EVOL.FRI

2012-09-02T13:57:00.000-07:00

Welcome to Evol.Fri! This is meant to be an informal reading group to accomplish the goal of staying current with the literature in evolutionary biology. It is hosted by the Eckert and Turbeville labs in the Department of Biology located at Virginia Commonwealth University.

I would like participants to nominate papers that are interesting. The only guideline is that it must fall broadly within the field of evolutionary biology. If you find papers of interest, please e-mail them to me (aeckert2@vcu.edu) and I will post them.

There will be no formal structure to this group. The person who nominates the paper will make a single statement about why the paper was chosen and that is it. The rest of the time will be open for discussion.

When: Every Friday at 4:00 pm

Where: We will wander off to a nice place with refreshments for the actual discussion after meeting at LSB 340/342.

Note the readings are in reverse order (future to past) and that additional posts can be located by clicking on the link "Older Posts" in the bottom right corner.

2012-01-25T16:27:00.000-08:00

February 24, 2012

An Ode to a Tree (with mutations added by A. J. Eckert):

I think that I shall never see
An herb as lovely as a tree.

A tree whose transcriptome is the best...

Wait a minute, I think that I have heard that one before! This week we will read a paper comparing and contrasting the transcriptomes of Populus and Arabidopsis. Maybe we can finally see what makes trees so unique. And before we go, one final mutation to the last line of that lovely little poem: "But only evolution can make a tree."

Quesada, T., et al. 2008. Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytologist 180: 408-420.

2012-01-24T16:08:00.000-08:00

February 17, 2012

Frogs are more than cute, they can inform us about processes that drive local-scale species diversity in the Amazon. It turns out that colonization time of a locality is more important in structuring local diversity than overall diversification rates, trait diversity or climatic diversity. Who would have thought?

Wiens, J. J., R. A. Pyron and D. S. Moen. 2011. Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity. Ecology Letters 14: 643-652.

2012-01-23T15:55:00.000-08:00

February 10, 2012

Is this important for evolution?

Jumping Jehosaphat! Is that gold? This week's paper uses a clever analogy between genome scans, whether they be GWAS or outlier approaches, and the Gold Rush of California in the 1840's and 1850's to examine the biological meaning of genomic outliers. In short, Rockman argues that like the distribution of gold, which is mostly contained in miniscule flakes and not huge nuggets, the distribution of functionally important genetic variation is hidden in effects that are too small to observe. He believes that outliers to date are abnormal (e.g. like those rare and shiny gold nuggets) and really do not inform us about the general material of evolution. Hopefully, we will not be too distracted by all those shiny yet uninformative objects on the way to read this paper!

Rockman, M. V. 2011. The QTN program and the alleles that matter for evolution: All that's gold does not glitter. Evolution 66: 1-17.

In addition, we will read a paper by Barrett and Hoekstra that cautions against over-interpretation of results from genome scans. Who says that history does not repeat itself?

Barrett, R. D. H. and H. E. Hoekstra. 2011. Molecular spandrels: tests of adaptation at the genetic level. Nature Reviews Genetics 12: 767-780

2012-01-22T15:29:00.000-08:00

February 3, 2012

Who says that basic science isn't useful? This week we will explore signals of positive selection in barley. The authors take an inferential approach based on nucleotide diversity to show that variation at eIF4E might be associated with local adaptation in response to mosaic virus infection. We'll have to toast the success of these authors, as barley is a key ingredient of one of Evol.Fri's main staples. Thanks to Chris for recommending this paper.

Hofinger, B. J., et al. 2011. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Molecular Ecology 20: 3653-3668.

2012-01-21T14:37:00.001-08:00

January 27, 2012

We will begin the semester with a trip down the road of statistical phylogeography, and what a trip it will be! Mardulyn et al. take a statistical approach to evaluate the phylogeographic history of a leaf beetle with regards to host plant shifts. Thanks to Serena for suggesting this paper.

Mardulyn, P., N. Othmezouri, Y. E. Mikhailov, J. M. Pasteels. 2011. Conflicting mitochondrial and nuclear phylogeographic signals and evolution of host-plant shifts in the boreo-montane leaf beetle Chrysomela lapponica. Molecular Phylogenetics and Evolution 61: 686-696.

Evol.Fri - Spring Semester 2012 - Call for Papers and Vote for Date and Time

2011-12-10T13:40:00.000-08:00

The meeting on December 9, 2011 marked the end of our first semester for the Evol.Fri reading group. Thank you to all who participated. Now, it's time to think about the future:

(1) With that said I would like to open a vote for a new date and time. Currently we meet on Fridays at 4:00. If you have an interest in changing this schedule, please e-mail me (aeckert2@vcu.edu) a preferred day and time.

