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 ==
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Every Friday at 11 am in the Bamford Room (TLS 171b).
  
'''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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== Schedule for Spring 2018 ==
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=== Jan. 26 ===
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We will begin with an overview of comparative methods:
  
'''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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Cornwell W, Nakagawa S. 2017. Phylogenetic comparative methods. Curr Biol. 27(9):R333-R336. [https://doi.org/10.1016/j.cub.2017.03.049 doi: 10.1016/j.cub.2017.03.049]
  
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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=== Feb. 2 (next meeting) ===
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Peter Turchin will be our guest to lead discussion of this paper:
  
'''Projector:'''
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Watts J, Sheehan O, Atkinson QD, Bulbulia J, Gray RD. 2016. Ritual human sacrifice promoted and sustained the evolution of stratified societies.Nature. 532:228-31. [https://doi.org/10.1038/nature17159  doi: 10.1038/nature17159]
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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=== Feb. 9 ===
* methods for detecting co-speciation (or the lack thereof)
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* 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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Noah Reid will lead a discussion of "Positive association between population genetic differentiation and speciation rates in New World birds." Proceedings of the National Academy of Sciences 114.24 (2017): 6328-6333. [https://doi.org/10.1073/pnas.1617397114 doi: 10.1073/pnas.1617397114]
  
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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=== Feb. 16 ===
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Suman gives a job talk!
  
== Meeting time and place ==
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=== Feb. 23  ===
For the Spring 2015 semester, we are meeting in the '''Bamford Room (TLS 171B) Tuesdays at 4'''
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Attend PhyloSeminar by Josef Uyeda:[https://www.youtube.com/watch?v=uzHz5jk_L7w On the need for phylogenetic history]
  
=== Topics ===
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=== Mar. 2 ===
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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Katie and Kevin discuss [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syy012/4877123 Contemporary Ecological Interactions Improve Models of Past Trait Evolution]
  
=== Tuesday, 20 January 2015 ===
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=== Mar. 9 ===
At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time
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Suman discusses [https://doi.org/10.1111/evo.13305 Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes)]
<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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=== Mar. 16 ===
'''Leader:''' Wagner
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SPRING BREAK WOO!
<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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===Mar. 23 ===
'''Leader:''' Nik and Jordan
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Katie discusses [https://doi.org/10.1093/sysbio/syy014 When Darwin’s Special Difficulty Promotes Diversification in Insects]
<br>
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'''Fossil record and macroevolutionary patterns'''
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Species Selection and the Macroevolution of Coral Coloniality and Photosymbiosis::{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Simpson_2013.pdf}}Simspon 2013
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=== Tuesday, 17 February 2015 ===
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=== Mar. 30 ===
'''Leader:''' Tim and Kevin
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Kevin and Diler discuss two papers at the heart of last week's paper:[https://doi.org/10.1073/pnas.1518659113 Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures] (Kevin) and [https://doi.org/10.1093/sysbio/syx037 Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models] (Diler)
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'''Insect-herbivore coevolution'''
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=== Tuesday, 24 February 2015 ===
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=== Apr. 6  ===
'''Leader:''' Lauren and Anna
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Eric discusses [https://doi.org/10.1093/sysbio/syx074 The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates]
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'''Pollination'''
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=== Tuesday, 3 March 2015 ===
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Supplemental reading: [https://academic.oup.com/sysbio/article/64/5/869/1685167 Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms]
'''Leader:''' Brigette and Joe
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<br>
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'''Mimicry'''
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=== Tuesday, 10 March 2015 ===
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=== Apr. 13 ===
'''Leader:''' Stanley and Yaowu
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Kristen discusses  [https://www.journals.uchicago.edu/doi/10.1086/689819 Trait Evolution in Adaptive Radiations: Modeling and Measuring Interspecific Competition on Phylogenies]
<br>
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=== Apr. 20 ===
'''Coevolution within the genome'''<br>
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Group discussion of Ree, R. H., & Sanmartın, I. (2009). Prospects and challenges for parametric models in historical biogeographical inference. Journal of Biogeography,36(7), 1211–1220. https://doi.org/10.1111/j.1365-2699.2008.02068.x
(we will meet at 5:15 after seminar)
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=== Tuesday, 17 March 2015 ===
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in preparation for Michael Landis' visit May 4th
'''SPRING BREAK'''
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=== Tuesday, 24 March 2015 ===
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=== Apr. 27 ===
'''Leader:''' Nik, Jordan, and Joe
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Landis, MH, WA Freyman, and BG Baldwin.  2018. Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeography uncertainty.  bioRxiv \16Apr18 http://biorxiv.org/cgi/content/short/301887v1
<br>
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'''Sexual coevolution: male-female arms race'''
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(we will meet at 5:15 after seminar)
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=== Tuesday, 31 March 2015 ===
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=== May 4th ===
'''Leader:''' Veronica, Beth, and Geert
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<br>
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'''Endosymbionts'''<br>
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=== Tuesday, 7 April 2015 ===
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'''Leader:''' Jimmy and Anna
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<br>
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'''Host-parasite'''
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=== Tuesday, 14 April 2015 ===
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Michael Landis, Postdoctoral Research Associate, Yale University will present his work on "Dating the silversword radiation using Hawaiian paleogeography"
'''Leader:''' Alison and Kaitlin
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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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Sign up here to talk to him: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Seminar_speaker_sign-up#Friday.2C_May_4th.2C_2018
'''Leader:''' Veronica
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<br>
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'''Coevolutionary methods'''
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=== Tuesday, 28 April 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.  
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'''Wrap up discussion'''
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<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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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.
*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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*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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'''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.
*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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'''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:
*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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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
*Charleston, M. 1998. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149: 191-223.
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
*Charleston, M. A. 2002. Principles of cophylogenetic maps.  Biological Evolution and Statistical Physics, Lecture Notes in Physics.  585: 122-147.
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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:
*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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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
*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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*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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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):
*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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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
*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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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:
*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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*Ehrlich, P. R. and P. H. Raven. 1964. Butterflies and plants: a study in coevolution. Evolution 18: 586-608.
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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
*Eichler, W. 1948. Some rules in ectoparasitism. Annals and Magazine of Natural History (Series 12) 1: 588–598.
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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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If you have ancillary papers, upload those to the dropbox individually and create separate links.  
*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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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.  
*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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'''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.  
*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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'''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.
*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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Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.
*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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'''Projector:'''
*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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The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.
*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 ==
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== Past Seminars ==
 +
* [[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]]

