Difference between revisions of "Systematics Seminar"

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This is the home page of the UConn EEB department's Co-evolution Seminar, taking the place of the Systematics Seminar this semester (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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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.  
<br><br>
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'''Seminar Format:''' Registered students should sign up for a subject/week by the 10th of February.  Because we may have more students than available class sessions, it may be necessary to co-lead some sessions. If you are interested in more than one subject, feel free to sign up for two sessions.  
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The leader(s) will be responsible both for (1) selection of readings, (2) an introductory presentation, (3) driving discussion and (4) setting up and putting away the projector. 
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
'''Readings:''' In consultation with the instructors, each leader should assign one primary paper /chapter for discussion and up to two other ancillary papers or resources.  The readings should be posted to EEBedia at least a week in advance.
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== Meeting time and place ==
  
'''Introductory PowerPoint:''' Introduce your topic with a 10- to 15-minute PowerPoint.  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.  
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
  
'''Discussion:''' You are responsible for driving the discussion.  Assume everyone in attendance has read the paper. There are excellent suggestions for generating class discussions on Chris Elphick’s Current Topics in Conservation Biology course site.  See section under expectations. 
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== Theme and Schedule for Fall 2019 ==
  
Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions the Friday before our class meeting.
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
  
'''Projector:'''
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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.
The presenter will be responsible for setting up the projector for each class session—you will need to get it from the EEB office, make sure you have appropriate adaptors and have it set up so that class can begin on schedule. Kathy has reserved the pink projector for our class. If you do not have a laptop, let Wagner know and he will bring his. (Nick McIntosh may also be able to provide a loaner.)
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'''Themes of the seminar will include:'''
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==August 30==
* methods for detecting co-speciation (or the lack thereof)
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Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
* the evolutionary consequences of mutualisms, e.g., to evolutionary diversification and extinction
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* when we should expect to find signals of co-speciation
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* what evolutionary forces resist coevolution
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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]
  
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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==September 13==
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Discussion of chapter 3 - Introduction to Brownian Motion
  
== Meeting time and place ==
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==September 20==
For the Spring 2015 semester, we are meeting in the '''Bamford Room (TLS 171B) Tuesdays at 4'''
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Discussion of chapter 4 - Fitting Brownian Motion
  
=== Topics ===
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==September 27==
This seminar will be split between class meetings that emphasize phylogenetic underpinnings, tree comparisons, and reconciliation methods, with those focused on the evolutionary processes underlying co-evolutionary phenomena (as well as the forces and circumstances that, more often than not, prevent it from occurring). And while parasites will figure large in our readings and discussions, we will also explore insect-plant co-evolution, endosymbionts and other mutualisms, mimicry, and others.
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Discussion of chapter 5 - Multivariate Brownian Motion
  
=== Tuesday, 20 January 2015 ===
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==October 4==
At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time
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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]
<br>
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=== Tuesday, 27 January 2015 ===
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(snow day)
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Futuyma%20and%20Slatkin%201983.pdf}}Futuyma and Slatkin, 1983. Coevolution.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Janzen%201980.pdf}}Janzen, 1980. What is coevolution?
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Ehrlich%20and%20Raven%201964.pdf}}Ehrlich and Raven, 1964. Butterflies and Plants: A Study in Coevolution.
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=== Tuesday, 3 February 2015 ===
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==October 11==
'''Leader:''' Wagner
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Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
<br>
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'''Introduction, classic papers, definitions'''<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Futuyma_Species%20Interactions.pdf}}Futuyma, Chapter 18. The Evolution of Interactions among Species.
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=== Tuesday, 10 February 2015 ===
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==October 18==
'''Leader:'''
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Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
<br>
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'''Fossil record and macroevolutionary patterns'''
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=== Tuesday, 17 February 2015 ===
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==October 25==
'''Leader:'''
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Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
<br>
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'''Insect-herbivore coevolution'''
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=== Tuesday, 24 February 2015 ===
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==November 1==
'''Leader:'''
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Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
<br>
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'''Pollination'''
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=== Tuesday, 3 March 2015 ===
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==November 8==
'''Leader:''' Zacharczenko
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Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
<br>
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'''Mimicry'''
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=== Tuesday, 10 March 2015 ===
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==November 15==
'''Leader:'''
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Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
<br>
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'''Coevolution within the genome'''<br>
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(we will meet at 5:15 after seminar)
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=== Tuesday, 17 March 2015 ===
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==November 22==
'''SPRING BREAK'''
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Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
  
