Population Genetics
sporte | August 21, 2006In which we see the results and come to our own conclusions.
If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide.
Ugh.
I prefer making my own decisions, thank you very much.
So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over time.
Let's see the results.
We're…
sporte | August 19, 2006Let the experiment begin.
We're experimenting with HIV in this series. And yes, you can try this at home!
If you want to see where we've been and get an idea where we're going, here are the links.
Part I. Meet HIV and learn how we're going to use it look at evolution. An introduction to the experiment and a link to a short flash movie on HIV.
Part II. Instructions for doing the experiment.
Part III. Look at the sequence results.
Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.
Let's move onward.
1. I made a data set of amino acids…
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
evolgen | August 17, 2006David 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…
evolgen | August 15, 2006Check out this nice primer of population genetics by Anya Plutynski and Warren Ewens from the Philosophy of Science Encyclopedia. A lot of it deals with classical population genetics (Wright, Fisher, et al), and I especially like their description of Hardy-Weinberg equilibrium:
Weinberg and Hardy independently established the "law of panmictic equilibrium" -- today known as the Hardy-Weinberg "law" or "principle". The law might be better described as a neutral or equilibrium model -- a mathematical derivation starting from assumptions (some known to be false) for the purposes of evaluating…
evolgen | August 13, 2006Seed's going buck-nutty for the 25th anniversary of the AIDS epidemic, including a new blog covering the 16th International AIDS Conference. This week's Ask A Science Blogger also deals with the disease:
To what extent do you worry about AIDS, either with respect to yourself, your children, or the world at large?
I am the youngest of the ScienceBlogs bloggers (about as old as the epidemic itself), and I cannot remember a world without AIDS. Aside from not going in without cover, how has the AIDS epidemic changed my behavior? The answer involves both a personal anecdote and some research in my…
sporte | August 10, 2006It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax.
Eh, what's that you say?
Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went in one ear and out the other. But then I read this really funny blog about a person, some ear wax, and an NMR machine, and well, you guessed it, I couldn't resist.
To me, it's been a jelly bean flavor that I studiously try to avoid. To several…
evolgen | July 31, 2006I have mentioned before that at one point in my life I wanted to study conservation genetics. This field can be thought of a subdiscipline of molecular ecology -- wherein researchers use molecular markers to test hypotheses regarding demography in their population of interest. Jacob at Salamander Candy has a post on the usefulness of neutral markers in conservation. Here's a taste:
The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers (refs 1-8). In the hypothetical species mentioned above, a…
sporte | July 28, 2006We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong.
We can do much, much more than identifying DNA sequences and obtaining crucial information, like who left their DNA behind on that little blue dress.
Today, we're going to a deeper question about who we are and who are our relatives.
Drumroll, okay, here it comes:
How similar are DNA sequences between humans and apes?
Your assignment is to find…
evolgen | July 17, 2006Last September, Bruce Lahn and colleagues published a couple of papers on the evolution of two genes responsible for brain development in humans (ASPM and Microcephalin). A group led by Sally Otto published a criticism of the analysis performed by Lahn's group in last week's issue of Science (JP has written a good summary on GNXP). Lahn and colleagues issued an excellent response to that criticism.
The original papers on ASPM and Microcephalin argued that the patterns of polymorphism and linkage disequilibrium at the two loci were inconsistent with our current understanding of demographic…
evolgen | July 16, 2006Here 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…
evolgen | July 3, 2006Mitochondrial DNA (mtDNA) is one of the most used markers in molecular ecology1. A good molecular marker for population level studies should be neutral, so that researchers can use it to infer things like:
Population size and changes in population size (expansions and bottlenecks);
Population structure;
And phylogeographic relationships.
A recent meta-analysis of mtDNA polymorphism revealed that there is no relationship between levels of diversity and population size. The authors of that study explain the lack of a relationship on recurrent selection on mtDNA genes, which affects the entire…
evolgen | June 15, 2006What is evolution? Razib started it. John Hawks joined in. I offered my opinion in the comments on GNXP. But I felt obliged to say more, here.
It seems like most of the readers in the ScienceBlogs universe don't understand the difference between evolution and natural selection. When Razib asked them to provide the thing they would want the public to understand about evolution (in ten words or less, mind you), most of them provided explanations of natural selection. Let me say it as clearly as I possibly can, evolution is more than natural selection.
I am not a neutralist. Check out the…
evolgen | June 15, 2006Andy 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…
evolgen | June 7, 2006I present for you an example of inferring a bit too much from inappropriate data. This isn't quite the same as making claims about demography based on 100 nucleotides from 6 individuals. But it's not much better given that this example is from a study of extant organisms. Abstracts to clarify what the hell I'm talking about are below the fold.
Exhibit A comes from a paper on human demography and mitochondrial DNA. Here is the abstract:
Human mitochondrial DNA (mtDNA) studies have entered a new phase since the blossoming of complete genome analyses. Sequencing complete mtDNAs is more expensive…
evolgen | June 4, 2006Billy 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…
evolgen | May 31, 2006...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…
evolgen | May 16, 2006Don'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…
evolgen | May 10, 2006Not all beneficial alleles come with deleterious side effects, in case I gave that impression. Of course, not all beneficial alleles come from mutations either. Hybridization between closely related species can lead to advantageous alleles introgressing into a population from another species. Loren Rieseberg, who has been studying hybridization between sunflower species for some time, has an article in the upcoming issue of the American Naturalist (press release here) on the introgression of an advantageous allele from one species to another. This is probably quite common and may have…
evolgen | May 2, 2006I'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…