(2) We will read any paper that address questions relevant to understanding evolution. So, please send along any paper you would like to read and I will post it. The schedule for next semester is wide open.

The first meeting of the group will be January 27, 2012. Happy Holidays and I hope to see everyone next semester.

2011-11-20T07:19:00.000-08:00

December 9, 2011

This week we will explore the effect of pathogen diversity on human evolution. The paper by Fumagalli et al. makes the strong claim that response to pathogens is the main driver of local adaptation among human populations. And I thought being sick all of the time was a bad thing! It also lays out a "new" method for inferring genetic variants involved with local adaptation.

Fumagalli, M., M. Sironi, U. Pozzoli, A. Ferrer-Admettla, L. Pattini, R. Nielsen. 2011. Signatures of environmental genetic adaptation pinpoint pathgens as the main selective pressure through human evolution. PLoS Genetics 7: e1002355.

2011-11-03T14:19:00.000-07:00

December 2, 2011

Who doesn't love a finch, especially one from the Galapagos Islands? This week we will inspect a paper looking at the phylogeography/historical demography of Darwin's finches. Of keen interest here is the use of multiple time points for inference of genetic diversity and model parameters. Maybe not as cool as using a 5,000 year old bristlecone pine to do the same, but, hey, those cute little guys helped Darwin create an entire field of study that unites all aspects of biology (and gives some us jobs). Thanks to Serena for suggesting this paper!

Farrington, H. L. and K. Petren. 2011. A century of genetic change and metapopulation dynamics in the Galapagos warbler finches (Certhidea). Evolution 65: 3148-3161.

2011-11-02T13:59:00.000-07:00

November 11, 2011

This week we will read a paper on the higher level systematics of marine worms. It highlights several of the challenges in performing such analyses and complements well our previous papers about low level phylogenetic inference, which has its own suite of issues. Thanks to Clint for suggesting this paper.

Phillipe, H., H. Brinkmann, R. Copley, et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470: 255-260.

2011-10-19T10:34:00.000-07:00

October 28, 2011

Note that this paper has been moved to Nov. 4, 2011

This week we will look at patterns of protein evolution in Arabidopsis. Several patterns of adaptive evolution described for Drosophila were examined in Arabidopsis and "surprisingly" differences were discovered. Boy, plants are so weird, but just might be worth the time to consider as good examples of adaptation in the broad sense.

Slotte, T., T. Bataillon, T. T. Hansen, K. St. Onge, S. I. Wright, M. H. Schierup. in press. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution.

2011-09-16T09:04:00.000-07:00

October 21, 2011

Note the change of date for this paper, as I will be out of town for the next couple of Fridays.

This week we will take a walk on the statistical side and examine whether or not proposed methods of species delimitation actually work, especially when gene flow is involved.

Zhang C, Zhang D-X, Zhu T, Yang Z. in press. Evaluation of a Bayesian coalescent method of species delimitation. Systematic Biology.

2011-09-15T14:29:00.000-07:00

September 30, 2011

This week we will explore the world of inbreeding and mating system evolution in hermaphroditic animals. Watch out, it might get interesting! This is also the first paper suggested by a member (thanks Serena), so please keep them coming.

Escobar, J. S. et al. Patterns of mating-system evolution in hermaphroditic animals: correlations among selfing rate, inbreeding depression, and the timing of reproduction. Evolution 65: 1233-1253.

2011-09-07T08:30:00.000-07:00

September 23, 2011

This week we will read a paper that address the role of genetic variation among founding lineages of a population when resource bases are novel. Further information can be found at Dan Bolnick's website.

Agashe D, Falk J J, Bolnick D L. 2011. Effects of founding genetic variation on adaption to a novel resource. Evolution 65: 2481-2491.

2011-09-02T10:28:00.000-07:00

September 16, 2011

This week we will read a fine example of how molecular phylogenies can (or cannot) reveal patterns about the tempo and mode of speciation within floristic hotspots.

Schnitzler J, et al. 2011. Causes of plant diversification in the Cape Biodiversity Hotspot of South Africa. Systematic Biology 60: 343-357.

2011-09-01T10:17:00.000-07:00

Rosenblum et al. PNAS 2009

September 9, 2011

This week we will read two papers about the molecular basis of ecological speciation by Erica Bree Rosenblum. She has been doing extremely awesome work in trying to understand the molecular basis of ecological speciation using coloration in animals as a model system.

1. Rosenblum E, Rompler H, Schoneberg T, Hoekstra H. 2009. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proceedings of the National Academy of Sciences USA 107: 2113-2117.

2. Rosemblum E, Harmon L. 2011. "Same same but different": Replicated ecological speciation at White Sands. Evolution 65: 946-960.