=== Tuesday, 24 March 2015 ===
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==December 6==
'''Leader:'''
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Discussion of chapter 14 - Summary
<br>
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'''Endosymbionts'''<br>
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(we will meet at 5:15 after seminar)
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=== Tuesday, 31 March 2015 ===
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== Information for discussion leaders ==
'''Leader:'''
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.
<br>
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'''Sexual coevolution: male-female arms race'''
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=== Tuesday, 7 April 2015 ===
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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. 
'''Leader:'''
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<br>
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'''Host-parasite'''
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=== Tuesday, 14 April 2015 ===
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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.
'''Leader:'''
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<br>
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'''Host-parasite'''<br>
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(we will meet at 5:15 after seminar)
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=== Tuesday, 21 April 2015===
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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:
'''Leader:'''
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<br>
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'''Coevolutionary methods'''
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=== Tuesday, 28 April 2015 ===
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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
'''Leader:'''
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
<br>
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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:
'''Wrap up discussion'''
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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
<br>
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=== Books ===
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*Futuyma, D. J. and M. Slatkin. 1983. Introduction. Pp. 1-13. In: D. J. Futuyma and M. Slatkin (eds.) Coevolution. Sinauer Assoc., Sunderland, MA.
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*Gilbert, L. E. and P. H. Raven. 1980. Coevolution of Animals and Plants. University of Texas Press, Austin, TX. 263 pp. [revised edition of 1975 book].
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*Page, R. D. M. 2003. Tangled Trees: Phylogeny, Cospeciation, and Coevolution.  University of Chicago Press, Chicago, IL.
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*Price, P. W. 1980. Evolutionary Biology of Parasites, Princeton University Press, Princeton, NJ.
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*Thompson, J. N. 1994. The Coevolutionary Process.  University of Chicago Press, Chicago, IL.
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*Thompson, J. N. 2014. Interaction and Coevolution. University of Chicago Press, Chicago, IL [reprint of 1982 book].
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*Also…be on the lookout for: Clayton, D. H., S. E. Bush, and K. P. Johnson. Coevolution of Life on Hosts: Integrating Ecology and History. University of Chicago Press.
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=== Some other papers ===
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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):
*Balbuena, J. A., R. Míguez-Lozano, and I. Blasco-Costa. 2013. PACo: A novel Procrustes application to cophylogenetic analysis. PLoS ONE 8: e61048.
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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
*Banks, J. C., R. L. Palma, and A. M. Paterson. 2006. Cophylogenetic relationships between penguins and their chewing lice. Journal of Evolutionary Biology 19: 156–166.
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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:
*Brockhurst, M. A. and B. Koskella. 2013. Experimental coevolution of species interaction. Trends in Ecology and Evolution. 28: 367-375.
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*Brooks, D. R. 1979. Testing the context and extent of host-parasite coevolution. Systematic Zoology 28: 299–307.
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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
*Brooks, D. R. 1981. Hennig's parasitological method: a proposed solution. Systematic Zoology 30: 229–249.
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*Brooks, D. R., M. G. P. van Veller, and D. A. McLennan. 2001. How to do BPA, really. Journal of Biogeography 28: 345–358. doi: 10.1046/j.1365-2699.2001.00545.x
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If you have ancillary papers, upload those to the dropbox individually and create separate links.  
*Charleston, M. 1998. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149: 191-223.
