genetics
razib | September 5, 2007Proceedings of the Royal Society B has a paper out which reports evidence of positive selection on genes which seem to have some relationship to the heritability of schizophrenia (Nature has a good summary). The authors imply that the genes in question were likely selected for reasons totally unrelated to schizophrenia, but that the new variants increase susceptibility toward the disease. This is understandable, rapid selective bursts can result in the increase in frequency of alleles which might have negative side effects that are on the balance erased by the benefits which they confer (a…
sporte | September 5, 2007If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)
You may be wondering, and rightly so: just what is a SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
purepedantry | September 4, 2007The issue of sympatric speciation -- or how to separate species emerge from a single species without geographic isolation -- is a contentious issue in evolutionary biology. How can two species emerge without reproductive isolation of two separate groups? Wouldn't they all just breed together, hiding any new genes in heterozygotes?
Bomblies et al. publishing in PLoS Bio have something interesting to say about that. The use a plant called Arabidopsis thaliana or thale grass to show that the answer might be in genes that regulate the immune response.
Just to get some background, the genes…
clock | September 3, 2007...that is, if you still think that a genome sequence tells all secrets about someone's success in science etc. ;-)
But the new paper actually uses Venter's personal genome to do some nifty stuff, as this is the first time a genome containing the sequences from BOTH sets of chromosomes of a single individual has been sequenced, with some interesting insights:
The Diploid Genome Sequence of an Individual Human:
We have generated an independently assembled diploid human genomic DNA sequence from both chromosomes of a single individual (J. Craig Venter). Our approach, based on whole-genome…
razib | September 3, 2007Curious about height? Check out this new paper in Nature Genetics, A common variant of HMGA2 is associated with adult and childhood height in the general population. Nature News has a nice report for public consumption.
Last week when I posted about heritable traits I used height as an illustrative example. The reasoning was pretty simple, it's a rather concrete phenotype which most humans have an intuitive grasp of in terms of the range of variation, and it also happens to exhibit high heritability in developed populations; on the order of 0.90, i.e., 90% of the variation in the…
razib | August 30, 2007When someone tells you that height is 80% heritable, does that mean:
a) 80% of the reason you are the height you are is due to genes
b) 80% of the variation within the population on the trait of height is due to variation of the genes
The answer is of course b. Unfortunately in the 5 years I've been blogging the conception of heritability has been rather difficult to get across, and I regularly have to browbeat readers who conflate the term with a. That is, they assume that if I say that a trait is mostly heritable I mean that its development is mostly a function of genes. In reality not…
razib | August 29, 2007Update: Comment from Chris Surridge of PLOS One:
Just a quick note. The paper is now formally published on PLoS ONE. The citation is:
Tuljapurkar SD, Puleston CO, Gurven MD (2007) Why Men Matter: Mating Patterns Drive Evolution of Human Lifespan. PLoS ONE 2(8): e785. doi:10.1371/journal.pone.0000785
As it is PLoS ONE you can rate the paper, annotate and discuss it there too.
There's a new preprint posted (PDF) on PLOS One titled Why Men Matter: Mating Patterns Drive Evolution of Human Lifespan. The basic question is this: why do humans live beyond the lifespan of the post-menopausal female…
razib | August 28, 2007Genetic and environmental contributions to prosocial behaviour in 2- to 9-year-old South Korean twins:
...The best-fitting model indicated that 55%...of the variance in the 2- to 9-year-olds' prosocial behaviour was due to genetic factors and 45%...was due to non-shared environmental factors. It is concluded that genetic and environmental influences on prosocial behaviour in young South Koreans are mostly similar to those in western samples.
This is the "standard" finding, most of the variation in behavior is due to genes or non-shared environment. In The Nurture Assumption Judith Rich…
razib | August 25, 2007Yesterday I posted on the resurrection of the "redheads going extinct" meme (as I noted, this story seems to cycle every few years). The current source is National Geographic Magazine, which doesn't have the "article" online. I went to the bookstore and checked out the September 2007 issue, and a write up does exist about the redheads going extinct. Unlike the secondary sources it isn't as sensationalist, and makes more than a passing nod to the Hardy-Weinberg logic from which the inference is derived.
