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.  
+
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 ==
Except for the first meeting, we will meet in the Bamford Room (TLS 171) '''Tuesdays at 4pm'''. The '''first meeting''' will be held in the '''BioPharm 3rd. floor fishbowl''' (Bamford room reserved at this time by ecology search committee).
+
Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
  
== Theme for Spring Semester 2008 ==
+
== Schedule for Fall 2017 ==
Unless there is loud objection, the theme this semester will be '''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:
+
=== Sep. 4 ===
* can you ever say that a clade is basal?
+
Labor day holiday (no meeting)
* do non-uniform clade priors make sense?
+
* what can and can't fossils say about node age
+
* when gene trees and species trees are both right, but different
+
* the signature of an adaptive radiation
+
Some suggested papers are listed below the schedule in the section entitled [[#Some possibilities|Some possibilities]].
+
  
== Schedule for Spring Semester 2008 ==
+
=== Sep. 11 ===
'''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].
+
Paul and Suman will lead the discussion of the paper:
  
=== Tuesday, January 22, 2008: Basal clades ===
+
Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. [https://doi.org/10.1093/sysbio/syw101 doi:10.1093/sysbio/syw101]
Discussion leader: Paul Lewis
+
  
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''.
+
=== Sep. 18 ===
:'''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}}
+
Noah Reid will lead discussion on this paper today:
:'''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}}
+
  
=== Tuesday, January 29, 2008 ===
+
Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.
Discussion leader:
+
  
=== Tuesday, February 5, 2008 ===
+
https://www.nature.com/articles/s41559-017-0126
Discussion leader:
+
Change meeting time (EEB Dept. Seminar conflicts)?
+
  
=== Tuesday, February 12, 2008 ===
+
We’ll be particularly interested in comparing it to this past Monday’s paper:
Discussion leader:
+
Change meeting time (EEB Dept. Seminar conflicts)?
+
  
=== Tuesday, February 19, 2008 ===
+
Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.
Discussion leader:
+
  
=== Tuesday, February 26, 2008 ===
+
https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
Discussion leader:
+
  
=== Tuesday, March 4, 2008 ===
+
=== Sep. 25 ===
Discussion leader:
+
  
=== Tuesday, March 11, 2008 ===
+
Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:
No meeting (Spring Break)
+
  
=== Tuesday, March 18, 2008 ===
+
Cadena, C. D., Zapata, F., & Jiménez, I. (2017). Issues and Perspectives in Species Delimitation using Phenotypic Data—Atlantean Evolution in Darwin’s Finches. Systematic Biology. [http://doi.org/10.1093/sysbio/syx071 DOI 10.1093/sysbio/syx071]
Discussion leader:
+
  
=== Tuesday, March 25, 2008 ===
+
=== Oct. 2  ===
Discussion leader:
+
  
=== Tuesday, April 1, 2008 ===
+
Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf
Watch out! (April Fool's Day)
+
  
Discussion leader:
+
Ziheng Yang; The BPP program for species tree estimation and species delimitation, Current Zoology, Volume 61, Issue 5, 1 October 2015, Pages 854–865, https://doi.org/10.1093/czoolo/61.5.854
  
=== Tuesday, April 8, 2008 ===
+
=== Oct. 9 ===
Discussion leader:
+
Seminar canceled for today
  
=== Tuesday, April 15, 2008 ===
+
=== Oct. 16 ===
Discussion leader:
+
Bernard Goffinet will lead the discussion using a study led by Nicholas Magain as part of his Ph.D. at Duke, which deals with species complexes in lichenized fungi. He compares multiple species delimitations in two complexes.
  
=== Tuesday, April 22, 2008 ===
+
'''Magain, N., et al. In press. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus ''Peltigera'' section ''Polydactylon.'' Molecular Phylogenetics and Evolution.''' [https://doi.org/10.1016/j.ympev.2017.08.013 DOI:10.1016/j.ympev.2017.08.013]
Discussion leader:
+
  
=== Tuesday, April 29, 2008 ===
+
Also, for those interested, here is a review of species delimitation methods (in 2015). Note: those on the Systematics-L list received a PDF of this paper (see instructions at the top of this page if you are not currently enrolled in this list and would like to be).
Discussion leader:
+
Leavitt, SD, CS Moreau, and HT Lumbsch. 2015. The Dynamic Discipline of Species 2 Delimitation: Progress Toward Effectively Recognizing Species Boundaries in Natural Populations. Chapter 2 in DK Upreti et al. (eds.), Recent Advances in Lichenology, Springer India.
 +
[https://doi.org/10.1007/978-81-322-2235-4_2 DOI:10.1007/978-81-322-2235-4_2]
  
