Phylogenetics

You may have thought that Orin Scrivello was the worst dentist ever. Well, have I got a story for you. This dentist isn't a sadist, and his follies were far from intentional. But the implications of his conduct greatly affected the lives of at least five of his patients. This week's Phylogeny Friday is story fit for CSI. Learn about the dentist, the virus, and his patients below the fold. The story revolves around Dr. David Acer, a Florida dentist who died in 1990 from complications of AIDS. Dr. Acer's death would have been far from remarkable at the time -- the AIDS epidemic was quite…
I wrote about the possibility of gene trees and species trees giving conflicting information in a previous Phylogeny Friday. In that example, the discordance was due to balancing selection maintaining multiple alleles across species boundaries. But can incongruities between genetic data and species history arise via entirely neutral processes? The answer is implied in the setup, but check out some of the details below the fold. Humans and chimpanzees share HLA alleles that have been maintained by selection. These loci are far from ideal for constructing evolutionary relationships between…
As I mentioned previously, I'm busy preparing some data for a meeting next week. I don't have much time to devote to Phylogeny Friday, so I'll be sharing some of my own data with you. This data is nothing special; it just happens to be the data I finished analyzing a few minutes ago. It's open, I could build a tree, and I'll show you that tree below the fold. This tree contains a scant three sequences. The two closely related sequences both come from Drosophila pseudoobscura and the outgroup is a gene from D. melanogaster. This gene was duplicated along the D. pseudoobscura lineage. In the…
I've been busy this past week (and I'll be busy in the next couple of weeks to come), so I don't have much time to post to evolgen. For this reason this week's Phylogeny Friday is a recycled post from the old site. Check out the comments on the original entry for some remarks from one of the authors of the paper I discuss. I'll try to get some original content up here, but blogging may be slow until the end of the month. Now that we have entered the post-genomics era, with the genomes of most model organisms completely sequenced (as well as the human genome), it is up to genome centers,…
Is it possible that you are more closely related to a chimpanzee than to another human? Ok, that's a bit of a loaded question. It depends on how we define 'related', or, more specifically, what we are measuring. If, for instance, you compared the anatomy or physiology of a human and a chimp, the conclusion would be obvious: all humans are more closely related to each other than any human is to a chimp. The same goes for a comparison of the entire genome. But what if we look at a small portion of the genome? This week's evolgen Phylogeny Friday deals with this question. More after the jump.…
Carl Zimmer (one of the best general audience science writers) has a post on his blog on how the human immune system differs from that of other primates and even other apes. It's a good example of why biomedical researchers need to understand evolutionary biology (and why dumb shits like this should not be trusted with the lives of their patients). That said, I've got a little nit to pick with Carl. He wrote: The scientists decided to compare human T cells directly to those of apes. It turns out that unlike humans apes produce a lot of Siglecs on their T cells. C'mon, Carl, you know…
Over at my old site, I lamented the apparent death of distance based tree building algorithms. Just as all of life on earth can be divided into three domains, phylogenetic methods can be split into three groups: distance based, maximum parsimony, and maximum likelihood. Distance and parsimony based approaches have been around for a while (and were used prior to the availability of molecular data). The combination of molecular data and more powerful computers allowed large molecular datasets to be analyzed using parsimony methods. Our great computing power has also allowed for the advent…
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.…
Via 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.
It's not the best way to kick of a new blog theme -- on Friday night with a half-hearted entry -- but I promised last week that I would begin Phylogeny Fridays today, so I need to deliver. For the first ever Phylogeny Friday, we have the greatest phylogeny of them all, the Tree of Life. Go explore the site, it's freakin' awesome.
After a short, and dirty, run, the evolgen Double Entendre Friday has shuffled off its mortal coil. I just can't keep it up week after week (double entendre not intended). Of course, if I do come across something particular distasteful with a dash of sexual innuendo I'll include it in the list of double entendres. But there is no way I could continue this as an every Friday tradition. As in network TV, whenever one series gets cancelled another steps in to take its place. At the old evolgen we had the Friday Random Ten. That was replaced by Double Entendre Fridays for the past month.…
A 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.
You, 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.…
As 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 [link] More after the jump... Well, I gotta say something about this, right?? I mean, I'm a retarded…
I am a big fan of The Science Creative Quarterly. I especially like how they integrate science with humor -- sort of like the Onion, but focused on science. Now they are getting into science education. If you know nothing about phylogenetics and systematics, this introduction to phylogenetics from the SCQ will be quite informative. Of course, if you're reading evolgen, you probably know something about phylogenetics -- and if you don't, read it and evolgen will make more sense. The treatment of phylogenetics isn't wrong, it's just not quite right. Take, for example, their distinction…
Are There Disagreements Between the Fossil Record and Molecular Data? Molecular biologists have a tradition of reworking a lot of the evolutionary relationships and timescales that morphologists and paleontologists worked so hard to figure out. This can really piss off the non-molecular folks, but I prefer to think of it as a cooperative relationship. The molecular clock, for example, would not be possible without calibration from the fossil record. It is important to note that molecular and morphological data tell two different stories, which I outline below the fold . . . When I wrote…