Molecular Evolution

There's an old paradigm in human population genetics that we each differ from each other by less than one percent at the DNA sequence level. While that may be true for our DNA sequences, recent work indicates that there's also quite a bit of variation amongst individuals in the actual content of their genomes. Such variation is known as copy number variation (CNV) or copy number polymorphism (CNP). What it means is that some people may have one copy of a genomic region, other may have two, and even others may have none. Nature thinks this research on CNV is quite important, as there are five…

At least in polyploids. So says this review of this paper. Take home message: polyploids use duplicates to buffer against mutations to important genes. The review is brought to you by the Science Creative Quarterly. SCQ is brought to you by David Ng, who has just introduced The Filter. If you don't know about SCQ, you should check it out. And if you know about SCQ but haven't discovered The Filter, you should check that out.

Don't worry, this one has nothing to do with mtDNA. There's been a bit of a hubbub recently in the ScienceBlogs community about science journalism. Sometimes we're a bit too hard on the journalists. In this week's issue of Nature, Robert Barton takes the journal to task for their coverage of the Pollard et al paper describing a rapidly evolving non RNA gene. Barton makes a good point at the beginning of his letter: You state in your News story on genetic differences between humans and other species . . . that research is beginning to pin down genes that "evolved rapidly during the transition…

Alex has been pondering the nature of non-protein-coding RNAs. So have the boys at Gene Expression (how appropriate). Coffee Mug and JP have pointed out that a large portion of the human genome is transcribed, and much of it has an unknown function. Now JP describes a paper that takes an evolutionary approach towards studying the function of intergenic transcripts. By comparing human and chimp transcription profiles, the authors "that intergenic transcripts show patterns of tissue-specific conservation of their expression which are comparable to exonic transcripts of known genes." This…

If you enjoyed my post on the evolution of sex chromosomes in tetrapods, you should check out Darwin Central for even more. It starts with the story of the vole, and goes into how mammalian sex chromosomes have evolved and what we can expect in the future.

Adam Eyre-Walker has published a review of adaptive evolution in a few well studied systems: Drosophila, humans, viruses, Arabidopsis, etc. These organisms have been the subject of many studies that used DNA polymorphism, DNA divergence, or a combination of the two to detect natural selection in both protein coding and non-coding regions of the genomes. Now that we have whole genome sequences for multiple closely related species from a few different taxa, many researchers are interested in determining the role of natural selection in the evolution of DNA sequences. Eyre-Walker claims that the…

A few months ago I wrote the following: 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 I'm going to have to write an entry on the evolutionary genetics of sex determination in everything other than mammals. I never did get around to writing that review of sex chromosomes. All is not lost, however, as the most recent issue of Current Biology is devoted to the evolution of sex. There is even an…

Nobel Intent has an excellent summary of a paper in the PNAS pipeline on the origin of new exons in the human genome. The authors compared genes between humans and seven other vertebrates to identify newly arisen exons. They found that many new exons are composed of repeat sequences, such as transposable elements. Also, recently evolved exons are more likely to be alternatively spliced, suggesting there is a "trial period" for a new exon before it can be fully incorporated into the protein coding sequence of a gene.

David Haussler and colleagues have identified a 118 base pair sequence that has evolved really fast along the human lineage relative to the chimpanzee lineage (Carl Zimmer has a good review). In fact, this sequence differs by two base pairs out of 118 between chimpanzees and chickens, and 18 out of 118 between chimps and humans. Differences in relative rates usually indicate changes in selection regimes along at least one lineage. These changes could be due to increased selective constraint along one lineage, relaxed constraint, or adaptive evolution. More on that later. Also interesting is…

Here are three interesting items that I don't plan on blogging, but are worth linking to: Here is a news release on indel variation in humans. SNPs are so 20th century. Deletions, duplications, and insertions are the molecular polymorphisms of the future. Speaking of deletions and duplications, Nobel Intent has a good review of three articles (available here, here, and here) that deal with structural polymorphism and disease on human chromosome 17. Interestingly, the same region examined the three papers harbors an inversion that may confer a fitness benefit. Finally, totally unrelated…

