
If this pans out the way we think it will, introgression from Neanderthals (and maybe with other archaics) may have been one of the two fundamental patterns underlying recent human evolution.
One of the two. [my emphasis -Razib]
What could John Hawks mean??? 1) Look at the category I placed this post under 2) Oh yes...a new round of teasing starts. But you won't have to wait that long this time....
pharyngula | November 8, 2006Fascinating stuff…read this paper in PNAS, Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage, or this short summary, or John Hawks' excellent explanation of the concepts, it's all good. It's strong evidence for selection in human ancestry for a gene, and just to make it especially provocative, it's all about a gene known to be involved in brain growth, and it's also showing evidence for interbreeding between Homo sapiens and Neandertal man.
The short short explanation: a population genetics study of a gene called…