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*Charleston, M. A. 2002. Principles of cophylogenetic maps.  Biological Evolution and Statistical Physics, Lecture Notes in Physics.  585: 122-147.
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.  
*Charleston, M. A. 2003. Recent results in cophylogeny mapping. Advances in Parasitology 54: 303–330. doi: 10.1016/s0065-308x(03)54007-6.
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*Charleston, M., and D. Robertson. 2002. Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology 51: 528–535.
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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.  
*Clark, M. A., N. A. Moran, P. Baumann, and J. J. Wernegreen. 2000. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 54: 517-525.
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*Clayton, D. H., and K. P. Johnson. 2003. Linking coevolutionary history to ecological process: doves and lice. Evolution 57: 2335–2341.
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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.
*Conow, C., D. Fielder, Y. Ovadia, and R. Libeskind-Hadas. 2010. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology 5: 16–26.
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*Demastes, J. W., T. A. Spradling, M. S. Hafner, G. R. Spies, D. J. Hafner, and J. E. Light. 2012. Cophylogeny on a fine scale: Goemydoecus chewing lice and their pocket gopher hosts, Pappogeomys bulleri. Journal of Parasitology 98: 262–270.
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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.
*Ehrlich, P. R. and P. H. Raven. 1964. Butterflies and plants: a study in coevolution. Evolution 18: 586-608.
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*Eichler, W. 1948. Some rules in ectoparasitism. Annals and Magazine of Natural History (Series 12) 1: 588–598.
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'''Projector:'''
*Futuyma, D. J. and M. Slatkin. 1983. Introduction. Pp. 1-13. In: D. J. Futuyma and M. Slatkin (eds.) Coevolution. Sinauer Assoc., Sunderland, MA.
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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.
*Gustafsson, D. R., and U. Olsson. 2012. Flyway homogenisation or differentiation? Insights from the phylogeny of the sandpiper (Charadriiformes: Scolopacidae: Calidrinae) wing louse genus Lunaceps (Phthiraptera: Ischnocera). International Journal for Parasitology 42: 93–102.
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*Hafner, M. S., and S. A. Nadler. 1988. Phylogenetic trees support the coevolution of parasites and their hosts. Nature 332: 258-259.
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*Hafner, M. S., and R. D. M. Page. 1995. Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system. Royal Society Philosophical Transactions Biological Sciences 349: 77–83.
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*Harbison, C. W., and D. H. Clayton. 2011. Community interactions govern host-switching with implications for host-parasite coevolutionary history. Proceedings of the National Academy of Sciences of the United States of America 108: 9525–9529. doi: 10.2307/25831263
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*Hommola, K., J. E. Smith, Y. Qiu, and W. R. Gilks. 2009. A permutation test of host-parasite cospeciation. Molecular Biology and Evolution 26: 1457–1468. doi: 10.1093/molbev/msp062
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*Hughes, J., M. Kennedy, K. P. Johnson, R. L. Palma, and R. D. M. Page. 2007. Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice. Systematic Biology 56: 232-251.
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*Huelsenbeck, J. P., B. Rannala, and B. Larget. 2000. A Bayesian framework for the analysis of cospeciation. Evolution 54: 352–364. doi: 10.1111/j.0014-3820.2000.tb00039.x
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*Johnson, K. P., R. J. Adams, R. D. M. Page, and D. H. Clayton. 2003. When do parasites fail to speciate in response to host speciation? Systematic Biology 52: 37–47. doi: 10.1080/10635150390132704
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*Johnson, K. P., J. D. Weckstein, M. J. Meyer, and D. H. Clayton. 2011. There and back again: switching between host orders by avian body lice (Ischnocera: Goniodidae). Biological Journal of the Linnean Society 102: 614–625. doi: 10.1111/j.1095-8312.2010.01612.x
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*Legendre, P., Y. Desdevises, and E. Bazin. 2002. A statistical test for host-parasite coevolution. Systematic Biology 51: 217–234. doi: 10.1080/10635150252899734
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*Light, J. E., and M. S. Hafner. 2007. Cophylogeny and disparate rates of evolution in sympatric lineages of chewing lice on pocket gophers. Molecular Phylogenetics and Evolution 45: 997-1013. doi: 10.1016/j.ympev.2007.09.001
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*Light, J. E., and M. S. Hafner. 2008. Codivergence in heteromyid rodents (Rodentia: Heteromyidae) and their sucking lice of the genus Fahrenholzia (Phthiraptera: Anoplura). Systematic Biology 57: 449-465. doi: 10.1080/10635150802169610