Revision as of 00:18, 1 May 2018

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

Every Friday at 11 am in the Bamford Room (TLS 171b).

Schedule for Spring 2018

Jan. 26

We will begin with an overview of comparative methods:

Cornwell W, Nakagawa S. 2017. Phylogenetic comparative methods. Curr Biol. 27(9):R333-R336. doi: 10.1016/j.cub.2017.03.049

Feb. 2 (next meeting)

Peter Turchin will be our guest to lead discussion of this paper:

Watts J, Sheehan O, Atkinson QD, Bulbulia J, Gray RD. 2016. Ritual human sacrifice promoted and sustained the evolution of stratified societies.Nature. 532:228-31. doi: 10.1038/nature17159

Feb. 9

Noah Reid will lead a discussion of "Positive association between population genetic differentiation and speciation rates in New World birds." Proceedings of the National Academy of Sciences 114.24 (2017): 6328-6333. doi: 10.1073/pnas.1617397114

Feb. 16

Suman gives a job talk!

Feb. 23

Attend PhyloSeminar by Josef Uyeda:On the need for phylogenetic history

Mar. 2

Katie and Kevin discuss Contemporary Ecological Interactions Improve Models of Past Trait Evolution

Mar. 9

Suman discusses Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes)

Mar. 16

SPRING BREAK WOO!

Mar. 23

Katie discusses When Darwin’s Special Difficulty Promotes Diversification in Insects

Mar. 30

Kevin and Diler discuss two papers at the heart of last week's paper:Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures (Kevin) and Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models (Diler)

Apr. 6

Eric discusses The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates

Supplemental reading: Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms

Apr. 13

Kristen discusses Trait Evolution in Adaptive Radiations: Modeling and Measuring Interspecific Competition on Phylogenies

Apr. 20

Group discussion of Ree, R. H., & Sanmartın, I. (2009). Prospects and challenges for parametric models in historical biogeographical inference. Journal of Biogeography,36(7), 1211–1220. https://doi.org/10.1111/j.1365-2699.2008.02068.x

in preparation for Michael Landis' visit May 4th

Apr. 27

Landis, MH, WA Freyman, and BG Baldwin. 2018. Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeography uncertainty. bioRxiv \16Apr18 http://biorxiv.org/cgi/content/short/301887v1

May 4th

Michael Landis, Postdoctoral Research Associate, Yale University will present his work on "Dating the silversword radiation using Hawaiian paleogeography"

Sign up here to talk to him: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Seminar_speaker_sign-up#Friday.2C_May_4th.2C_2018

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