Molecular Evolution
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 3, 2007A new article in Nature Genetics brings together two themes that I've blogged about before: human brains and King and Wilson. In fact, I've even already blogged about the article, but this post contains a more thorough treatment of the science.
The long and short of it is that some people think that differences in protein coding sequences can't explain the morphological differences between humans and chimps. Additionally, there are other phenotypes that differ between the species, including cognitive abilities and dietary preferences. There is evidence for adaptive evolution in protein…
evolgen | September 2, 2007Massimo Pigliucci has reviewed Mike Lynch's book on genome evolution for Science [Postgenomic Musings]. In his review, Pigliucci writes the following:
One of the central theses of the book is that natural selection is not necessarily the central evolutionary mechanism, as quite a bit of the details of genomic structures and evolution can be accounted for by invoking the neutral mechanisms of mutation, recombination, and drift. Lynch is certainly correct on this point, and he backs his argument with much empirical and theoretical detail. Yet, we must be hanging around with different crowds,…
evolgen | August 31, 2007
Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the host, but there are also transposable elements (TEs), sequences from mitochondria (numts), and endogenous retroviruses (ERVs). In addition to those examples, other symbionts also infect eukaryotes and leave traces of their presence in the genomes of the hosts. One such parasite of many invertebrates is Wolbachia, a bacteria that invades the germ cells of its host and inflicts odd behaviors such as male killing, feminization of males, and reproductive…
evolgen | August 31, 2007Genome rearrangements are fast becoming one of the most interesting aspects of comparative genomics (I may be slightly biased in my perspective). We have known for quite some time that genomes of different species (and even within species) differ by inversions of their chromosomes (this was first studied in Drosophila). In fact, some of the early work on the evolutionary relationships of species was done using chromosomal rearrangements. Additionally, there's a whole lot of important biological implications of rearrangements, including speciation, human disease, and the function of genes…
evolgen | August 30, 2007
A group of researchers from France and Italy have sequenced the genome of the finest grape varietal, Pinot Noir. The genome has hallmarks of ancient triploidization, shared by other dicotyledons, but there is no evidence for recent polyploidization. That meant sequencing and assembling this genome is easier than doing so for other agricultural plants that experienced genome doubling (and tripling) as a result of domestication.
Comparisons of gene content with Arabidopsis thaliana reveals an enrichment of various gene families responsible for protein products that produce favorable features…
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 13, 2007King and Wilson are the bee's knees for all the kids who want to hype the effect of gene expression divergence between humans and chimps. The argument boils down to a few points: humans and chimps are mad different, their protein sequences are mad similar, therefore expression of the proteins must be important for those phenotypic differences. There are some people who point out that looking at straight sequence divergence between orthologous sequences neglects the importance of copy number differences between species.
In a channeling of King and Wilson, a new paper looks at differences in…
evolgen | August 2, 2007One of the primary hypotheses of Sean Carroll's model of evo-devo is that cis-regulatory elements (CREs) are the primary drivers of morphological evolution (see here). This hypothesis is controversial in the evolutionary genetics community. Because it's hard to examine the effect of CREs on phenotypes at a genome-wide scale, the problem must be reduced into smaller elements. One such element that has been the subject of previous studies is the role of cis and trans mutations in the evolution of gene expression. I have previously discussed some results that shed light on this issue. The basic…
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 15, 2007I've recently come across two articles on junk DNA. The first one, from New Scientist, includes a pretty thorough coverage of recent studies that have identified functions for non-protein-coding regions of the human genome ("Why 'junk DNA' may be useful after all"). The article is set up as if it will present the demise of junk DNA, but it paints the accurate picture that a large portion of the human genome is non-functional. And TR Gregory like the article too.
The second article tries to do that, but fails. It's from The Scientist and entitled Junk Worth Keeping: Is it time to retire…
evolgen | July 9, 2007I thought I had come to grips with evo-devo. Then along come Hopi Hoekstra and Jerry Coyne to call shenanigans on Sean Carroll's model of evo-devo. This is nothing new for Coyne, but I can't recall Hoekstra ever getting involved in the debate before now.
Before we get to Hoekstra and Coyne, let's allow Carroll to describe evo-devo in his own words. His most recent summary of the evolution of transcriptional regulatory regions can be found in this paper from a recent National Academies Sackler Colloquium. Here's how he and his colleagues explain the importance of cis regulatory regions (CREs)…
evolgen | June 22, 2007
Sensing and reacting to one's environment is necessary for survival. Different species have different expertise in regards to how they sense their environment. Humans, for example, have reduced olfactory abilities relative to other mammals, but excellent color vision. Cats have good night vision, but poor vision during day light. These proficiencies and deficiencies in sensory abilities hold for non-mammalian taxa as well.
Olfaction and taste have been well studied in a variety of taxa. Amongst the invertebrates, the genes responsible for olfaction and taste in Drosophila are one of the best…
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 5, 2007
This year's meeting of the Society for Molecular Biology and Evolution will take place at Dalhousie University in Halifax, Nova Scotia (conference webpage). I'm going, and so are Reed Cartwright and Jason Stajich. Additionally, Rosie Redfield and John Logsdon have each been invited to give a talk at the conference. As you can see, there will be a blogger presence at the meeting.
Are you going to the conference? If you are (whether you're a blogger or not), you should join the SMBE 2007 group on the Nature Network. And if you haven't already signed up for the Nature Network (it's like…
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 26, 2007
The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links:
ERV linked with a tone of disgust.
I restated my frustration with the term junk DNA.
JR Minkel, the author of the Scientific American article, responded to my criticisms.
Ryan Gregory replied to Minkel's SciAm blog post, introducing the term "junctional DNA" to replace junk DNA describe sequences with unknown function. Gregory also tells us how a genome is like an onion (let me count the ways), or something of the sort wonders why onions…
evolgen | April 24, 2007Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they're at it again.
The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can't find published anywhere (neither can ERV). Is Scientific American describing unpublished research on their website? Either way, they're doing it poorly. The study described in the article identified non-coding sequences that were conserved across all sequenced mammalian genomes but missing from the chicken genome. Five percent of the…
evolgen | April 23, 2007Because my browser consists of a growing forest of tabs containing stuff waiting to be blogged, and there is no way I can write a complete entry on each one, and I want to at least link to the relevant sites so that I can close those tabs, I give you a link dump with maximal run-on sentences:
Remember my post on the evolution of zombie populations? If so, you've got a good memory. If not, who cares? Anyway, there's an article in arXiv about ghosts, vampires and zombies. (Via Ortholog).
The evolution of snake venom genes. They make up part of the venome.
Jonathan Eisen on the Human…
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…