Systematics Seminar

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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.  
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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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<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.  
  
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
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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. 
  
== Meeting time and place ==
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'''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.
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''
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=== Monday, 23 January 2012 ===
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'''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.  
At this meeting we will discuss possible themes for this semester's seminar, but just to get the ball rolling I have uploaded a short Nature paper for us to discuss:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/MoluscsNature.pdf}}Smith et al. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367 (Dec. 2011). [http://www.nature.com/nature/journal/v480/n7377/full/nature10526.html doi:10.1038/nature10526]
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Images created from the data sets provided online showing extent of missing data. The color red indicates new data collected for this study, black indicates existing data, white indicates missing data. Note, if you choose to display these in your browser (rather than downloading them and using Preview or Photoshop to view them), you should be aware that they are very wide but not very tall, so you will have to zoom your browser to see anything (unless you have really good eyes).
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'''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.
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]
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:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]
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The links below are images of the same two datasets, but wrapped to 1000 pixels wide for easier viewing:
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Prepare 3-5 questions that you expect will spur discussion.  Ideally, you would distribute questions the Friday before our class meeting.
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_50930sites.png small_50930sites.png]
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:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_216402sites.png large_216402sites.png]
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=== Monday, 30 January 2012 ===
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'''Projector:'''
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fu&#269;&iacute;kov&aacute; will lead a discussion on the following shakeup in the green plant tree:
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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.)
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PLoS%20One%202012%20Timme.pdf}}Timme, R. E., T. R. Bachvaroff and C. R. Delwiche. 2012. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. PLoS One 7: e29696.
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Images created from the data sets provided online showing extent of missing data. The color black indicates existing data, white indicates missing data. Admonitions for similar images posted for last week's paper apply here as well.
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'''Themes of the seminar will include:'''
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed.png S10897_trimmed.png]
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* methods for detecting co-speciation (or the lack thereof)
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full.png S10897_full.png]
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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
  
The same as above, but wrapped to 1000 pixels wide (easier to see):
 
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed_wrap.png S10897_trimmed_wrap.png]
 
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full_wrap.png S10897_full_wrap.png]
 
  
=== Monday, 6 February 2012 ===
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[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
Switching gears a bit, Russ Meister will lead a discussion on some Mosquito phylogenetics work.  Additionally he will talk about the Digital Mosquito Project he is working on.
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== Meeting time and place ==
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For the Spring 2015 semester, we are meeting in the '''Bamford Room (TLS 171B) Tuesdays at 4'''
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Phylogenetic%20analysis%20and%20temporal%20diversification%20of%20mosquitoes.pdf}}Phylogenetic analysis and temporal diversification of mosquitoes.pdf
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=== Topics ===
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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.  
  
=== Monday, 13 February 2012 ===
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=== Tuesday, 20 January 2015 ===
Brigette Zacharczenko will discuss some of the challenges of lepidoptera systematics.  
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At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/cho%20et%20al%202011.pdf}}Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
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<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.
  
=== Monday, 20 February 2012 ===
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=== Tuesday, 3 February 2015 ===
Emily Ellis
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'''Leader:''' Wagner
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/tinn%20and%20oakley%202008.pdf}}Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda
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<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.
  
=== Monday, 27 February 2012 ===
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=== Tuesday, 10 February 2015 ===
Beth Timpe
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'''Leader:''' Nik and Jordan
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<br>
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'''Fossil record and macroevolutionary patterns'''<br>
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Species Selection and the Macroevolution of Coral Coloniality and Photosymbiosis:<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Simpson%202013.pdf}}Simpson 2013<br>
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Extra readings:<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Barbeitos%20et%20al.%202010.pdf}}Barbeitos et al. 2010<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Kitahara%20et%20al.%202010.pdf}}Kitahara et al. 2010
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Badets%20et%20al.%202011.pdf}} Badets et al. 2011. ''Correlating Early Evolution of Parasitic Platyhelminths to Gondwana Breakup''
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=== Tuesday, 17 February 2015 ===
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'''Leader:''' Tim and Kevin
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<br>
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'''Nematode-Insect-Plant coevolution'''
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nelson_et_al.pdf}}Nelson_et_al_2014.pdf
  