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*Janzen, D. H. 1980. What is coevolution? Evolution. 34: 611-612.
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*Manter, H. W. 1966. Parasites of fishes as biological indicators of recent and ancient conditions. Pp. 59–71. Proceedings of the 26th Annual Biology Colloquium on Host-Parasite Relationships, Oregon State University Biology Colloquium.
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*McCutcheon, J. P., B. R. McDonald, and N. A. Moran. 2009. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proceedings of the National Academy of Sciences America USA 106: 15394-15399.
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*McCutcheon, J. P., and N. A. Moran. 2007. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. of the National Academy of Sciences America USA 104: 19392-19397.
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*Meier-Kolthoff, J. P., A. F. Auch, D. H. Huson, and M. Göker. 2007. CopyCat: cophylogenetic analysis tool. Bioinformatics 23: 898–900. doi: 10.1093/bioinformatics/btm027
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*Merkle, D., and M. Middendorf. 2005. Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory in Biosciences 123: 277–299. doi: 10.1016/j.thbio.2005.01.003
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*Morse, S. F., C. W. Dick, B. D. Patterson, and K. Dittmar. 2012. Some like it hot: Evolution and ecology of novel endosymbionts in bat flies of cave-roosting bats (Hippoboscoidea, Nycterophiliinae). Applied and Environmental Microbiology 78: 8639-8649.
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*Page, R. D. M. 1994. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173.
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*Page, R. D. M., and M. S. Hafner. 1996. Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system. Pp. p. 255–270. In New Uses for New Phylogenies, P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee (eds.). Oxford University Press, Oxford.
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*Page, R. D. M., P. L. M. Lee, S. A. Becher, R. Griffiths, and D. H. Clayton. 1998. A different tempo of mitochondrial DNA evolution in birds and their parasitic lice. Molecular Phylogenetics and Evolution 9: 276–293. doi: http://dx.doi.org/10.1006/mpev.1997.0458
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*Paterson, A., G. Wallis, L. Wallis, and R. Gray. 2000. Seabird louse coevolution: complex histories revealed by 12S rRNA sequences and reconciliation analyses. Systematic Biology 49: 383- 399.
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*Reed, D. L., and M. S. Hafner. 1997. Host specificity of chewing lice on pocket gophers: a potential mechanism for cospeciation. Journal of Mammalogy 78: 655–660. doi: 10.2307/1382916
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*Ricklefs, R. E., S. M. Fallon, and E. Bermingham. 2004. Evolutionary relationships, cospeciation, and host switching in avian malaria parasites. Systematic Biology 53: 111–119. doi: 10.1080/10635150490264987
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*Schardl, C. L., K. D. Craven, S. Speakman, A. Stromberg, A. Lindstrom, and R. Yoshida. 2008. A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses. Systematic Biology 57: 483–498. doi: 10.1080/10635150802172184
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*Sloan, D. B., and N. A. Moran. 2012. Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Molecular Biology and Evolution 29: 3781-3792.
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*Takiya, D. M., P. L. Tran, C. H. Dietrich, and N. A. Moran. 2006. Co-cladogenesis spanning three phyla: leafhoppers (Insecta: Hemiptera: Cicadellidae) and their dual bacterial symbionts. Molecular Biology 15: 4175-4191.
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*Thompson, J. N. 2012. The role of coevolution. Science 335: 410-411.
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*Thompson, J. N. 2014. Natural selection, coevolution, and the web of life. American Naturalist 183: iv-v.
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*Thompson, J. N. 2014. Coevolution and speciation. Pp. 535-542. In Losos, J. B. (ed.) The Princeton Guide to Evolution. Princeton University Press, Princeton, NJ
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*Urban, J. M., and J. R. Cryan. 2012. Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea). BMC Evolutionary Biology 12:87.
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*Weckstein, J. D. 2004. Biogeography explains cophylogenetic patterns in toucan chewing lice. Systematic Biology 53: 154–164. doi: 10.1080/10635150490265085
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*Whiteman, N. K., D. Santiago-Alarcon, K. P. Johnson, and P. G. Parker. 2004. Differences in straggling rates between two genera of dove lice (Insecta: Phthiraptera) reinforce population genetic and cophylogenetic patterns. International Journal for Parasitology 34: 1113-1119.
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== Past Systematics Seminars ==
+
== Past Seminars ==
 +
* [[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 2014|Fall 2014]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]

Latest revision as of 17:47, 25 October 2019

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