Phylogenetics
awild | February 29, 2008
Out today is a preprint version (subscription only) of Corrie Moreau's Pheidole phylogeny. At first glance this seems a nice piece of work: the evolutionary history of one of the world's most diverse ant genera inferred from 140 species and 5 genes.
This is some extremely cool ant evolution research, and the first salvo from the nascent Pheidole working group. Once I get a chance to digest all 50+ pages I'll post the highlights.
source: Moreau, C. S. 2008. Unraveling the Evolutionary History of the Hyperdiverse Ant Genus Pheidole (Hymenoptera: Formicidae). Molecular Phylogenetics and…
evolgen | February 1, 2008Paraphyly in Drosophila
Many biology students have hands-on experience working with Drosophila melanogaster. This little fly is one of the major workhorses of genetics. It may not be for long. That's not to say people will stop working with the fly, but the fly may no longer be named "Drosophila melanogaster". That's because the Drosophila genus is paraphyletic and should be split into multiple genera. Oh, and D. melanogaster doesn't hold the rights to the name Drosophila. Those rights belong to D. funebris, the first species named in the Drosophila genus. (Christopher Taylor at the Catalogue…
evolgen | December 28, 2007Historical Inaccuracy Edition
A lot of us who work in well established biological systems take for granted how those systems were first discovered or established. Sometimes this involves the choice by an individual to begin studying development using a small worm. Other times it's the fortunate discovery of visible chromosomes allowing for physical maps of genomes to be constructed decades prior to genome sequencing. Or it could be the fortuitous choice of a taxon to use a model system for molecular evolution. This post deals with that last scenario, specifically the Drosophila melanogaster…
evolgen | October 1, 2007This is a repost (with some edits) of an introduction to publishing original research on blogs -- a series I am reintroducing. The original entry can be found here.
Previous entries:
Part 1 - Introduction
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 2 of this series (The Backstory) can be found below.
The Backstory
The reason you and I and all other animals (and most other forms of life) can do things (like live) is because we combine oxygen with sugars to make energy. Eventually, the oxygen…
evolgen | September 14, 2007
I'm sure by now you've heard of the ginormous spider web that was spun in Texas. The thing was huge -- 200 yards long -- and it was spun by multiple different species. That interspecific collaboration got Bill Poser thinking, so he blogged about it at Language Log:
The web covers hundreds of square meters. Not only was it built by hundreds of spiders, who normally build isolated webs and eat each other if they get too close, but entomologist Allen Dean reports that they belong to twelve different families! We're talking massive inter-species communication here folks, and not particularly…
evolgen | September 2, 2007
Remember when I said that the near future of eukaryotic genome sequence would involve sequencing EST libraries (collections of mRNA, or transcribed genes) rather than de novo sequencing of whole genomes? Well, I did, even if you don't remember. Anyway, a new paper in PLoS ONE puts that approach to the test for the purpose of generating sequence data to study mammalian evolution. Here is the last paragraph from the paper, summarizing why EST sequencing projects are useful in phylogenetics:
While complete genomes are the ultimate data sets for resolving phylogenetic and evolutionary issues of…
evolgen | July 6, 2007This week's phylogeny takes a look at the green portion of the eukaryotic tree. These are the eukaryotes capable of photosynthesis. Eukaryotes first obtained the ability to perform photosynthesis when a eukaryotic cell absorbed a photosynthetic cyanobacterium. This was followed by a few subsequent horizontal transmissions of the endosymbiont between unrelated eukaryotic lineages. Although eukaryotic chloroplasts can trace their origins to a single endosymbiosis, they don't share that organelle based on simple common descent.
Green plants -- one of the photosynthetic eukaryotic lineages --…
evolgen | April 27, 2007This week's phylogeny comes from this paper on molecular dating of speciation events. I won't be addressing molecular dating per se, but I will be dealing with what molecular clocks tell us. Like, do they actually reveal the speciation time of a pair of species?
The divergence date of a pair of species can refer to two things: when the two populations became two species (no longer exchanging alleles) or when the two genetic lineages split. The splitting of genetic lineages happens prior to the speciation event. That's because within a population there is variation throughout the genome. It's…
evolgen | April 13, 2007Today's password is coevolution.
First of all, here is a pair of phylogenies. The one on the left shows the relationships of a bunch of dove species, and the one on the right shows a bunch of lice that parasitize the doves. The lines connecting doves and lice indicate lice that parasitize each dove species..
Notice that parts of the tree mirror each other. We see that closely related dove species are infected by closely related lice. But that tree is nowhere as clean as this one:
On the left is an aphid phylogeny, and the tree on the right is from their obligate symbionts (speaking of…
evolgen | March 30, 2007Mammals did not rapidly radiate after the K/T boundary.
That's the punch line of a paper published in this week's issue of Nature. This has been all over the news, including the New York Times twice (#1 and #2). You see, there's this idea that when the dinosaurs (technically, the non-avian dinosaurs) disappeared, mammals quickly filled in the vacated niches. That means there should have been a rapid radiation of mammalian lineages following the dinosaur mass extinction -- marked by the boundary between the Cretaceous and Tertiary periods (known as the K/T boundary).
