Difference between revisions of "Systematics Seminar"
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− | This is the home page of the UConn EEB department's Systematics Seminar. 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 | + | 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. |
− | + | [[Systematics Listserv|Click here for information about joining and using the Systematics email list]] | |
− | == | + | == Meeting time and place == |
− | : | + | For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm''' |
− | === | + | === Topics === |
− | + | 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. | |
− | : | + | {| border="1" cellpadding="1" |
− | : | + | !style="background:#C0C0C0;" width="250"|Systematic Error |
+ | !style="background:#C0C0C0;" width="350"|Tests for Systematic Error | ||
+ | !style="background:#C0C0C0;" width="350"|Programs / Methods Accounting for Systematic Error | ||
+ | !style="background:#C0C0C0;" width="200"|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) || || || | ||
+ | |||
+ | |- | ||
+ | |||
+ | || Heterotachy || || || | ||
+ | |||
+ | |- | ||
+ | |||
+ | || Paralogy || || || | ||
+ | |||
+ | |- | ||
+ | |||
+ | || Functional Convergence in Proteins / Selection || || || [[:File:Parker_et_al_2013.pdf|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans | ||
+ | |||
+ | |- | ||
+ | |||
+ | || Missing Data (?) || || || [[:File:Wiens_and_Moen_2008.pdf|Wiens and Moen 2008]], but see | ||
+ | [[:File:Lemmon_et_al_2009.pdf|Lemmon et al. 2009]] | ||
+ | |||
+ | |- | ||
+ | |||
+ | || 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 | ||
+ | :[[:File:Rodriguez-Ezpeleta et al 2007. SystBiol.pdf|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 | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2014-Xi-sysbio_syu055.pdf}} Xi et al. 2014 | ||
+ | |||
+ | === 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 <br/> | ||
+ | |||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Chifman%20and%20Kubatko%20-%202014%20-%20Quartet%20Inference%20from%20SNP%20Data%20Under%20the%20Coalesce.pdf}} Chifman and Kubatko 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. | ||
+ | |||
+ | [https://molevol.mbl.edu/index.php/Laura_Kubatko Kubato lecture] | ||
+ | |||
+ | Symposium talk recordings: | ||
+ | :Part 1 http://www.ustream.tv/recorded/52713111 <br/> | ||
+ | :Part 2 http://www.ustream.tv/recorded/52716590 (The first half of Swofford's talk starts towards the end of this recording) <br/> | ||
+ | :Part 3 http://www.ustream.tv/recorded/52720049 (The second half Swofford's talk picks up at the beginning of this recording) <br/> | ||
+ | |||
+ | Symposium schedule and abstracts: | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/2014FrontiersSymposiumSchedule.pdf}} 2014 Frontiers in Phylogenetics Symposium Schedule | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/2014FrontiersSymposiumAbstracts.pdf}} 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" | ||
+ | :https://www.youtube.com/watch?v=kHa57G1imNY | ||
+ | |||
+ | Here is the paper referenced in Paul's talk: | ||
+ | |||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genome%20Biology%20and%20Evolution%202011%20Zhong.pdf}} 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 === | ||
+ | |||
+ | :[[:File:Parker_et_al_2013.pdf|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans | ||
+ | |||
+ | === Monday, 20 October 2014 === | ||
+ | Topic: Hybridization/reticulate evolution | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/dc/Cui_2013.pdf}} 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. | ||
+ | |||
+ | === Monday, 27 October 2014 === | ||
+ | |||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wisecaver-Hackett-MPE%202.pdf}}Wisecaver-Hackett-MPE 2.pdf | ||
+ | |||
+ | === Monday, 3 November 2014 === | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nakhleh_TrendsInEcologyAndEvolution_2013.pdf}}Nakhleh Trends In Ecology And Evolution 2013 | ||
+ | |||
+ | === Monday, 10 November 2014 === | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Mol%20Biol%20Evol-2013-Roure-197-214.pdf}}Mol Biol Evol-2013-Roure-197-214.pdf | ||
+ | |||
+ | === Monday, 17 November 2014 === | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2014-De%20Oliveira%20Martins-sysbio_syu082.pdf}}Syst Biol-2014-De Oliveira Martins-sysbio_syu082.pdf | ||
+ | |||
+ | === Monday, 1 December 2014=== | ||
+ | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lambert%20et%20al.%20-%202015%20-%20When%20do%20species-tree%20and%20concatenated%20estimates%20di.pdf}}Lambert et al. - 2015 - When do species-tree and concatenated estimates di.pdf | ||
== Past Systematics Seminars == | == Past Systematics Seminars == | ||
− | * Fall 2006 | + | * [[Systematics Seminar Fall 2013|Fall 2013]] |
− | * Spring 2005 | + | * [[Systematics Seminar Spring 2012|Spring 2012]] |
− | * Fall 2004 | + | * [[Systematics Seminar Fall 2011|Fall 2011]] |
− | * | + | * [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester) |
+ | * [[Systematics Seminar Fall 2010|Fall 2010]] | ||
+ | * [[Systematics Seminar Spring 2010|Spring 2010]] | ||
+ | * [[Systematics Seminar Fall 2009|Fall 2009]] | ||
+ | * [[Systematics Seminar Fall 2008|Fall 2008]] | ||
+ | * [[Systematics Seminar Spring 2008|Spring 2008]] | ||
+ | * [[Systematics Seminar Fall 2007|Fall 2007]] | ||
+ | * [[Systematics Seminar Spring 2007|Spring 2007]] | ||
+ | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2006.html Fall 2006] | ||
+ | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemSpring2005.html Spring 2005] | ||
+ | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004] | ||
+ | * [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004] | ||
+ | |||
+ | [[Category:EEB Seminars]] |
Revision as of 18:15, 20 November 2014
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.
Click here for information about joining and using the Systematics email list
Contents
- 1 Meeting time and place
- 1.1 Topics
- 1.2 Monday, 25 August 2014
- 1.3 Monday, 1 September 2014
- 1.4 Monday, 8 September 2014
- 1.5 Monday, 15 September 2014
- 1.6 Monday, 22 September 2014
- 1.7 Monday, 29 September 2014
- 1.8 Monday, 6 October 2014
- 1.9 Monday, 13 October 2014
- 1.10 Monday, 20 October 2014
- 1.11 Monday, 27 October 2014
- 1.12 Monday, 3 November 2014
- 1.13 Monday, 10 November 2014
- 1.14 Monday, 17 November 2014
- 1.15 Monday, 1 December 2014
- 2 Past Systematics Seminars
Meeting time and place
For the Fall 2014 semester, we are meeting in the Bamford Room (TLS 171B) Mondays 2:30-3:30pm
Topics
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) | |||
Heterotachy | |||
Paralogy | |||
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.
Monday, 27 October 2014
Monday, 3 November 2014
Monday, 10 November 2014
Monday, 17 November 2014
Monday, 1 December 2014
Past Systematics Seminars
- Fall 2013
- Spring 2012
- Fall 2011
- Spring 2011 (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
- Fall 2010
- Spring 2010
- Fall 2009
- Fall 2008
- Spring 2008
- Fall 2007
- Spring 2007
- Fall 2006
- Spring 2005
- Fall 2004
- Spring 2004