Systematics Seminar Fall 2013
This is the home page of the UConn EEB department's Systematics Seminar (EEB 6486). This is a graduate seminar devoted to issues of interest to graduate students and faculty who make up the syastematics program at the University of Connecticut.
- 1 Meeting time and place
- 1.1 Monday, 26 August 2013
- 1.2 Monday, 2 September 2013
- 1.3 Monday, 9 September 2013
- 1.4 Monday, 16 September 2013
- 1.5 Monday, 23 September 2013
- 1.6 Monday, 30 September 2013
- 1.7 Monday, 07 October 2013
- 1.8 Monday, 14 October 2013
- 1.9 Monday, 21 October 2013
- 1.10 Monday, 28 October 2013
- 1.11 Monday, 4 November 2013
- 1.12 Monday, 11 November 2013
- 1.13 Monday, 18 November 2013
- 1.14 Monday, 2 December 2013
- 2 Past Systematics Seminars
Meeting time and place
For the Fall 2013 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2-3pm
Monday, 26 August 2013
At this meeting we will discuss possible themes for this semester's seminar:
Monday, 2 September 2013
Labor Day, no meeting
Monday, 9 September 2013
Elizabeth Jockusch will lead the discussion this week.
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.
- Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. link
Monday, 16 September 2013
Lily Lewis will lead the discussion this week
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
- Wagner et al. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology 22(3):787-798 link
Here is a link to a supplementary paper folks may be interested in for an overview of the applications of RAD-sequencing (or at least those conceived of thus far):
- Davey, J. W., and M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9(5-6):416-423 link
Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
- Etter, P. Sequenced RAD markers for rapid SNP disovery and genetic mapping. link
Finally, here is a PowerPoint concatenation of a few figures from various papers laying out how the RAD-seq process works. This may be a helpful supplement for understanding the methods in the cichlid paper link
Monday, 23 September 2013
Paul Lewis will lead the discussion this week.
- Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. link
- Paul's handout on calculating internode certainty measure link
Monday, 30 September 2013
Brigette Zacharczenko will lead the discussion this week.
- Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using LikelihoodLink
Monday, 07 October 2013
Veronica Bueno will lead the discussion this week.
- Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf
Monday, 14 October 2013
Paul Lewis will lead the discussion.
Main paper for discussion:
- Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.
Optional followup paper describing improvements in technical details:
- Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.
Monday, 21 October 2013
Simona Augyte will lead the discussion this week.
Monday, 28 October 2013
Paul Lewis will lead the discussion this week.
- link Goremykin et al. 2013. The evolutionary root of flowering plants. Systematic Biology 62(1): 50-61
Monday, 4 November 2013
There are two things to do to prepare for this week:
- Come up with an example of speciation that does not follow the classic bifurcating tree structure.
- Read this article
link Mindell, D. 2013. The Tree of Life: Metaphor, Model, and Heuristic Device. Syst. Biol. 62:479-489.
Monday, 11 November 2013
Paper for this week:
- Leaché A.D., Harris R.B., Rannala B., Yang Z. 2013. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology. doi:10.1093/sysbio/syt049 (Advance Access, August 13, 2013)
Monday, 18 November 2013
Veronica Bueno will lead the discussion this week. Zhang et al., 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. doi:10.1093/bioinformatics/btt499
Monday, 2 December 2013
Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading.
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
The Effect of Geographical Scale of Sampling on DNA Barcoding