Difference between revisions of "Systematics Seminar"

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<span style="color:red">The home page of the Systematics Seminar has moved to [https://uconneeb.github.io/systseminar/ https://uconneeb.github.io/systseminar/]. This EEBedia page is no longer maintained or updated.</span>
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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.  
 
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.  
  
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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)
 
  
== Schedule for Fall Semester 2011 ==
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
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Several themes were identified for this semester's Systematics Seminar. We will spend 2-3 weeks on each one.
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== Theme and Schedule for Fall 2019 ==
* Ancestral state reconstruction
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* Use of niche modeling in delimiting species
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
* Informativeness of genes
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* Cryptic species
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Students registered for the course shall pick one chapter of the book to elaborate on, either by choosing and assigning a paper relevant to the chapter, or by bringing in their own project/data to present.
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==August 30==
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Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
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==September 6==
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Discussion of chapter 2 - Fitting Statistical Models to Data, [http://phytools.org/mexico2018/ex/2/Intro-to-phylogenies.html Introduction to phylogenies in R]
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==September 13==
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Discussion of chapter 3 - Introduction to Brownian Motion
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==September 20==
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Discussion of chapter 4 - Fitting Brownian Motion
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==September 27==
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Discussion of chapter 5 - Multivariate Brownian Motion
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==October 4==
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Discussion of chapter 6 - Beyond Brownian Motion<br>[https://github.com/kevinliam/Miscellaneous/blob/master/add_tree_info.zip Kevin shows us how to add images to plotted trees in R]
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==October 11==
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Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
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==October 18==
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Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
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==October 25==
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Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
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==November 1==
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Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
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==November 8==
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Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
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==November 15==
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Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
  
=== Tuesday, September 6, 2011 ===
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==November 22==
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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Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
  
=== Tuesday, September 13, 2011 ===
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==December 6==
Eric Schultz will lead a discussion of the following paper:
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Discussion of chapter 14 - Summary
:{{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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== Information for discussion leaders ==
Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion of the following paper:
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
:{{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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The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector.
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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'''Readings:''' In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources. The readings should be posted to EEBedia at least 5 days in advance.
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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'''Announcing the reading:''' The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:
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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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
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In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with <code><nowiki>http://dx.doi.org/</nowiki></code>. Here is how the above link looks embedded in this EEBedia page:
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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
  
Hamid Razifard will lead a discussion of the following paper:
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2. If the paper is not available through the library, upload a PDF of the paper to [http://dropbox.uconn.edu the UConn dropbox], being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the [[Dropbox Test]] page for other examples):
:{{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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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
"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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In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:
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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===Tuesday, October 25th, 2011===
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:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.] Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041
Ursula King will present some Les Lab research and will lead a discussion on cryptic speciation.
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The following paper gives some background information:
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Viinikka, Y. (1976) Najas marina L. (Najadaceae). Karyotypes, cultivation and morphological variation.Ann. Bo. Fennici 13, 119-131:
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If you have ancillary papers, upload those to the dropbox individually and create separate links.  
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/marina.pdf}}marina.pdf
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.  
  
===Tuesday, November 1st, 2011===
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'''Introductory PowerPoint/KeyNote Presentation:''' Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation.  Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes.  (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.).  Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging.  Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated).  You may also want to provide more detail and background about ancillary readings which likely have not been read by all.
  
Russ Meister will lead a discussion on the following paper:
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'''Discussion:''' You are responsible for driving the discussion.  Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site.  See section under expectations. 
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Co-Cladogenesis%20spanning%20three%20phyla%20%28Moran%202006%29.pdf}}Co-Cladogenesis spanning three phyla (Moran 2006).pdf
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Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.
  
And possibly talk about his proposed doctorate work.
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'''Projector:'''
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The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.
  
== Past Systematics Seminars ==
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== Past 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 Spring 2019|Spring 2019]]
 +
* [[Systematics Seminar Fall 2018|Fall 2018]]
 +
* [[Systematics Seminar Spring 2018|Spring 2018]]
 +
* [[Systematics Seminar Fall 2017|Fall 2017]]
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[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 Fall 2010|Fall 2010]]
 
* [[Systematics Seminar Spring 2010|Spring 2010]]
 
* [[Systematics Seminar Spring 2010|Spring 2010]]

Latest revision as of 18:03, 26 August 2021

The home page of the Systematics Seminar has moved to https://uconneeb.github.io/systseminar/. This EEBedia page is no longer maintained or updated.

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

We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).

Theme and Schedule for Fall 2019

We will be reading Luke J. Harmon's book on comparative phylogenetic methods

Students registered for the course shall pick one chapter of the book to elaborate on, either by choosing and assigning a paper relevant to the chapter, or by bringing in their own project/data to present.

August 30

Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting

September 6

Discussion of chapter 2 - Fitting Statistical Models to Data, Introduction to phylogenies in R

September 13

Discussion of chapter 3 - Introduction to Brownian Motion

September 20

Discussion of chapter 4 - Fitting Brownian Motion

September 27

Discussion of chapter 5 - Multivariate Brownian Motion

October 4

Discussion of chapter 6 - Beyond Brownian Motion
Kevin shows us how to add images to plotted trees in R

October 11

Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova

October 18

Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova

October 25

Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan

November 1

Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch

November 8

Discussion of chapter 11 - Fitting birth-death models — Tanner Matson

November 15

Discussion of chapter 12 - Beyond birth-death models - Katie Taylor

November 22

Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes

December 6

Discussion of chapter 14 - Summary

Information for discussion leaders

Seminar Format: Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.

The leader(s) will be responsible both for (1) selection of readings, (2) announcing the selection, (3) an introductory presentation, (4) driving discussion and (5) setting up and putting away the projector.

Readings: In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources. The readings should be posted to EEBedia at least 5 days in advance.

Announcing the reading: The leader should add an entry to the schedule (see below) by editing this page. There are two ways to create a link to the paper:

1. If the paper is available online through our library, it is sufficient to create a link to the DOI:

:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]

In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with http://dx.doi.org/. Here is how the above link looks embedded in this EEBedia page:

Doyle et al. 2015. Syst. Biol. 64:824-837.

2. If the paper is not available through the library, upload a PDF of the paper to the UConn dropbox, being sure to use the secure version so that it can be password protected. Copy the URL provided by dropbox, and create a link to it as follows (see the Dropbox Test page for other examples):

:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]

In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:

Doyle et al. 2015. Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041

If you have ancillary papers, upload those to the dropbox individually and create separate links.

Finally, send a note to the Systematics Listserv letting everyone know that a paper is available.

Introductory PowerPoint/KeyNote Presentation: Introduce your topic with a 10- to 15-minute PowerPoint or KeyNote presentation. Dedicate at least 2/3 of that time to placing the subject into the broader context of the subject areas/themes and at most 1/3 of it introducing paper, special definitions, taxa, methods, etc. Never exceed 15 minutes. (For example, for a reading on figs and fig-wasps, broaden the scope to plant-herbivore co-evolution.). Add images, include short movie clips, visit web resources, etc. to keep the presentation engaging. Although your presentation should not be a review of the primary reading, showing key figures from the readings may be helpful (and appreciated). You may also want to provide more detail and background about ancillary readings which likely have not been read by all.

Discussion: You are responsible for driving the discussion. Assume everyone in attendance has read the main paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site. See section under expectations.

Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.

Projector: The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.

Past Seminars