Population Genetics
evolgen | March 5, 2008Brian Charlesworth has reviewed Michael Lynch's The Origins of Genome Architecture for Current Biology. Charlesworth's review is generally positive, and he agrees that population size may be an important factor in genome evolution. However, he thinks that Lynch overplays the role relaxed selective constraint in small populations plays in the evolution of genomic complexity.
Charlesworth argues that sexual reproduction may be partly to blame for some of the features found in the bloated genomes of many eukaryotes. For example, the abundance of transposable elements may be the result of sexual…
evolgen | March 2, 2008One of the drums I beat around here pertains to inferring demographic history using molecular markers (i.e., DNA data). I've been known to go off on people who make claims about ancestral population sizes based on studies of a single locus or gene. You see, studying a single locus only gives you the evolutionary history of that locus. There is no way to untangle the affects of natural selection from those of demography without examining multiple loci.
The coalescent is a popular statistical technique used to study DNA sequence polymorphism. Combining bayesian analysis with coalescent theory…
evolgen | January 14, 2008While much of the research in evolutionary biology is purely academic in nature -- designed for the purpose of understanding the biology of a system rather than for immediate human benefit -- there is some research that yields immediate practical uses. One research area that is particular fruitful in this regard involves applying evolutionary theory toward combating infectious disease agents. The metaphor of an arms race is often used to describe the evolutionary dynamics of parasites and their hosts. This true for the naturally evolved reactions in hosts, but also for human engineered…
evolgen | December 30, 2007Can positive selection drown out neutral evolution? That's what John Hawks claims in response to my post on accelerated evolution. Hawks points out that, rather than looking at the neutral fixation rate (which is equal to the mutation rate, u), we should be more interested in the average time to fixation of a neutral mutation (the product of 4 times the effective population size, 4Ne). On the time scale he's looking at (40,000 years), neutral evolution shouldn't really matter because Hawks says that the Ne=100,000, which makes 4Ne>40,000.
Therefore, the majority of new mutations that arose…
sporte | December 26, 2007Genetics textbooks abound with stories of European royalty and the hazards of having children after you've married one of your cousins. It struck me as an interesting parallel that the lion is such a popular symbol in so many royal coats of arms. Like the royal families of Europe, certain lion populations have also suffered from a few too many copies of certain recessive genes.
I first read about the Florida panthers a few years ago while researching material for a class that I teach on using bioinformatics. It wasn't my first encounter with big cats and their DNA. Years before, while…
evolgen | December 21, 2007There's been a whole lot of hype around the Hawks et al. paper describing a recent burst of adaptive evolution in the human genome. The problem is a lot of people are conflating accelerated adaptive evolution with accelerated evolution. Take this for example:
12/11: Accelerated Human Evolution
In recent years, humans have evolved at a much higher rate than previously thought, according to a new paper in PNAS. By analyzing genome variations, researchers found that the rate of human evolution was fairly stagnant until about 50,000 years ago, and then--because of larger populations, climate…
evolgen | December 14, 2007For those of you interested in recent adaptive evolution in some insignificant bipedal primate, John Hawks and pals have published a paper in PNAS describing something you'll find interesting. Of course, if you're interested in such things, you already know that. Here are some links related to Hawks et al. paper:
The Hawks et al. paper presents data to suggest a recent burst in adaptive evolution along the human lineage. The reason for this burst is an increase in populations size, allowing for more beneficial mutations in the species. Eventually, the paper itself will be available here.…
evolgen | December 4, 2007
I previously described where in a genome we would expect to find sexually antagonistic genes. Briefly, depending on whether a gene is male-biased or female-biased and whether beneficial mutations are dominant or recessive, we can predict whether these sexually antagonistic genes will be on X chromosomes or autosomes. As I mentioned in that post, the theoretical results can only be translated into realistic predictions if we have reliable estimates of the relevant parameters. We do not have such estimates, but we can study the distribution of sex-biased genes throughout genomes. The results…
evolgen | November 23, 2007Brian at Laelaps has written a post entitled "What's good for the gander isn't always good for the goose", in which he describes some examples of sexual dimorphism in charismatic vertebrates. Studying the phenotypes of these traits is interesting, but what's happening on the genomic level? That is, how do differences between males and females affect the distribution of genes on chromosomes?
