Population Genetics
evolgen | July 8, 2007I've got far too many tabs open in my browser window, and I gotta blog them ASAP so that I can clean up the ol' computer. Here are a few things I've been meaning to blog, in list form:
Nature Genetics has published an issue devoted to structural variation in genomes. There appears to be a bias toward human genomes, but it's cool nonetheless. Also, I'm pretty sure all the articles are FREE ACCESS.
The most recent issue of Molecular Ecology has a bunch of articles on the genetics of speciation. There's also an article on the genetics of pigmentation variation in Drosophila melanogaster.
Peter…
evolgen | July 3, 2007In a post at the Panda's Thumb, Ian Musgrave cites this paper by Bakewell et al claiming that 154 genes out of 13,888 surveyed show evidence for adaptive evolution in humans since the divergence with chimps (this is the "chimps more evolved than humans" paper). Ian brings this up in a discussion of Haldane's dilemma -- which is only a dilemma to creationists (biologists are more interested in his sieve and his rule) -- but he cites the paper as an authority on the amount of adaptive evolution in humans. A discussion of adaptive evolution in human genes would be incomplete without mentioning…
evolgen | June 27, 2007H.J. Muller is famous for (among other things) his argument for the evolution of recombination involving the purging of deleterious alleles (dubbed Muller's Ratchet). In a nutshell, Muller observed that, in the absence of recombination, deleterious mutations will fix in populations because every chromosome will, eventually, obtain a mutation which decreases the fitness of the organism. Recombination allows for the movement of deleterious mutations off of chromosomes, which decreases the genetic load in a population (because fewer deleterious mutations will fix).
Much of the recent work in…
evolgen | June 16, 2007
Last year, Katie Pollard and colleagues published a couple of papers in which they identified regions of the human genome that had recently undergone an acceleration in their rate of evolution and characterized the expression pattern of an RNA gene located in one of those regions. The RNA gene is expressed in the developing brain, which lead people to speculate that it played some important role in making humans smarter than chimps (my round-up and stab at speculation can be seen here). Their approach toward identifying those regions is quite simple, but the cause of accelerated evolution in…
evolgen | June 1, 2007For some reason, John Hawks thinks my disc flipping calculations have something to do with population genetics. He extends it to FST, which is just plain ridiculous. There is nothing about binomial sampling that can be related to popgen theory. Nothing.
evolgen | May 27, 2007Given the amount of attention I devoted to the effect of selection on the relationship between mitochondrial DNA polymorphism and population size (see here, here, here, here, here, and here), it's only appropriate that I link to this article by Meiklejohn, Montooth, and Rand on selection on mtDNA. Here's the abstract:
Several recent studies have confirmed that mitochondrial DNA variation and evolution are not consistent with the neutral theory of molecular evolution and might be inappropriate for estimating effective population sizes. Evidence for the action of both positive and negative…
evolgen | May 3, 2007Here's some interesting science:
A commonly used medicinal leach may have been misidentified as the wrong species.
Here is a description of the Human Variome Project, which seems more focused on mapping disease genes than doing cool population genetics. That's too bad.
Science has an article on the benefits of undergraduate research. The most important one: to get into grad school.
You can use molecular markers to determine that a lonesome tortoise has no reason to feel alone.
The central nervous system is homologous across all animals.
What is the greatest innovation? I've tackled this…
evolgen | April 21, 2007Over at GNXP, Razib has posted a few links to papers concerning adaptive evolution (aka, positive selection or Darwinian selection) in humans and chimps. He's been following the coverage of this paper from George Zhang's group which provides evidence that more genes have been under positive selection along the chimpanzee lineage than the human lineage. The popular press are advertising this finding as "chimps more evolved than humans", and Razib's gotten a kick out of the phrasing (part 1, part 2, part 3). Zhang and colleagues interpret their finding the in framework of the nearly neutral…
evolgen | April 20, 2007It seems like everything is coming in twos the past couple of days. Yesterday we mentioned two books on the evolution of genomes and two stories involving either Wolbachia or sex determination. Today, we have two stories involving criticisms of scientific papers. One deals with the evolution of the bacterial flagellum, and the other addresses natural selection on the brain expressed gene ASPM in humans.
The first story involves everyone's favorite irreducibly complex cellular apparatus: the bacterial flagellum. During the Kitzmiller v. Dover trial, Nick Matzke worked with the plaintiffs (the…
evolgen | April 19, 2007Oxford University Press will be releasing a new book in June entitled Darwinian Detectives: Revealing the Natural History of Genes and Genomes. From the OUP description of the book:
Molecular scientists exploring newly sequenced genomes have stumbled upon quite a few surprises, including that only one to ten percent of the genetic material of animals actually codes for genes. What does the remaining 90-99% of the genome do? Why do some organisms have a much lower genome size than their close relatives? What were the genetic changes that were associated with us becoming human?
