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 systematics program at the University of Connecticut.
Meeting time and place
For the Fall 2014 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2:30-3:30pm
As the semester progresses, please feel free to add to this running list of sources of systematic error, tests for that error, methods to account for that error, and relevant literature for that error.
|Systematic Error||Tests for Systematic Error||Programs / Methods Accounting for Systematic Error||Associated Literature|
|Nucleotide Composition Bias||Include additional taxa, RY recoding|
|Amino Acid Composition Bias||Dayhoff recoding|
|Incomplete Lineage Sorting|
|Horizontal Gene Transfer / Hybridization / Gene Flow|
|Among Site Rate Heterogeneity (ASRV)|
|Among Lineage Rate Heterogeneity (ALRV)|
|Functional Convergence in Proteins / Selection||Parker et al. 2013, sequence convergence in echolocating bats and cetaceans|
|Missing Data (?)||Wiens and Moen 2008, but see|
|Taxon Sampling (?)|
|Non-Independence of Sites|
|Overly Restrictive Priors|
|Sequencing Hardware Error|
Monday, 25 August 2014
At this meeting we will discuss possible themes for this semester's seminar:
Monday, 1 September 2014
Labor Day, no meeting
Monday, 8 September 2014
For this meeting, please come with an example (or examples) of a source of systematic error in datasets, and a paper that attempts to address this source of systematic error. We will use these examples and papers as a basis for discussions in upcoming weeks.
Monday, 15 September 2014
Topic: An overview of potential systematic errors found in phylogenomic data sets
- Rodriguez-Ezpeleta et al. 2007, Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
Monday, 22 September 2014
Topic: Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
Monday, 29 September 2014
Topic: David Swofford's presentation at the Frontiers in Phylogenetics Symposium, "Filtering and Partitioning Strategies for Phylogenomic Analyses", and SVDQuartets method from Chifman and Kukatko 2014
Optional (but a nice supplement to the paper above and also reviews most other species tree methods): Laura Kubatko talked about SVDQuartets in her lecture at the Woods Hole Molecular Evolution Workshop this past summer. Click on the link below, then click on "Slides (draft)" to download the PDF: the SVDQuartets explanation begins at slide 63.
Symposium talk recordings:
- Part 1 http://www.ustream.tv/recorded/52713111
- Part 2 http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording)
- Part 3 http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording)
Symposium schedule and abstracts:
- 2014 Frontiers in Phylogenetics Symposium Schedule
- 2014 Frontiers in Phylogenetics Symposium Abstracts
Monday, 6 October 2014
Topic: Paul Lewis's presentation at Evolution 2014, "Bayesian estimation of phylogenetic information content and implications for site-stripping"
Here is the paper referenced in Paul's talk:
- Zhong B., Deusch O., Goremykin V.V., Penny D., Biggs P.J., Atherton R.A., Nikiforova S.V., Lockhart P.J. 2011. Systematic error in seed plant phylogenomics. Genome Biology and Evolution. 3:1340–1348.
Monday, 13 October 2014
- Parker et al. 2013, sequence convergence in echolocating bats and cetaceans
Monday, 20 October 2014
Topic: Hybridization/reticulate evolution
- Cui, R., Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., Rosenthal, G.G. 2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution. 67(8):2166-2179.