genetics
razib | December 5, 2006Over at agnostic's blog p-eter points out that lactose tolerance can be considered "dominant." Most of you know I have issues with terms like dominant or recessive because I think the simple heuristic is infectious and tends to persist and spread throughout the discourse to the point where it obstructs rather than illuminates. That being said, I can see where he's coming from. We know a bit about the primary European mutation which confers the ability to digest milk as an adult. It's a cis-acting element which works to maintain transcription from the LCT gene, and so results in a level of…
razib | December 4, 2006RPM discusses hybrid speciation while agnostic waxes skeptical about the relevance of more symmetry among multiracial humans. The comments on agnostic's posts are interesting as well.
razib | December 4, 2006A few weeks ago I presented a tentative model for how lactose tolerance (the ability of adults to digest milk easily and efficiently) spread throughout the world. Here is what I offered:
1) A haplotype block, A, associated with the LCT gene, and a particular SNP on that block, -13910*T, is responsible for Eurasian lactose tolerance (here are some numbers across populations)
2) In African populations which are lactose tolerant this haplotype, A, and the SNP, -13910*T, are not always found.
3) This implies that separate mutational events resulted in alternative genetic strategies which…
evolgen | December 4, 2006
The ninth edition of Mendel's Garden has been posted by the collective of Oregon State grad students known as Salamander Candy. Go read the month's best genetics blogging.
razib | December 3, 2006The Associated Press has an article on the genetics of taste and its relevance in everyday life. I've posted on the genetics of taste in the past, it's an interesting topic. Basically, you have three phenotypes:
Super-taster
Taster
Non-taster
Until recently the "super-taster" category was unknown, the crude assays (e.g., tasting PTC doped paper) only distinguished between tasters and non-tasters. The inheritance pattern would have suggested a recessive pattern for the non-tasters, but the super-taster category suggests that we are simply seeing a more additive process where two "on"…
razib | December 2, 2006RPM and Kambiz comment on a paper which argues for the utility of mtDNA in phylogeography.
Remember,
there is lots of mtDNA that is easy to extract because there are so many mitochondria within eukaryotic cells
it mutates fast, building up a lot of genetic variation, in a neutral matter (i.e., perfect "clock")
it is uniparental, passed from mother to daughter, making the coalescent model congenially tractable
evolgen | November 29, 2006A couple of years ago, one of the rear tail lights went out on my car. I'm kinda handy with tools, so I figured it would be an easy fix. I poked around in the trunk area with my screw driver, removing every screw within spitting distance of the lamp. I tugged on the lamp in every possible direction, but the sucker wouldn't budge. Just because I could sequence DNA or parse a genome into the interesting bits and discard the boring stuff, didn't mean I could perform simple maintenance on my car. I admitted defeat and had the lamp fixed the next time I brought my car in for an inspection.
Why did…
razib | November 27, 2006Orac has a rather thorough post on eugenics, and what Richard Dawkins has recently had to say on it. Here is the dictionary.com definition of eugenics:
...the study of or belief in the possibility of improving the qualities of the human species or a human population, esp. by such means as discouraging reproduction by persons having genetic defects or presumed to have inheritable undesirable traits (negative eugenics) or encouraging reproduction by persons presumed to have inheritable desirable traits (positive eugenics).
First, in a historical context Dawkins' addressing the question of…
razib | November 23, 2006A new paper in Nature, Global variation in copy number in the human genome, suggests that it isn't just SNPs that matter in regards to human variation. Those of you who are "in the know" aren't surprised, so this press release is a bit much. Along with a focus on gene regulation, this is a fascinating new area which expands our understanding of how we are how we are beyond the raw sequence. p-etr at my other blog has a lot more. RPM has a post scheduled on this topic, I saw a preview when he published it to make sure it looked right. The press is making a big deal out of this, so we'll…
razib | November 23, 2006Gene-culture coevolution is a topic of interest for me. Consider adult milk digestion. It's weird, and seems like a new adaptation. The lactase gene has been under such strong selection that it is often used (or the region around it) as a control to test whether new methods for detecting selection actually work where we think they should work.
Here are a few maps I reworked from this paper:
The area where cattle genes which produce milk are diverse is relevant because that is the region where milk producing cattle have likely been resident the longest. The logic is similar to why Africans…
razib | November 22, 2006Nick Anthis, he of the fake British accent, has a follow up post on "ethical stem cells."
evolgen | November 21, 2006John Hawks reports that the gene that, when mutated, can turn male flies gay and females into lesbians can also make boy flies fight like girls and vice-versa. This research will be published in an upcoming edition of Nature Neuroscience. And be sure to check out the videos from the fruit fly Drosophila Fight Club.
razib | November 20, 2006I don't have time to comment in detail, but I thought I'd give readers a heads up, there is a preprint in The American Journal of Human Genetics which confirms that a few SNPs on one locus is responsible for 3/4 of the variation between blue and brown eyes in white populations. This locus, OCA2, is the third longest haplotype in the European genome from the HapMap sequence (the European HapMap data comes from Utah Mormons). The length of this haplotype is suggestive of recent strong positive selection within the European population (the further back in time and the weaker the selective…
pharyngula | November 20, 2006
I've been writing a fair amount about early pattern formation in animals lately, so to do penance for my zoocentric bias, I thought I'd say a little bit about homeotic genes in plants. Homeotic genes are genes that, when mutated, can transform one body part into another—probably the best known example is antennapedia in Drosophila, which turns the fly's antenna into a leg.
Plants also have homeotic genes, and here is a little review of flower anatomy to remind everyone of what 'body parts' we're going to be talking about. The problem I'll be pursuing is how four different, broadly defined…
razib | November 19, 2006A new paper, A Maternal-Offspring Coadaptation Theory for the Evolution of Genomic Imprinting (open access), presents a theory of genomic imprinting which purports to explain some facets of the phenomenon via maternal-child interaction:
Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother-offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but…
razib | November 17, 2006This week's Ask a ScienceBlogger:
Who would you nominate for Scientist Laureate, if such a position existed?...
E.O. Wilson. Wilson combines the skills of a serious researcher with literary grace and social/political prominence. With the passing from the scene of Carl Sagan I can't think of any other great scientist who can compare. Yes, there are greater stars in the heavens such as Edward Witten, but none who burn so brightly for the delicate eyes of the common man.
razib | November 17, 2006You want more links to Neandertal related stuff? OK...Afarensis hits the morphology, while Kambiz hits the genetics. On Science Friday they interviewed one of the authors of one of the archeo-genomics papers (Rubin) as well as paleoanthropologist Richard Klein.
razib | November 16, 2006Finally Nick Wade is wading in on the Neandertal genomics story. Wade is a top level reporter, so when he covers a story I am pretty sure he is getting "inside" information that allows him to frame his piece appropriately. So when he says, "Researchers also hope to resolve such questions as whether the Neanderthals spoke, their hair and skin color...." Well, that is definite confirmation of the obvious fact that FOXP2 and MC1R are in the sights. One thing, Wade refers to "founding population." Remember to be careful of terms like this...long term effective population can be tricky, and it…