=== Monday, 5 March 2012  ===
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=== Tuesday, 24 February 2015 ===
Ursula King
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'''Leader:''' Lauren and Anna
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Zhang%20et%20al.%202011%20High-Throughput%20Sequencing%20of%20Six%20Bamboo%20Chloroplast%20Genomes.pdf}}Zhang et al. 2011. High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)
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<br>
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'''Pollination'''<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whittall_Hodges_2007_Pollinator_shifts.pdf}}Whittall and Hodges 2007<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nilsson_1988_The_evolution_of_flowers.pdf}}Nilsson 1988
  
=== Monday, 12 March 2012 ===
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=== Tuesday, 3 March 2015 ===
'''SPRING BREAK''' - no meeting this week
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'''Leader:''' Brigette and Joe
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<br>
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'''Mimicry'''<br>
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Main paper: Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/cuthill_2012_mimicry_heliconius.pdf}}Cuthill and Charlston 2012
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Extra reading
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/mallet_1999_mimicry.pdf}}Mallet 1999
  
=== Monday, 19 March 2012 ===
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=== Tuesday, 10 March 2015 ===
Lily Lewis
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'''Leader:''' Stanley and Yaowu
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Popp%20et%20al.%202011%20PNAS%20%2B%20SI.pdf}}Popp et al. 2011 PNAS + SI.pdf  A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum).
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<br>
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'''Coevolution within the genome'''<br>
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(we will meet at 5:15 after seminar)
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue%20Commentary%20PNAS%202011.pdf}}Donoghue Commentary PNAS 2011.pdf This is a commentary on the Popp et al. paper if you're interested.
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=== Tuesday, 17 March 2015 ===
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'''SPRING BREAK'''
  
=== Monday, 26 March 2012 ===
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=== Tuesday, 24 March 2015 ===
Geert Goemans and Ben Price
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'''Leader:''' Nik, Jordan, and Joe
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<br>
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'''Sexual coevolution: male-female arms race'''
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(we will meet at 5:15 after seminar)
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moulton%20et%20al%202010.pdf}}Moulton et al 2010.pdf
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=== Tuesday, 31 March 2015 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/J%20Hered-2007-Rodr%C3%ADguez-243-9.pdf}}J Hered-2007-Rodríguez-243-9.pdf
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'''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'''
  
=== Monday, 2 April 2012 ===
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=== Tuesday, 14 April 2015 ===
Veronica Bueno
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'''Leader:''' Alison and Kaitlin
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Harrington%26Near%2C%202012%20-%20Phylogenetic%20and%20Coalescent%20Strategies%20of%20Species%20Delimitation%20in%20Snubnose%20Darters.pdf}}Harrington&Near, 2012 - Phylogenetic and Coalescent Strategies of Species Delimitation in Snubnose Darters.pdf
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<br>
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'''Host-parasite'''<br>
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(we will meet at 5:15 after seminar)
  
=== Monday, 9 April 2012 ===
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=== Tuesday, 21 April 2015===
Timothy Moore
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'''Leader:''' Veronica
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Barrkman%20et%20al%202007.pdf}}Barrkman et al 2007.pdf
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<br>
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'''Coevolutionary methods'''
  
=== Monday, 16 April 2012 ===
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=== Tuesday, 28 April 2015 ===
Erica Lasek-Nesselquist will lead discussion on the following paper:
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'''Leader:'''
Philippe, H, H. Brinkmann, DV Lavrov, DTJ Littlewood, M Manuel, G W&ouml;rheide and D. Baurain. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology 9(3): e1000602.
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<br>
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pbio.1000602.pdf}}pbio.1000602.pdf
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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.
  
