Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
We are meeting this semester in the '''Bamford Room (TLS 171B) Tuesdays 4-5pm''' (except Sept. 6, when we will meet in TLS 154; see below)
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For the Fall 2014 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2:30-3:30pm'''
  
== Schedule for Fall Semester 2011 ==
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=== Topics ===
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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.
Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.
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* Ancestral state reconstruction
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* Use of niche modeling in delimiting species
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* Informativeness of genes
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* Cryptic species
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=== Tuesday, September 6, 2011 ===
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{| border="1" cellpadding="1"
We will attend the special seminar by Chris Bird, an EEB BS alum and presently a postdoctoral associate at the University of Hawaii. The talk will be at '''4 pm in TLS 154''', and is entitled “Sympatric Speciation on the Seashore.”
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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
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!style="background:#C0C0C0;" width="200"|Associated Literature
  
=== Tuesday, September 13, 2011 ===
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|-  
Eric Schultz will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/whitehead%202010%20evolution.pdf}}Whitehead, A. 2010. The evolutionary radiation of diverse osmotolerant physiologies in killifish (''Fundulus'' sp.). Evolution 64(7): 2070-2085. [http://dx.doi.org/10.1111/j.1558-5646.2010.00957.x doi:10.1111/j.1558-5646.2010.00957.x].
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Note: you will need a user name and password to access the PDF above. These were sent out via the Systematics listserv on Sept. 6, 2011, but feel free to write to [mailto:paul.lewis@uconn.edu Paul Lewis] if you missed it.
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=== Tuesday, September 20, 2011 ===
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|| Nucleotide Composition Bias ||  || Include additional taxa, RY recoding ||
Karolina Fučíková will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Laszlo%20et%20al%202010%20-%20shrooms.pdf}}Nagy et al. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution 57:1037-1048.
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=== Tuesday, September 27, 2011 ===
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|-
Chris Owen will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2011-Tsang-616-29.pdf}}Tsang et al. 2011.pdf. Hermit to King, or Hermit to All: Multiple Transitions to Crab-like Forms from Hermit Crab Ancestors. Systematic Biology 60:616–629.
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I have also included the classic Cunningham et al. 1992 paper, which originally proposed the "Hermit to King" hypothesis (short and worth the read) and another paper from the Cunningham group that uses DNA and mtDNA gene rearrangements to explore the phylogeny of decapods and the evolution of the crab-like form.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cunningham%20et%20al.%201992.pdf}}Cunningham et al. 1992.pdf. Evolution of king crabs from hermit crab ancestors. Nature 355:539-542.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MorrisonProcRoyB2002.pdf}}Morrison et al. 2002.pdf. Mitochondrial gene rearrangements confirm the parallel evolution of crab-like form. Proc. R. Soc. Lond. B 269:345-350.
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===Tuesday, October 4th, 2011===
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|| Amino Acid Composition Bias ||  || Dayhoff recoding ||
Beth Timpe will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Pagel%20et%20al.%202004.pdf}} Pagel et al. 2004<br>
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''Bayesian estimation of ancestral character states on phylogenies''. Syst. Biol. 53(5):673–684, 2004.<br><br>
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===Tuesday, October 11th, 2011===
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|-
Don Les will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Paris1989.pdf}}Paris1989.pdf<br>
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''Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns''. American Fern Journal, Vol. 79, No. 2.<br><br>
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===Tuesday, October 18th, 2011===
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|| Incomplete Lineage Sorting ||  ||  ||
  
Hamid Razifard will lead a discussion of the following paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hay%20et%20al.%202010.%20Tuatara.pdf}}Hay et al. 2010. Tuatara.pdf<br>
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"Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia)". Conserv Genet (2010) 11:1063–1081.<br><br>
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|| Horizontal Gene Transfer / Hybridization / Gene Flow ||  ||  ||
The authors provide a good review of the previous studies (using allozymes, mtDNA) with conflicting results. They also provide a thorough analysis of all sampled tuatara populations using different techniques (microsats, mtDNA, and PCA on allozyme data obtained by others). The paper is good example of getting different results using different techniques, since the markers probably have different evolutionary history. Therefore, using various techniques (and not focusing on a few evidence from morphology, or molecular data) seems necessary for future taxonomic studies.
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|-
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|| Among Site Rate Heterogeneity (ASRV) ||  ||  ||
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|-
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|| Among Lineage Rate Heterogeneity (ALRV) ||  ||  ||
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|-
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|| Heterotachy ||  ||  ||
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|-
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|| Paralogy ||  ||  ||
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|-
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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
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|-
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|| Missing Data (?) ||  ||  || [[:File:Wiens_and_Moen_2008.pdf‎|Wiens and Moen 2008]], but see
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[[:File:Lemmon_et_al_2009.pdf‎|Lemmon et al. 2009]]
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|-
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|| Taxon Sampling (?) ||  ||  ||
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|-
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|| Non-Independence of Sites ||  ||  ||
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|-
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|| Overly Restrictive Priors ||  ||  ||
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|-
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|| Sequencing Hardware Error ||  ||  ||
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|}
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=== Monday, 25 August 2014 ===
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At this meeting we will discuss possible themes for this semester's seminar:
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=== Monday, 1 September 2014 ===
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Labor Day, no meeting
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=== Monday, 8 September 2014 ===
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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.
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=== Monday, 15 September 2014 ===
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Topic: An overview of potential systematic errors found in phylogenomic data sets
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:[[:File:Rodriguez-Ezpeleta et al 2007. SystBiol.pdf|Rodriguez-Ezpeleta et al. 2007]], Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
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=== Monday, 22 September 2014 ===
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=== Monday, 29 September 2014 ===
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=== Monday, 6 October 2014 ===
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=== 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 ===
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=== Monday, 1 December 2014===
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2010] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
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* [[Systematics Seminar Fall 2013|Fall 2013]]
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* [[Systematics Seminar Spring 2012|Spring 2012]]
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* [[Systematics Seminar Fall 2011|Fall 2011]]
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* [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 Fall 2010|Fall 2010]]
 
* [[Systematics Seminar Spring 2010|Spring 2010]]
 
* [[Systematics Seminar Spring 2010|Spring 2010]]

Revision as of 19:55, 10 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

Monday, 29 September 2014

Monday, 6 October 2014

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