Many of the traits that are beneficial for males are deleterious in females (and vice versa). For example, male sheep with big horns will mate more and leave more offspring, but females with big horns…
sporte | November 14, 2007Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread.
Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used to look at ancestry.
Genetic markers in the mitochondrial DNA are used to trace ancestry through the maternal line and markers on the Y chromosome can be used to learn about one's father.…
evolgen | November 7, 2007The world of genomics is changing. It was initially about sequencing the genome a single representative individual from a particular species. Now, there's a large focus on polymorphism -- that is, sequencing multiple individuals from a single species to study the genomic variation in that species. That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale.
That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans, a sibling…
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…
evolgen | August 25, 2007
Remember the story about how we inherited the gene that gives us human brains from Neanderthals? The genetic data that were used to reach that conclusion (or a slightly less over-the-top conclusion) were part of a couple of other studies that identified signatures of adaptive evolution in genes involved in brain development. Those results were poorly criticized over a year ago, and they've recently come under fire yet again -- and again (I've compiled a list of the relevant papers below the fold).
The two most recent attacks come in two different flavors. The first attack (previously…
evolgen | August 23, 2007The University of Michigan has put out a press release entitled:
Bits of 'junk' RNA aid master tumor-suppressor gene
With a title like that, how could I not blog the hell out of this bastard? I mean, they even put the scare quotes around "junk". Like that -- like I just did. Amazing!
The story is about three micro RNA genes (miRNAs) that interact with p53 -- the cancer gene -- and are not expressed properly in some lung cancer cells. Not only have these researchers cured cancer, Guido Bommer, the lead author, seems to think they've found the cure amidst piles of junk:
"In the 'junk' lies…
evolgen | August 20, 2007
There's been a lot of recent interest in sequences that are highly conserved between humans and other mammals (and even other non-mammalian vertebrates). These sequences are thought to be under purifying selection, which prevents the accumulation of substitutions after two evolutionary lineages diverge. We cannot rule out, however, that the sequences are conserved by either pure chance (ie, in a large enough dataset, there will be a substantial amount of outliers that are still part of the same distribution) or because they have a lower mutation rate.
David Haussler is one of the leaders in…
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…
sporte | August 8, 2007Some maggots have gotten good press lately because of their helpful ability to clean out wounds by consuming dead tissue. Screwworms however; also known as Cochliomyia hominivorax, will never be welcomed in an operating room or anywhere else.
USDA Agricultural Research Service
These are the creatures of nightmares. During part of their lives, they live and travel as flies, and lay their eggs in the wounds of warm-blooded animals. When the eggs hatch, the screwworm maggots feed on the living flesh of the infested animals.
Fortunately, we've learned how to control the screwworm and we…
evolgen | July 16, 2007
Mike Lynch has been getting a fair bit of hype recently for his nearly neutral model of genome evolution (see here and here). The nearly neutral theory riffs off the idea that the ability of natural selection to purge deleterious mutations and fix advantageous mutations depends on the effective population size of the population in which the mutations arise. From here, the nearly neutral theory predicts that more slightly deleterious mutations and fewer slightly advantageous mutations will fix in small populations compared to large populations (see here and here for previous posts on this…
evolgen | July 11, 2007Bad tests for natural selection are bad at detecting selection.
Austin Hughes has published a fairly critical review of some methods used to detect natural selection in protein coding sequences. His attack on current methods for detecting natural selection is threefold. First, he claims that comparing non-synonymous to synonymous substitutions (see here) does not allow one to differentiate between adaptive evolution and relaxed selective constraint. Second, he argues that comparing polymorphism and divergence of synonymous and non-synonymous sites (see here) does not allow one to…