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.  
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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]]
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
 
== Meeting time and place ==
 
== Meeting time and place ==
We are meeting this semester in the '''Bamford Room (TLS 171) Fridays from 2-3pm'''. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays.
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
== Theme for Spring Semester 2008 ==
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=== Topics ===
The theme this semester is '''Tree Thinking'''. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these:
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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.
* can you ever say that a clade is basal?
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* do non-uniform clade priors make sense?
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* what can and can't fossils say about node age
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* when gene trees and species trees are both right, but different
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* the signature of an adaptive radiation
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Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
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== Schedule for Spring Semester 2008 ==
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{| border="1" cellpadding="1"
'''Note: the papers linked here require a user name and password to access.''' If you have forgotten the user name and/or password, contact [mailto:paul.lewis@uconn.edu Paul Lewis].
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!style="background:#C0C0C0;" width="250"|Systematic Error
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!style="background:#C0C0C0;" width="350"|Tests for Systematic Error
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!style="background:#C0C0C0;" width="350"|Programs / Methods Accounting for Systematic Error
 +
!style="background:#C0C0C0;" width="200"|Associated Literature
  
=== Tuesday, January 22, 2008: Basal clades ===
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|-
Discussion leader: Paul Lewis
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Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''.
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|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}} '''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}} '''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281.
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=== Friday, February 1, 2008 ===
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|-
Discussion leader: Frank Smith
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}} '''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974.
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|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
  
In this paper, Kevin de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc.
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|-
  
=== Friday, February 8, 2008 ===
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|| Incomplete Lineage Sorting ||  ||  ||
Discussion leader: Karolina Fucikova
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''Donoghue, P. C. J., and M. J. Benton'''. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
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=== Friday, February 15, 2008 ===
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|-
Discussion leader: Yu(Daniel) Fan
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
+
  
Suggested reading
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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|-
  
=== Friday, February 22, 2008 ===
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|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
Discussion leader:
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=== Friday, February 26, 2008 ===
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|-
Discussion leader:
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=== Friday, February 29, 2008 ===
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|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
Discussion leader:
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=== Friday, March 7, 2008 ===
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|-
No meeting (Spring Break)
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=== Friday, March 14, 2008 ===
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|| Heterotachy ||  ||  ||
Discussion leader:
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=== Friday, March 21, 2008 ===
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|-
Discussion leader:
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=== Friday, March 28, 2008 ===
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|| Paralogy ||  ||  ||
Discussion leader:
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=== Friday, April 4, 2008 ===
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|-
Discussion leader:
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=== Friday, April 11, 2008 ===
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|| Functional Convergence in Proteins / Selection ||  ||  || [[:File:Parker_et_al_2013.pdf‎|Parker et al. 2013]], sequence convergence in echolocating bats and cetaceans
Discussion leader:
+
  
=== Friday, April 18, 2008 ===
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|-
Discussion leader:
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=== Friday, April 25, 2008 ===
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|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
Discussion leader:
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[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
  
== Some possibilities ==
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|-
Feel free to expand this list, and there is of course no requirement that papers for discussion be chosen from this list. To upload a PDF (and receive a free email describing how to make a link to it here), click [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html this link to the upload form]. You will need to know the username and password to upload a PDF (same combination needed to download PDFs from this web site).
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=== Paraphyly vs. Polyphyly ===
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|| Taxon Sampling (?) ||  ||  ||
  
Farris' paper is not recent, but would almost certainly be cited by more recent treatments of this subject.
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|-
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Farris_1974_SystZool_23_548-554.pdf}} '''Farris, J. S.''' 1974. Formal definitions of paraphyly and polyphyly. Systematic Zoology 23: 548-554.
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|| Non-Independence of Sites ||  ||  ||
  
=== Tree terms ===
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|-
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}} '''Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley'''. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22:114-115.
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|| Overly Restrictive Priors ||  ||  ||
  
=== Necessity of unequal split priors: undesirable? ===
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|-
  
The Velasco response in combination with one of the other two would make for an interesting discussion.
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|| Sequencing Hardware Error ||  ||  ||
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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|}
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}} '''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586.
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=== Monday, 25 August 2014 ===
 +
At this meeting we will discuss possible themes for this semester's seminar:
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
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=== Monday, 1 September 2014 ===
 +
Labor Day, no meeting
  
=== Using fossils in dating lineages ===
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=== 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.
  
Among other things, this paper explains why fossils cannot indicate actual branching dates.
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=== 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
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''Donoghue, P. C. J., and M. J. Benton'''. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
+
=== 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
  
=== Signature of adaptive radiations ===
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=== 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/>
  
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
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:{{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
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}} '''Whitfield, J. B., and P. J. Lockhart'''. 2007. Deciphering ancient rapid radiations. TREE 22:258-265.
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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.
  
[[#top|Back to top]]
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[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 ===
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=== Monday, 20 October 2014 ===
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=== Monday, 27 October 2014 ===
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 +
=== Monday, 3 November 2014 ===
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 +
=== Monday, 10 November 2014 ===
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 +
=== Monday, 17 November 2014 ===
 +
 
 +
=== Monday, 1 December 2014===
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
 +
* [[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 Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
Line 121: Line 147:
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
__NOTOC__
 
  
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Revision as of 19:33, 29 September 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

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

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

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

Pdficon small.gif 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

Pdficon small.gif 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.

Kubato lecture

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:

Pdficon small.gif 2014 Frontiers in Phylogenetics Symposium Schedule
Pdficon small.gif 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:

Pdficon small.gif 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

Monday, 20 October 2014

Monday, 27 October 2014

Monday, 3 November 2014

Monday, 10 November 2014

Monday, 17 November 2014

Monday, 1 December 2014

Past Systematics Seminars