evolgen | September 10, 2007Mendel's Garden is the original blog carnival devoted to genetics. A new carnival is traditionally posted on the first Sunday of the month (although the date is somewhat flexible). The newest edition of Mendel's Garden has been posted at balancing life.
Sandy at Discovering Biology in a Digital World will be hosting the next edition. If you would like to submit a post, visit the blog carnival submission page. If you would like to host a future edition, email me (evolgen--at--yahoo--dot--com) or leave on a comment on this post.
evolgen | September 6, 2007Among my many pet peeves are when people refer to Drosophila as fruit flies (they are not). Real fruit flies (Tephritids) feed, mate, and lay their eggs on live fruit -- for this reason, many are agricultural pests (e.g., the medfly). Drosophila, on the other hand, feed on the micro-organisms found primarily on rotting fruit or other rotting plant parts. For this reason, I like to think of Drosophila as one of the most refined insects because they prefer fermented sugars (like beers and wines).
While the majority of Drosophila feed on rotting plant material, some have found an even more…
evolgen | September 4, 2007Lookie here -- they've sequenced Craig Venter's genome. What did they learn about Craig? Well, he's European. He has 46 chromosomes. He's got some structural differences from the reference genome. Venter also differs from the reference genome by insertions and deletions.Like every other human, he's got a boat load of repetitive sequences in his genome. And he differs from that reference genome in coding sequences.
Levy et al. 2007. The diploid genome sequence of an individual human. PLoS Biol 5: e254 doi:10.1371/journal.pbio.0050254
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 | 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 | September 1, 2007Shelley's posted some pictures of nerd cakes. She calls 'em geek cakes, but I see no headless chickens. Anyway, I've got my own little nerd cake:
We had it made for a party we threw during recruitment weekend for our grad program this past spring. Sadly, the icer responsible for the art couldn't spell, so I put a sprig of something green on the cake for the missing "C" in Lamarck. And if you don't get it, see here.
evolgen | September 1, 2007According to this press release Trends in Genetics (TIG) is "the most established monthly journal in Genetics". I have no idea what that means, but if I were asked to name the top journals in genetics, TIG wouldn't crack the top four. In fact, here is my top four:
Nature Genetics
PLoS Genetics
Genetics
Heredity
Additionally, TIG is published by Elsevier, which means TIG sold guns to terrorists and rogue nations (but they don't anymore). Well, TIG is also publishing an article in November (according to the press release) that will "shed new and unexpected light on some of the long standing…
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, 2007BioMed Central has posted videos of interviews of some notable scientists. Included is a video of friend of evolgen (and enemy of Prof. Steve Steve) Michael Ashburner espousing the virtues of open access. Ashburner was a signatory on the letter to Science encouraging publishers to make their journals publicly available. He also walks the walk, proclaiming that he will not publish in non-open access journal, nor review articles for non-open access journals. Not only is he in favor of open access publishing, he also pushes for open access software.
One of Ashburner's recent project has involved…
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 29, 2007
That's the poster for the upcoming football season at Penn State. It's purpose is both utilitarian (it's got the schedule of games printed on it) and motivational (it's supposed to get you all geeked up for the upcoming season). This year's poster is using the slogan "FIGHT ON!", and I bet someone in the athletic department thought they were real clever when they came up with that. It also sounds mighty familiar, almost as if I'd heard it before. Oh, yeah, it's the name of the USC fight song (see here). It's not as bad as Auburn printing "Roll Tide" on their poster or Ohio State printing "Go…
evolgen | August 26, 2007Why should advisers encourage their students to publish? For the answer, read this post by TR Gregory.
Why is the publishing industry afraid of open access? I can't answer that question, but I can point you to the evidence for their fear: it's right here. Jonathan Eisen points out why PRISM, the anti-open access lobbying group, is total bullshit. The Open Reading Frame doesn't like it either.
evolgen | August 25, 2007
Remember the story about how we inherited the gene that gives us human brains from Neanderthals? The genetic data that were used to reach that conclusion (or a slightly less over-the-top conclusion) were part of a couple of other studies that identified signatures of adaptive evolution in genes involved in brain development. Those results were poorly criticized over a year ago, and they've recently come under fire yet again -- and again (I've compiled a list of the relevant papers below the fold).
The two most recent attacks come in two different flavors. The first attack (previously…
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 21, 2007Nautilus, Nature's blog for authors, has a guest post by Robin Rose on long author lists, entitled "What's an author?". The post is representative of a certain brand of curmudgeonliness mixed with a dash of either ignorance or naivete. Rose has seen author list with more than 20 authors, and he's confused. Did each author contribute equally? How could the manuscript possibly have gotten written? How do you evaluate each author's contribution? Should we cite these long author publications differently? These are all questions running through Dr. Rose's mind, and he has bothered to share them…
evolgen | August 20, 2007
There's been a lot of recent interest in sequences that are highly conserved between humans and other mammals (and even other non-mammalian vertebrates). These sequences are thought to be under purifying selection, which prevents the accumulation of substitutions after two evolutionary lineages diverge. We cannot rule out, however, that the sequences are conserved by either pure chance (ie, in a large enough dataset, there will be a substantial amount of outliers that are still part of the same distribution) or because they have a lower mutation rate.
David Haussler is one of the leaders in…
evolgen | August 17, 2007
I'd be remiss to not mention this paper from Hopi Hoekstra's group after I previously discussed the anti-evo-devo paper she wrote with Jerry Coyne. The premise of the paper from Hoekstra and Coyne is that Sean Carroll overplays the importance of cis-regulatory changes in the evolution of form. Well, Hoekstra and colleagues mapped the genes responsible for natural coat color variation in subspecies of a beach mouse. They isolated two QTLs, and they identified one candidate gene for each. One candidate gene contains a substitution in a protein coding region, while the other gene has no change…
evolgen | August 15, 2007Finally, using a series of related MMEJ substrates, we investigated the inhibitory effect of Pku70 on fission yeast MMEJ unraveled in this study and the impact of both length and position of the microhomologous region on MMEJ efficiency.
That quote comes at the end of the introduction of this paper entitled "Microhomology-Mediated End Joining in Fission Yeast Is Repressed by Pku70 and Relies on Genes Involved in Homologous Recombination" by Anabelle Decottignies. It's unremarkable as far as passages from scientific papers go, but I chose it for a reason. The paper from which the quote is…