The new study reveals that…
evolgen | March 16, 2007New Terms in Phylogenetics
I'm a cladist, and as a cladist I want all of my taxa monophyletic. That means anything given a name (animals, plants, vertebrates, insects, etc.) should include all the organisms that descend from the most recent common ancestor (MRCA) shared by the organisms you claim are in that group. Confused? Well, allow me to direct you to Wilkins's post on clades and this handy diagram:
In the tree above, grouping species A, B, C, and D into a single taxon results in a monophyletic clade. But if we exclude species A (calling species B, C, and D a single taxon), we create a…
evolgen | December 7, 2006The five nurses and one doctor (the Tripoli Six) accused of infecting hundreds of patients with HIV in Libya are awaiting the verdict of their trial, expected to be handed down on December 19. The second trial concluded on November 4 -- the original guilty verdict was overturned. I previously mentioned that the molecular evidence (DNA sequences from HIV taken from the patients) did not support a guilty verdict. Nature has published the results of an analysis of those DNA sequences that suggests the doctors were not responsible for the HIV infection. A description of that evidence is below the…
evolgen | December 1, 2006What if some phylogenies were simply irresolvable? That is, what if, no matter how much data we collected, it would be impossible to reconstruct, with a high level of certainty, an accurate representation of the tree of life? That would suck. A lot. I have mentioned how this can result from long branch attraction or lineage sorting. But are there any taxa where this appears to be a major problem?
Antonis Rokas and Sean Carroll have published an essay in PLoS Biology that addresses the issue of bushes (or irresolvable nodes) in the tree of life. They point out four clades in which no single…
evolgen | November 19, 2006Like a lot of evolutionary biologists not studying the root of the tree of life, I assumed the three domain hypothesis was fairly well supported by the research community. This model posits that the tree of life can be broken up into three taxa at its most basal level: eukaryotes, bacteria, and archaea. It's the hypothesized evolutionary relationships of these taxa that caused researchers to break the tree of life into three domains.
It turns out the three domain model isn't as supported as many of us assume. Larry Moran put me in my place, pointing out arguments against the three domain…
evolgen | November 3, 2006When Phylogeny Friday last made an appearance on this blog, we were exploring the vertebrates. This was part of a larger series in which we were working our way through the eukaryotes, focusing on animals. I've come to realize that weekly phylogenies are too much, so we're scaling Phylogeny Friday back to appear on the first Friday of the month.
Today, we will take a look at another group of eukaryotes: the fungi. (We'll return to the animals in a future edition.) Both fungi and animals are unikonts, and the clade containing fungi is sister to the clade containing the animals:
This is one…
evolgen | September 22, 2006We've been working our way across through the tree of life in the past few editions of Phylogeny Friday. Last week we took a look at the evolutionary relationships of the animals, and we realized that many of the branching orders are extremely difficult to resolve. Today we're going to zoom in on one of those branches: the vertebrates. Why? Because we're vertebrates and we want to know about ourselves. Also, we know more about this taxon than any other taxon. These are the same rules than have governed us throughout our journey.
After last week's disappointingly unresolved tree, I have a…
evolgen | September 15, 2006A few weeks ago I introduced the tree of life, albeit to some criticisms. The following week I zoomed in on one branch of that tree, the eukaryotes. I pointed out that animals were a mere twig in the eukaryotic tree, yet they have been the focus of a large amount of biological research. This disproportionate attention is due in part to our ignorance regarding the majority of eukaryotic taxa. We have only become aware of many of the eukaryotes recently, so we have a lot of catching up to do in order to understand their evolutionary relationships.
Because animals are the best studied eukaryotes…
evolgen | September 8, 2006And they're doing it open access style.
Jonathan Eisen and Michael Eisen have each published papers in the PLoS journals using newly available genome sequence data. Jonathan is lead on author on the paper describing the genome sequence of the ciliate, Tetrahymena thermophila. He has blogged about the publication here and provides a wrap-up of a bunch of the coverage here. This single celled eukaryote is a model organism for cell biology, although not at the same level as Saccromyces cerevicea.
Michael Eisen's lab is heavily involved in the Drosophila genomes project. He is the senior author…
evolgen | August 25, 2006Last week's Phylogeny Friday introduced the three domains of life: bacteria, archaea, and eukaryotes. The bacteria and archaea are commonly referred to as prokaryotes, although that creates a paraphyletic taxon. Today, we will focus on the eukaryotes (organisms with nuclei and organelles). This taxon contains plants, animals, fungi, and a bunch of other lineage with which you are probably not familiar. Recently, a group of Canadian researchers reviewed our current understanding of the evolutionary relationships of the eukaryotes, creating the following phylogeny.
The eukaryotes can be…
evolgen | August 18, 2006Phylogeny Friday is back, bitches! Katherine's gotta add me to her list ASAP. In the glorious return of PhyFridays, I give you the root of the tree of life. In the upcoming editions we'll zoom in on a few parts of the tree to illustrate the diversity of certain taxa of interest. It'll be kind of like a reverse Ancestor's Tale.
The image on your left shows the evolutionary relationships of the three domains of life: bacteria, archaea, and eukaryotes. Traditionally, the bacteria and archaea are known as prokaryotes, but prokaryotes are a paraphyletic taxon. Oh, how I hate paraphyletic taxa.…