Molecular Evolution
evolgen | April 24, 2006Bora has been pushing the idea of publishing original research (hypotheses, data, etc) on science blogs. As a responsible researcher, I would need to obtain permission from any collaborators (including my advisor) before published anything we have been working on together. But what about small side projects or minor findings that I don't expect to publish elsewhere? As it turns out, such a project has been laying dormant since I first started working on it at a class project a few years ago. I will reveal more information about this project in subsequent posts, but suffice it to say this…
evolgen | April 24, 2006Via nodalpoint comes this UPGMA tree of sequence alignment algorithms from this paper. The first thing that comes to mind is that there are way too many sequence alignment methods. The second, it's kinda cool to see one method used to understand another. And Nucleic Acids Research gets mad props for being entirely open access while still being published by the evil empire that is Oxford University Press.
evolgen | April 21, 2006Pharyngula has a good summary of the new Sean Carroll Drosophila wing dot paper. Eventually Sean's gonna try to mess around with a hawaiin species and blow the roof off this mother.
evolgen | April 4, 2006I previously alluded to Junk Non-coding DNA evolving into a gene in my last post on junk DNA. Here is another example of this phenomenon:
Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA.
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"This appears to be a new mechanism for the evolution of a gene from non-coding DNA", says Professor Cheng, "3.5 billion years of evolution of life has produced many coding genes and conventional thinking assumes that new genes must come from pre-existing ones because the probability of a random stretch of DNA…
evolgen | March 27, 2006My little screed on junk DNA elicited some good feedback, including a comment from Dan Graur. In a somewhat ill-thought out rant, I implied that anyone who uses the term 'junk DNA' should be ostracized from the scientific community (or something along those lines). I restated my opinion in a far more diplomatic manner in the discussion that followed in the comments: junk DNA is an appropriate term for DNA that serves no function (non-transcribed, non-regulatory, and non-structural), but we should refrain from using that term for all non-coding DNA. I elaborate my opinion and reference a…
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 23, 2006The term "Junk DNA" is bullshit. There, I said it. The moment I hear someone utter that phrase, I immediately lose respect for him or her. No one whose opinion is worth anything will refer to non-coding DNA as junk. That's why this article bothers me. The title, "Junk DNA may not be so junky after all" has nothing to do with the content of the article. The research being described is not about showing that non-coding DNA has a function. The function has already been determined. The researchers have used zebrafish to identify enhancers for human genes. The subtitle to the article (…
evolgen | March 19, 2006The human Y, that is. The Science Creative Quarterly has a very thorough (ie, make sure you have some time to spare) review of the mammalian Y chromosome (focusing on the human Y). The article covers the origin and evolution of the mammalian Y and what the degeneration of the Y means for the future of human male fertility and sex determination. I should point out that the mammalian Y chromosome is an anomaly in origin and sex determination. In fact, every single sex determination system and sex chromosome system that I know of differs from all of the others in some manner. It looks like…
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 15, 2006Hey, Myers, two can play at this game. An article in the Journal of Molecular Evolution presents structural and sequence analysis of hemocyanin (an oxygen carrying protein) from the cephalopod, Nautilus pomilius (shown at the left). They also compared the sequence to another cephalopod, Octopus dofleini, and found that the two species diverged approximately 415 million years ago.
Bergmann, S, B Lieb, P Ruth, and J Markl. 2006. The Hemocyanin from a Living Fossil, the Cephalopod Nautilus pompilius: Protein Structure, Gene Organization, and Evolution. J Mol Evol 62: 362-374.
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 8, 2006Kevin White (aka, Mr. Drosophila microarray data) has a paper coming out in tomorrow's issue of Nature. The paper (which is not available on the Nature website yet) compares the expression of over 1,000 genes from humans, chimpanzees, orangutans and rhesus monkeys. From a news write up of the findings:
When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased…
evolgen | March 6, 2006A very pretty picture (click on the image to make it larger):
Go read what Carl Zimmer and Rhosgobel have to say. For more on the Tree of Life, go here.
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, 2006You, me, your pet dog, and any other animal with a backbone are deuterostomes. So are sea stars, sea urchins, and sea cucumbers. During early development you, me, and echinoderms (sea stars et al) are a round ball of cells. The ball of cells invaginates and that opening becomes our anus. This differs from other animals like flies, worms, and snails whose first opening becomes a mouth. A second opening forms later in development, and it becomes our mouth (hence the name "deuterostome", or mouth second). The deuterostomes can be broken into two groups: the chordates and the echinoderms.…
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 24, 2006My apologies for the utter lack of posting over the past week. I've got stuff sitting around waiting to be written about, and I just haven't been writing. I'm not going to make excuses; I just haven't been managing my time well. While you wait for me to post again (soon, I promise), I give you this article on "intelligently designing" promiscuous enzymes to perform specific functions. Here's a quote from the write up:
According to the theory of divergent molecular evolution, primordial enzymes and other proteins started out as "promiscuous" so that primitive organisms would be better able…
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 1, 2006As I mentioned before, you should definitely check out the Tangled Bank. This bi-week's issue is quite diverse (and all the astronomers seem to be talking about the "earth-like" planet). One entry comes from an extremely opinionated anthropologist who calls out quantitative geneticists:
Chimps More Like Humans Than Apes??? What does it mean to be human? And why quantitative geneticists should stick to their jobs.
Retarded Geneticists With No Understanding of the Word 'Phenotype' Mouth Off
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More after the jump...
Well, I gotta say something about this, right?? I mean, I'm a retarded…