That being said, the write up in National Geographic Magazine simply recycles older…
razib | August 25, 2007p-ter points me to a new paper which documents interspecies hybridization in monkeys whose lineages putatively diverged about 3 million years ago. Note that the hybridization follows Haldane's rule: the heterogametic sex (in mammals the males) exhibits sterility while the other sex does not. Whatever genetic incompatibilities built over the period during which the two populations became distinct the less robust sex (males have only one copy of the X chromosome, ergo, sex-linked diseases) naturally exhibits greater breakdown in hybrids. In any case, the story is obviously relevant to…
razib | August 24, 2007Every few years it seems that a new meme declares that "blondes will go extinct!" or that "red hair will go extinct!" I've only been blogging for 5 years, and this story has already cycled multiple times. A co-blogger of mine told me that he did some digging and it seems that this meme is of old vintage, with "blondes going extinct!" stories dating back to the 19th century. The current craze (as evidenced by blogs) seems to have started at an Australian newspaper. But, it is sourced originally to National Geographic Magazine.
First, the story doesn't appear on National Geographic Magazine…
razib | August 24, 2007RPM pointed me to this new paper, Major Histocompatibility Complex Heterozygosity Reduces Fitness in Experimentally Infected Mice:
...Our results show that MHC effects are not masked on an outbred genetic background, and that MHC heterozygosity provides no immunological benefits when resistance is recessive, and can actually reduce fitness. These findings challenge the HA hypothesis and emphasize the need for studies on wild, genetically diverse species.
MHC are a group of loci which are critical in the adaptive immune systems of "higher" organisms. They are also among the most polymorphic…
razib | August 22, 2007This is more of a quick note than a post. In Africa (and to a lesser extent other regions) the rise of malaria has resulted in an extreme evolutionary response, basically the heterozygote is extremely fit vis-a-vis mutant homozygotes (which exhibit Sickle Cell Anemia) and the wild type homozygotes. This is a case of balancing selection via overdominance, the frequencies of the alleles are determined by the fitness of the three genotypes (mutant homozygote, heterozygote and wild type homozygote). Naturally polymorphism will be maintained since the heterozygote by necessity needs the…
pharyngula | August 20, 2007If it existed, it might also be profoundly autistic and … diabetic? So science cannot disprove the existence of a soul, but one thing we're learning is how much valued human properties such as love and attachment and awareness of others are a product of our biology — emotions like love are an outcome of chemistry, and can't be separated from our meaty natures.
The latest issue of BioEssays has an excellent review of the role of the hormone oxytocin in regulating behaviors. It highlights how much biochemistry is a determinant of what we regard as virtues.
Anyone with a little familiarity with…
evolgen | August 17, 2007
I'd be remiss to not mention this paper from Hopi Hoekstra's group after I previously discussed the anti-evo-devo paper she wrote with Jerry Coyne. The premise of the paper from Hoekstra and Coyne is that Sean Carroll overplays the importance of cis-regulatory changes in the evolution of form. Well, Hoekstra and colleagues mapped the genes responsible for natural coat color variation in subspecies of a beach mouse. They isolated two QTLs, and they identified one candidate gene for each. One candidate gene contains a substitution in a protein coding region, while the other gene has no change…
razib | August 14, 2007I'm on the road/traveling for the near future, so posting will be light, but these four papers look interesting (haven't had a time to look closely).
Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
Varying environments can speed up evolution
Evolution in the hypervariable environment of Madagascar
Innovation and robustness in complex regulatory gene networks
razib | August 13, 2007Ezra Klein asks "How Quickly Do Genes Change?" in response to Andrew Sullivan gushing over Greg Clark's new book, A Farewell to Alms. Clark offers the hypothesis that the industrial revolution in England was catalyzed in part by changes in behavior which might have been reinforced by selection for particular alleles. In terms of the specific hypothesis, I'm skeptical and would probably bet that Clark has overplayed his hand and put too many eggs in one basket. But, in response to Ezra's question I threw down a flurry of comments (with a lot of grammatical errors due to my haste) which you…
purepedantry | August 10, 2007Nicholas Wade reports in the NYTimes about a UCD professor, Gregory Clark, and his theory of the Industrial Revolution. His answer is that high fertility rates in the upper classes caused them to steadily supplant lower classes. They brought productive values with them such that when the population reached a critical mass of individuals with middle class breeding so to speak, the Industrial Revolution occurred:
A way to test the idea, he realized, was through analysis of ancient wills, which might reveal a connection between wealth and the number of progeny. The wills did that, but in…
razib | August 9, 2007Update: Another post on this topic at my other blog.
A few days ago I pointed to a new paper, Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans. Knowing my interest in the topic you might assume that I would be "all over this." Well, I finally read the paper (twice) and I have to say it's a really interesting piece of work.
To the left is a map of the proportion of the T-13910 SNP near the LCT locus in selected populations. In Eurasia the correlation between this allele and "Lactase Persistence" (LP) is very strong (r ~ 0.97 in terms of LP…