=== Monday, 23 April 2012 &lArr; ===
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=== Some other papers ===
Chris Owen will present the following paper: Sanderson, M.J., M.M. McMahon, and M. Steel. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10:155.<br/>
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*Balbuena, J. A., R. Míguez-Lozano, and I. Blasco-Costa. 2013. PACo: A novel Procrustes application to cophylogenetic analysis. PLoS ONE 8: e61048.
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Sanderson%20et%20al.%202010.pdf}}Sanderson et al. 2010.pdf
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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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*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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*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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*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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*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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*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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*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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*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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*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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*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.
 +
*Thompson, J. N. 2012. The role of coevolution. Science 335: 410-411.
 +
*Thompson, J. N. 2014. Natural selection, coevolution, and the web of life. American Naturalist 183: iv-v.
 +
*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
 +
*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.
 +
*Weckstein, J. D. 2004. Biogeography explains cophylogenetic patterns in toucan chewing lice. Systematic Biology 53: 154–164. doi: 10.1080/10635150490265085
 +
*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.
  
 
== Past Systematics Seminars ==
 
== Past Systematics Seminars ==
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]
 
* [[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)
 
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)

Latest revision as of 20:05, 25 February 2015

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.

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.

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.

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.

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.

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.

Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions the Friday before our class meeting.

Projector: 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.)

Themes of the seminar will include:

  • methods for detecting co-speciation (or the lack thereof)
  • the evolutionary consequences of mutualisms, e.g., to evolutionary diversification and extinction
  • when we should expect to find signals of co-speciation
  • what evolutionary forces resist coevolution


Click here for information about joining and using the Systematics email list

Contents

Meeting time and place

For the Spring 2015 semester, we are meeting in the Bamford Room (TLS 171B) Tuesdays at 4

Topics

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.

Tuesday, 20 January 2015

At this meeting we will discuss possible themes for this semester's seminar, and determine the meeting time

Tuesday, 27 January 2015

(snow day)

Pdficon small.gifFutuyma and Slatkin, 1983. Coevolution.
Pdficon small.gifJanzen, 1980. What is coevolution?
Pdficon small.gifEhrlich and Raven, 1964. Butterflies and Plants: A Study in Coevolution.

Tuesday, 3 February 2015

Leader: Wagner
Introduction, classic papers, definitions

Pdficon small.gifFutuyma, Chapter 18. The Evolution of Interactions among Species.

Tuesday, 10 February 2015

Leader: Nik and Jordan
Fossil record and macroevolutionary patterns
Species Selection and the Macroevolution of Coral Coloniality and Photosymbiosis:

Pdficon small.gifSimpson 2013

Extra readings:

Pdficon small.gifBarbeitos et al. 2010
Pdficon small.gifKitahara et al. 2010

Tuesday, 17 February 2015

Leader: Tim and Kevin
Nematode-Insect-Plant coevolution

Pdficon small.gifNelson_et_al_2014.pdf

Tuesday, 24 February 2015

Leader: Lauren and Anna
Pollination

Pdficon small.gifWhittall and Hodges 2007
Pdficon small.gifNilsson 1988

Tuesday, 3 March 2015

Leader: Brigette and Joe
Mimicry
Main paper: Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

Pdficon small.gifCuthill and Charlston 2012

Extra reading

Pdficon small.gifMallet 1999

Tuesday, 10 March 2015

Leader: Stanley and Yaowu
Coevolution within the genome
(we will meet at 5:15 after seminar)

Tuesday, 17 March 2015

SPRING BREAK

Tuesday, 24 March 2015

Leader: Nik, Jordan, and Joe
Sexual coevolution: male-female arms race (we will meet at 5:15 after seminar)

Tuesday, 31 March 2015

Leader: Veronica, Beth, and Geert
Endosymbionts

Tuesday, 7 April 2015

Leader: Jimmy and Anna
Host-parasite

Tuesday, 14 April 2015

Leader: Alison and Kaitlin
Host-parasite
(we will meet at 5:15 after seminar)