Ignoring the…
evolgen | April 18, 2007Dan Hartl was inducted into the National Academy of Sciences of the USA in 2005 for his contributions to the field of evolutionary genetics. His inaugural article as an Academy member was published this week in the Proceedings of the National Academy of Sciences (PNAS, pronounce pee-nas, hehe). Hartl and colleagues compared levels of polymorphism in 91 genes from Drosophila melanogaster with divergence from D. simulans. They were interested in determining the effect of natural selection on nonsynonymous mutations, kind of like what was done in this paper (reviewed here).
Hartl and colleagues…
evolgen | April 17, 2007A lot of interesting evolutionary genetics research gets published, and I don't have time to write an insightful commentary on all of it (some may argue that I have never written an insightful commentary on anything). Here's a brief overview of the stuff I have missed in the past few weeks:
A population of sheep was started with the introduction of two individuals on a remote island in the southern region of the Indian Ocean. Surprisingly, genetic diversity has increased over time in this population (reported here). This increase in heterozygosity (measured by the amount of microsatellite…
evolgen | April 12, 2007In addition to the paper on adaptive evolution in the Drosophila melanogaster genome (reviewed here yesterday), Chung-I Wu is also senior author on a sort-of companion paper studying adaptive evolution in the human genome. Yeah, I know, who really cares about the human genome, human evolution, or humans? The real interest is in Drosophila. But, believe it or not, there are some people who find human population genetics totally engrossing.
The paper using sequences from the human genome, which Wu co-authored with Jun Gojobori (who is not this Gojobori), Hua Tang and Josh Akey, looks at…
evolgen | April 11, 2007Not all regions of the genome are equal in the eyes of evolution. For example, natural selection is more effective on genes in regions of higher recombination. We have known this for a while. The connection between recombination rate and natural selection was nicely refined when it was shown that DNA polymorphism is lower in regions of low recombination and higher in regions of high recombination (see Begun and Aquadro). This could be due to higher mutation rates in regions of high recombination (and vice versa), greater reach of selective sweeps in regions of low recombination (the…
evolgen | March 29, 2007Last week, I linked to an article in Seed about synonymous mutations with deleterious effects in humans. It's heavy with errors, but I didn't linger too much on them. Larry Moran, on the other hand, got a bit more riled up than I did, and John Logsdon (whose blog has the potential to be something cool) agrees with Larry. And I agree with both of them.
The issue here is with the neutral theory, which Larry describes quite well (see also the coverage in this primer to population genetics). Many people misinterpret the neutral theory and think that it claims that all mutations in some class (non…
evolgen | March 16, 2007If you happen to be a yeast population geneticist, then you probably already know about the Saccharomyces Genome Resequencing Project. They have resequenced 32 strains of S. cerevisiae and 27 strains of S. paradoxus at between 1x and 3x coverage. The nice thing about resequencing is that SNP discovery and genotyping occur simultaneously. That's in contrast to the human HapMap project which identified polymorphism in a few individuals, then searched for those polymorphisms in a larger panel. That means you can do some good population genetic analyses on the yeast data, which are not possible…
evolgen | March 13, 2007The New York Times has published an article in their Science section on the evolution of human parasites, and it's not by Carl Zimmer. In the article, Nicholas Wade (another good science writer at the NYTimes) presents a few vignettes of human-parasite co-evolution, including a bacterium that causes tooth decay, the ulcer causing Heliobacter, and a tapeworm we share with pigs. I guess Carl called dibs on the pubic lice. Anyway, Wade made me smile when he presented the phylogeography of one human parasite:
The latest organism to be identified as a longtime member of the human biota club is…
evolgen | February 15, 2007Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American's website about Junk DNA. I'm a little late to the game because, well, I've been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It's an opportunity to discuss semantics, and I love semantics.
Those of you who have hung around here for a while know this topic often comes up at evolgen (remember this, this, and this . . . hell, here's what a search for Junk DNA turns up). Long story short, I can't stand the term junk DNA, but I do agree…
evolgen | February 5, 2007I've been chatting up Wilkins about the role of natural selection in speciation (and when I say "speciation" I mean "reproductive isolation"). Wilkins listed a few cases where speciation would occur independently of natural selection. Amongst the mechanisms in Wilkins's list was speciation via karyotypic changes (polyploidy, inversions, fusions or fissions). I cried shenanigans, and this is why.
The karyotype refers to the organization of an organism's genome -- chromosome number, fusions/fissions of chromosomes, and gene order within chromosomes. One way to change the karyotype is to…
evolgen | January 10, 2007Mutations are the fuel that drives the engine of evolution. Without mutations there would be no variation upon which natural selection and other evolutionary forces could act. Furthermore, much of the theoretical results regarding evolutionary genetics depend on estimates of mutation rates. For example, Kimura showed that the rate of fixation of neutral mutations is equal to the neutral mutation rate. Additionally, many models to explain the evolution of sex and recombination depend on the amount of deleterious mutations per genome per generation (U).
A group led by Peter Keightly (DOI) have…