Population Genetics
evolgen | April 24, 2006If you read evolgen, you've probably been following the race riots that Wilkins started. It's pretty much died down now, and it was more a debate about semantics rather than an actual scientific disagreement. This is usually the case in evolutionary biology -- take, for example, the neutralist-selection debate or the recent junk DNA fun we had here at evolgen. I have refrained from offering my opinion on Wilkins's post due to my poor understanding of human population genetics (as evidenced by my attempt to discuss marketing BiDil to African Americans), but I have a few comments I would…
evolgen | March 23, 2006Alex Palazzo managed to piss off some people with his taxonomy of biomedical disciplines. We have also learned that there are different types of physics geeks and anthropologists. (By the way, don't ever call me a geek; geeks bite the heads off of chickens. I'm a nerd.) I previously attempted to classify evolutionary biologists and named them after the important names in their particular field. It was actually a satire of the creationist ploy to call people Darwinists, so laugh. Now I'm going to further divide up the evolutionary geneticists (already a sub-set of biologists) into a bunch…
evolgen | March 20, 2006Robert Skipper took issue with Dick Lewontin's definition of natural selection. Skipper did not like how Lewontin removed the struggle for existence and interaction with the environment from the requirements for evolution by natural selection. John Hawks points out that the environment encompasses everything outside of the genome (the proteome, cell environment, extracellular physiology, the extra-organismal environment, and even culture), and I agree with him -- as a reductionist, I like to view the nucleotide as the unit of selection and everything else as the environment. Skipper agrees…
evolgen | March 17, 2006PLoS Computational Biology has an article in the pipeline on detecting natural selection in humans in chimps. The authors looked for genes evolving at unequal rates between the two species and genes with signals of positive selection. I have not read the entire article, but it looks like a good attempt to distinguish actual positive selection from changes in selective constraint.
evolgen | March 14, 2006PLoS Biology (the people that brought you the recent paper from Jonathan Pritchard on detecting selection in the human genome and George Zhang's paper on selection on human pseudogenes) has published an editorial on detecting natural selection. It is a good follow up to my series on detecting natural selection using molecular data.
evolgen | March 10, 2006I commented a couple of days ago on a news item about a journal article on the evolution of gene expression in primates that had yet to be published. Well, the article has been published, and I've read it (Nature has also published a news and views piece on the study by Rasmus Nielsen). I have a few comments on why this research is unique, what the researchers found, and the implications of this research below the fold.
WHY THIS STUDY IS UNIQUE: This is the first large scale study to examine gene expression in primates using species specific probes. Gene expression can be measured by…
evolgen | March 7, 2006This paper is rather timely considering I just finished reviewing methods for detecting natural selection. Jonathan Pritchard's group has scanned SNP data from three populations (Europeans, East Asians, and Nigerians) for signatures of positive natural selection. The authors used measures of polymorphism to detect natural selection. In their approach, they polarized polymorphic SNPs as ancestral and derived (kind of like a Fay and Wu test) using the other populations as outgroups. In this type of test, high frequency derived SNPs are a hallmark of recent positive selection; the authors…
evolgen | March 6, 2006I have to say, it's kinda cool to have my opinion acknowledged and used to correct an error. It looks like I pull some weight around here (not as much as some folks, but the 100 or so page views a day mean something).
But I ain't done yet. In honor of my dedication to correcting errors in the popular press, I have added a new category called "Science News" to this blog. In this installment, I will point out another error published by Seed. Not all of my posts will be devoted to copy-editing my bosses, it just so happens that they're now one hit away from a trifecta for the day.
This one…
evolgen | March 5, 2006Polymorphism and Divergence
This is the eighth of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The introduction can be found here. The first post described the organization of the genome, and the second described the organization of genes. The third post described codon based models for detecting selection, and the fourth detailed how relative rates can be used to detect changes in selective pressure. The fifth post dealt with classical population genetics methods for detecting selection using allele and genotype frequencies…
evolgen | February 27, 2006I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…
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 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…
evolgen | February 2, 2006I wrote previously about a couple of misconceptions in evolutionary genetics (random mutation and natural selection and decoding genomes). Razib and John Hawks have been rapping on genetic drift and neutrality. Razib thinks it's important to distinguish between molecular evolution and phenotypic evolution -- I agree, by the way, but drawing the line can be difficult. As John pointed out in another post on misconceptions, the one gene, one protein model is greatly flawed. However, there is a relationship between the genotype and the phenotype, and if much of molecular evolution can be…
evolgen | January 20, 2006The first thing I think when I read the title to this post is, "Man, that's a long friggen title, and it's not at all catchy." The next thing I think is, "I thought I said I wasn't going to write about ecology." Well, I actually wrote:
"I am in no way, shape, or form an organismal biologist nor am I an ecologist, and if you catch me out of my element, by all means, please set me straight."
So, I invite you to put me in place if I'm talking out of my ass. But why would I write about an ecological concept like interspecific competition? This actually stems from a course that I am TAing…
evolgen | January 17, 2006PZ Myers is reposting some of his greatest hits from the old Pharyngula website to his new digs at ScienceBlogs. In one post he gets into the deficiencies of modern evolutionary theory using West-Eberhard's book as a guide. I agree with most of the thing he says (and I'll get into how I agree with him below), but first I need to scratch a pet-peeve itch:
"You can see this in any textbook of population genetics: the effect of selection is to impose a gradual shift in the mode of a pattern of continuous variation. Stabilizing selection chops off both tails of the distribution, directional…
evolgen | January 14, 2006Nucleotide Polymorphism and Selection
This is the seventh of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The introduction can be found here. The first post described the organization of the genome, and the second described the organization of genes. The third post described codon based models for detecting selection, and the fourth detailed how relative rates can be used to detect changes in selective pressure. The fifth post dealt with classical population genetics methods for detecting selection using allele and genotype…
evolgen | January 12, 2006I have been describing some recently published worked on polymorphic deletions (see here and here for the previous two posts) on the old site. I will conclude that series here at ScienceBlogs with a discussion of linkage disequilibrium and deletions.
In the previous two posts I outlined two different approaches for identifying polymorphic deletions using single nucleotide polymorphisms (SNPs). I also described some of the analysis performed on that data set, which revealed that many of the deletions resulted in the elimination of at least a portion of a gene (some removed complete genes,…