Systematics Seminar Fall 2013
Note: this web site is now obsolete. See Systematics Seminar for the current Systematics Seminar web site.
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