Tuesday, 21 April 2015

Leader: Veronica
Coevolutionary methods

Tuesday, 28 April 2015

Leader:
Wrap up discussion

Books

  • Futuyma, D. J. and M. Slatkin. 1983. Introduction. Pp. 1-13. In: D. J. Futuyma and M. Slatkin (eds.) Coevolution. Sinauer Assoc., Sunderland, MA.
  • 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].
  • Page, R. D. M. 2003. Tangled Trees: Phylogeny, Cospeciation, and Coevolution. University of Chicago Press, Chicago, IL.
  • Price, P. W. 1980. Evolutionary Biology of Parasites, Princeton University Press, Princeton, NJ.
  • Thompson, J. N. 1994. The Coevolutionary Process. University of Chicago Press, Chicago, IL.
  • Thompson, J. N. 2014. Interaction and Coevolution. University of Chicago Press, Chicago, IL [reprint of 1982 book].
  • 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.

Some other papers

  • Balbuena, J. A., R. Míguez-Lozano, and I. Blasco-Costa. 2013. PACo: A novel Procrustes application to cophylogenetic analysis. PLoS ONE 8: e61048.
  • 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.
  • Brockhurst, M. A. and B. Koskella. 2013. Experimental coevolution of species interaction. Trends in Ecology and Evolution. 28: 367-375.
  • Brooks, D. R. 1979. Testing the context and extent of host-parasite coevolution. Systematic Zoology 28: 299–307.
  • Brooks, D. R. 1981. Hennig's parasitological method: a proposed solution. Systematic Zoology 30: 229–249.
  • 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
  • Charleston, M. 1998. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149: 191-223.
  • Charleston, M. A. 2002. Principles of cophylogenetic maps. Biological Evolution and Statistical Physics, Lecture Notes in Physics. 585: 122-147.
  • Charleston, M. A. 2003. Recent results in cophylogeny mapping. Advances in Parasitology 54: 303–330. doi: 10.1016/s0065-308x(03)54007-6.
  • 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.
  • 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.
  • Clayton, D. H., and K. P. Johnson. 2003. Linking coevolutionary history to ecological process: doves and lice. Evolution 57: 2335–2341.
  • 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.
  • 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.
  • Ehrlich, P. R. and P. H. Raven. 1964. Butterflies and plants: a study in coevolution. Evolution 18: 586-608.
  • Eichler, W. 1948. Some rules in ectoparasitism. Annals and Magazine of Natural History (Series 12) 1: 588–598.
  • Futuyma, D. J. and M. Slatkin. 1983. Introduction. Pp. 1-13. In: D. J. Futuyma and M. Slatkin (eds.) Coevolution. Sinauer Assoc., Sunderland, MA.
  • 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.
  • Hafner, M. S., and S. A. Nadler. 1988. Phylogenetic trees support the coevolution of parasites and their hosts. Nature 332: 258-259.
  • 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.
  • 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
  • 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
  • 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.
  • 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
  • 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
  • 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
  • Legendre, P., Y. Desdevises, and E. Bazin. 2002. A statistical test for host-parasite coevolution. Systematic Biology 51: 217–234. doi: 10.1080/10635150252899734
  • 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
  • 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
  • Janzen, D. H. 1980. What is coevolution? Evolution. 34: 611-612.
  • 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.
  • 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.
  • 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.
  • 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
  • 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
  • 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.
  • Page, R. D. M. 1994. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173.
  • 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.
  • 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
  • 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.
  • 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
  • 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
  • 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
  • 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.
  • 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.
  • Thompson, J. N. 2012. The role of coevolution. Science 335: 410-411.
  • Thompson, J. N. 2014. Natural selection, coevolution, and the web of life. American Naturalist 183: iv-v.
  • 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
  • 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.
  • Weckstein, J. D. 2004. Biogeography explains cophylogenetic patterns in toucan chewing lice. Systematic Biology 53: 154–164. doi: 10.1080/10635150490265085
  • 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.

Past Systematics Seminars

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