Difference between revisions of "Systematics Seminar"

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This is the home page of the UConn EEB department's Systematics Seminar. 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.  
  
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
 
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
  
 
== Meeting time and place ==
 
== Meeting time and place ==
We are meeting this semester in the '''Bamford Room (TLS 171) Fridays from 2-3pm'''. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays.
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Every Friday at 11 am in the Bamford Room (TLS 171b).
  
== Theme for Spring Semester 2008 ==
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== Schedule for Spring 2018 ==
The theme this semester is '''Tree Thinking'''. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these:
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=== Jan. 26 ===
* can you ever say that a clade is basal?
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We will begin with an overview of comparative methods:
* do non-uniform clade priors make sense?
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* what can and can't fossils say about node age
+
* when gene trees and species trees are both right, but different
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* the signature of an adaptive radiation
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Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
+
  
== Schedule for Spring Semester 2008 ==
+
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]
'''Note: the papers linked here require a user name and password to access.''' If you have forgotten the user name and/or password, contact [mailto:paul.lewis@uconn.edu Paul Lewis].
+
  
=== Tuesday, January 22, 2008: Basal clades ===
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=== Feb. 2 (next meeting) ===
Discussion leader: Paul Lewis
+
Peter Turchin will be our guest to lead discussion of this paper:
  
Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''.
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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]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}} '''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}} '''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281.
+
  
=== Friday, February 1, 2008 ===
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=== Feb. 9 ===
Discussion leader: Frank Smith
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}} '''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974.
+
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]
  
In this paper, Kevin de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc.
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=== Feb. 16 ===
 +
Suman gives a job talk!
  
=== Friday, February 8, 2008 ===
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=== Feb. 23  ===
Discussion leader:
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Attend PhyloSeminar by Josef Uyeda:[https://www.youtube.com/watch?v=uzHz5jk_L7w On the need for phylogenetic history]
  
=== Friday, February 15, 2008 ===
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=== Mar. 2 ===
Discussion leader:
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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]
  
=== Friday, February 22, 2008 ===
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=== Mar. 9 ===
Discussion leader:
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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)]
  
=== Friday, February 26, 2008 ===
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=== Mar. 16 ===
Discussion leader:
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SPRING BREAK WOO!
  
=== Friday, February 29, 2008 ===
+
===Mar. 23 ===
Discussion leader:
+
Katie discusses [https://doi.org/10.1093/sysbio/syy014 When Darwin’s Special Difficulty Promotes Diversification in Insects]
  
=== Friday, March 7, 2008 ===
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=== Mar. 30 ===
No meeting (Spring Break)
+
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)
  
=== Friday, March 14, 2008 ===
+
=== Apr. 6  ===
Discussion leader:
+
Eric discusses [https://doi.org/10.1093/sysbio/syx074 The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates]
  
=== Friday, March 21, 2008 ===
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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]
Discussion leader:
+
  
=== Friday, March 28, 2008 ===
+
=== Apr. 13 ===
Discussion leader:
+
Kristen discusses  [https://www.journals.uchicago.edu/doi/10.1086/689819 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
  
=== Friday, April 4, 2008 ===
+
in preparation for Michael Landis' visit May 4th
Discussion leader:
+
  
=== Friday, April 11, 2008 ===
+
=== Apr. 27 ===
Discussion leader:
+
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
  
=== Friday, April 18, 2008 ===
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=== May 4th ===
Discussion leader:
+
  
=== Friday, April 25, 2008 ===
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Michael Landis, Postdoctoral Research Associate, Yale University will present his work on "Dating the silversword radiation using Hawaiian paleogeography"
Discussion leader:
+
  
== Some possibilities ==
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== Information for discussion leaders ==
Feel free to expand this list, and there is of course no requirement that papers for discussion be chosen from this list. To upload a PDF (and receive a free email describing how to make a link to it here), click [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html this link to the upload form]. You will need to know the username and password to upload a PDF (same combination needed to download PDFs from this web site).
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
  
=== Paraphyly vs. Polyphyly ===
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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.
  
Farris' paper is not recent, but would almost certainly be cited by more recent treatments of this subject.
+
'''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.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Farris_1974_SystZool_23_548-554.pdf}} '''Farris, J. S.''' 1974. Formal definitions of paraphyly and polyphyly. Systematic Zoology 23: 548-554.
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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:
  
=== Tree terms ===
+
1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
 +
<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
 +
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:
 +
:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}} '''Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley'''. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22:114-115.
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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):
 +
<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
 +
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:
  
=== Necessity of unequal split priors: undesirable? ===
+
:[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
  
The Velasco response in combination with one of the other two would make for an interesting discussion.
+
If you have ancillary papers, upload those to the dropbox individually and create separate links.  
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.  
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}} '''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586.
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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.  
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
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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.
  
=== Using fossils in dating lineages ===
+
Prepare 3-5 questions that you expect will spur discussion.  Ideally, you would distribute questions a day or two before our class meeting.
  
Among other things, this paper explains why fossils cannot indicate actual branching dates.
+
'''Projector:'''
 +
The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} '''Donoghue, P. C. J., and M. J. Benton'''. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
+
== Past Seminars ==
 
+
* [[Systematics Seminar Fall 2017|Fall 2017]]
=== Signature of adaptive radiations ===
+
* [[Systematics Seminar Fall 2014|Fall 2014]]
 
+
* [[Systematics Seminar Fall 2013|Fall 2013]]
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
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* [[Systematics Seminar Spring 2012|Spring 2012]]
 
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* [[Systematics Seminar Fall 2011|Fall 2011]]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}} '''Whitfield, J. B., and P. J. Lockhart'''. 2007. Deciphering ancient rapid radiations. TREE 22:258-265.
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* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
 
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* [[Systematics Seminar Fall 2010|Fall 2010]]
[[#top|Back to top]]
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* [[Systematics Seminar Spring 2010|Spring 2010]]
 
+
* [[Systematics Seminar Fall 2009|Fall 2009]]
== Past Systematics Seminars ==
+
* [[Systematics Seminar Fall 2008|Fall 2008]]
 +
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Fall 2007|Fall 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
 
* [[Systematics Seminar Spring 2007|Spring 2007]]
Line 115: Line 112:
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004]
 
__NOTOC__
 
  
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Revision as of 23:52, 17 April 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"

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