Wednesday, November 20, 2013

Paper for Monday 25th

Paper for the discussion on the 25th...

Microevolutionary processes generate phylogenomic discordance at ancient divergences

http://onlinelibrary.wiley.com/doi/10.1111/evo.12047/abstract


Wednesday, November 13, 2013

Reading for Nov. 18th

Hi all,

Take a peek at
Cui, R., Schumer, M., Kruesi, K., Walter, R., Andolfatto, P. and Rosenthal, G. G. (2013), PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION IN XIPHOPHORUS FISHES. Evolution, 67: 2166–2179. doi: 10.1111/evo.12099
http://onlinelibrary.wiley.com/doi/10.1111/evo.12099/full
for next week's discussion.  Let me know if you have any questions beforehand.

Cheers,
Blaine

Wednesday, October 30, 2013

Reading for Nov. 4th

Hi guys!

the paper for Monday is Gene discordance in phylogenomics of recent plant radiations, an example from the Hawaiian Cyrtandra (Gesneriaceae).

It touches on a number of topics related to the use of multiple nuclear loci for phylogenetic studies of closely related species.  I don't think it'll be too hard of a read, but if you find yourself short on time or the details of the analyses are challenging but you still want to participate in the discussion, I'd suggest focusing on the first two paragraphs of the intro, methods 2.3-2.7, and the results/discussion.

Please write down one thing you liked about the paper and one thing you think should have been done differently and bring it for discussion.

Attached are definitions and brief explanations of the software/programs used that might be helpful to have on hand while you're reading if issues of gene discordance are new to you.


Wednesday, October 23, 2013

Paper for Oct. 28

Hello everyone,

And now for something completely different, here is next week's paper:


Wheat, Christopher W., and Niklas Wahlberg. "Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda."Systematic Biology 62.1 (2013): 93-109.

http://sysbio.oxfordjournals.org/content/62/1/93.long

Monday, October 14, 2013

Paper for October 21st

Yo,

Here is next Monday's paper.


Rabosky, D.L. & Matute, D.R. (2013). Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds. Proceedings of the National Academy of Sciences 110: 15354-15359.


http://www.pnas.org/content/110/38/15354.full

Low Coverage Problem

Hi guys!

Below are two papers that discuss one solution to low coverage.  I'm not sure if something like this method could also be used to address Heather Rose's points about paralogous v. orthologous loci.  Just to clarify, this is NOT the paper for next week (not to say future presentations can't use these haha).


1. ALEX BUERKLE, C. & GOMPERT, Z. Population genomics based on low coverage sequencing: how low should we go? Mol Ecol (2012).


2. GOMPERT, Z. et al. GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES. Evolution 66, 2167–2181 (2012).

Thanks for a great discussion!
Best,
Kelly