Jacob at Salamander Candy has written the post that I have been meaning to write. With so much freely available sequence data in GenBank and loads of free software with which to analyze it, we should encourage the general public to start looking for 'interesting things' (building phylogenies, comparing rates of evolution along lineages, testing for natural selection, etc). There are tons of armchair astronomers, so why not develop a community of armchair molecular genetics data miners? Here's a taste of Jacob's essay: The more non-professionals we have doing science, the better, because not…

Here is some light reading for your Sunday: Mosquitoes sing to each other by flapping their wings. This paper reports sexually dimorphic responses to wing beat patterns in mosquitoes (PZ Myers has a good review). This leads me to wonder whether we can study intra- and inter-specific differences in flight behavior and response, which then gets me wondering whether we can find QTLs responsible for these differences. And (this should come as no surprise to those who know me) I also wonder whether these QTLs will map to within inversions for sympatric species pairs more so that allopatric…

Andy Clark has written a review of comparative evolutionary genomics for Trends in Ecology and Evolution. His review deals with identifying functional regions of the genome and inference of both positively and negatively selected sequences. Clark is one of the leaders in the field of evolutionary genetics (and now genomics), actively participating in the analysis of both the human and Drosophila genomes. He also brings a solid understanding of biology, as well as an appreciation of statistical rigor. You can sense his excitement about the union of molecular biology and evolution in the…

Billy D (no, not that Billy Dee) is pimping an anti-evolution book by John Sanford. I refuse to link to outright liars, but you can find a link to Bill's blog here. More after the jump. From what I can gather, the author postulates that the human genome is deteriorating, and this is evidence against Darwinian evolution. This is another argument -- in a long line of many others -- that basically amounts to the same bullshit: natural selection cannot explain the diversity of life on earth. Interestingly, Michael Lynch used a similar argument (albeit without supernatural forces) in describing…

...or how a learned to stop worrying and love evo-devo. As my mind gets a chance to process some of the stuff I heard and talked about at the meeting I just returned from, I'll post some thoughts that will help me organize my ideas (hopefully better organized than that last sentence). This is the first (of perhaps few, perhaps many) of those (possibly incoherent) ramblings -- interrupted by as few paranthetical remarks as possible. In this post, I'll try to tie together: A talk by Sean Carrol on the evolution of wing pigmentation. A talk by Peter Andolfatto on the evolution of Drosophila non…

Don't expect much from me in terms of substantial posting. I'm getting prepared for the SMBE meeting, and devoting most of my time to finishing up some data analysis and putting together my talk. If you want to read about some evolutionary genetics research, here are some links: Check out this report on genome duplications in angiosperms from Claude dePamphilis's lab (Indian Cowboy has more here). I'm pretty interested in copy number variation, so I definitely need to read this article comparing copy number polymorphisms in humans and chimps (news release here). From the snippets I've…

Razib linked to some press surrounding an unpublished (although presented at a conference) finding that an allele that causes deafness in homozygotes may allow wounds to heal better in heterozygotes. This appears to be another example of an allele simultaneously under balancing selection (due to overdominance) and purifying selection. Other such examples include the sickle cell allele and the cystic fibrosis allele (despite some initial skepticism, I now admit that the evidence for selection maintaining the CF allele in European populations is quite convincing). I discuss another potential…

I'm trying to emerge from hibernation, and I'll hopefully have some good blogging material up in the next few days. In lieu of my own ideas, I'm going to link to what other people have written. Read them, because I ain't saying much right now. The list can be found below the fold. Neil Saunders points us to this article from the BBC on a new function for "junk DNA". I hope Neil is right: "one day the term 'junk DNA' will fall into disuse." John Hawks has a good discussion of a recent paper on inferring population size using mtDNA. Apparently cytoplasmic DNA is under selection, and that…

Ian Musgrave has a good summary of genes appearing from non-coding DNA (ORFans) on the Panda's Thumb. I have written about ORFans here and here (dude's gotta link to himself sometimes). Ian's post is targeted at some claims made by the creationist Paul Nelson, but he focuses more on the science that on the ignorant blowhard.

Bora has been pushing the idea of publishing original research (hypotheses, data, etc) on science blogs. This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts can be found below. Part 2 of this series (The Backstory) can be found after the jump. Previous entries: Part 1 - Introduction The Backstory The enzyme fructose-1,6-bisphosphate aldolase (hereafter referred to as aldolase) is responsible for splitting fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate during glycolysis.…