== Some possibilities ==
+
=== Oct. 23 ===
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).
+
Diler Haji will lead us in a discussion of the paper below:
  
=== Tree terms ===
+
Ferla, MP,  J Cameron Thrash, SJ Giovannoni, and WM Patrick. 2013. New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability. PLoS One 8(12): e83383. [http://dx.doi.org/10.1371/journal.pone.0083383 doi 10.1371/journal.pone.0083383]
  
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 22114-115
+
The central question for this week is: What exactly is a species of ''Hodgkinia''? ''Hodgkinia'' is a cicada-specific alphaproteobacterial endosymbiont within the Rhizobiales that can be more than 20% divergent across its genome and still be considered ''Hodgkinia''. This is a paper looking at alphaproteobacterial phylogeny and the placement of a rhizobiales bacterium.
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}}
+
  
=== Necessity of unequal split priors: undesirable? ===
+
=== Oct. 30 ===
  
The Velasco response in combination with one of the other two would make for an interesting discussion.
+
Kevin Keegan will lead discussion of:
  
:'''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}}
+
Beaulieu, Jeremy M., and Brian C. O’Meara 2016 Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction. Systematic Biology 65(4): 583–601. [https://doi.org/10.1093/sysbio/syw022 doi:10.1093/sysbio/syw022]
  
:'''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}}
+
=== Nov. 6  ===
  
:'''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}}
+
Paul Lewis will lead discussion of:
  
=== Phylocode: how to name a clade ===
+
[http://doi.org/10.1093/sysbio/syw103 Allman, E. S., Kubatko, L. S., & Rhodes, J. A. (2017). Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data. Systematic Biology, 66(4), 620–636.]
  
Discusses tree terms such as ''crown group'', ''stem lineage'', etc.
+
=== Nov. 13  ===
  
:'''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}}
+
Lee Deininger will lead discussion of:
  
=== Using fossils in dating lineages ===
+
Hadfield, JD, BR Krasnov, R Poulin, and S Nakagawa. 2014. A tale of two phylogenies: comparative analyses of ecological interactions. The American Naturalist 183(2):174-187. [http://dx.doi.org/10.1086/674445 doi: 10.1086/674445] (supplementary material at [http://dx.doi.org/10.5061/dryad.jf3tj doi: 10.5061/dryad.jf3tj])
  
Among other things, this paper explains why fossils cannot indicate actual branching dates.
+
=== Nov. 20 ===
 +
Everyone should contemplate:
  
: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 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}}
+
Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ. 2009. The mitochondrial genome sequence and molecular phylogeny of the turkey, ''Meleagris gallopavo''.  Anim Genet. 2009 Apr;40(2):134-41. [http://dx.doi.org/10.1111/j.1365-2052.2008.01810.x doi: 10.1111/j.1365-2052.2008.01810.x]
  
=== Signature of adaptive radiations ===
+
Happy Thanksgiving!
  
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
+
=== Nov. 27 (next meeting) ===
  
:Whitfield, J. B., and P. J. Lockhart. 2007. Deciphering ancient rapid radiations. TREE 22:258-265 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}}
+
=== Dec. 4 ===
  
[[#top|Back to top]]
 
  
== Past Systematics Seminars ==
+
== 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:
 +
<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.]
 +
 
 +
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:
 +
 
 +
:[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
 +
 
 +
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 ==
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 +
* [[Systematics Seminar Spring 2012|Spring 2012]]
 +
* [[Systematics Seminar Fall 2011|Fall 2011]]
 +
* [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography  Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
 +
* [[Systematics Seminar Fall 2010|Fall 2010]]
 +
* [[Systematics Seminar Spring 2010|Spring 2010]]
 +
* [[Systematics Seminar Fall 2009|Fall 2009]]
 +
* [[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 116: Line 139:
 
* [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]
 
__NOEDITSECTION__
 
__NOTOC__
 
  
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Revision as of 19:12, 20 November 2017

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 Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).

Schedule for Fall 2017

Sep. 4

Labor day holiday (no meeting)

Sep. 11

Paul and Suman will lead the discussion of the paper:

Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. doi:10.1093/sysbio/syw101

Sep. 18

Noah Reid will lead discussion on this paper today:

Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.

https://www.nature.com/articles/s41559-017-0126

We’ll be particularly interested in comparing it to this past Monday’s paper:

Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.

https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896

Sep. 25

Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:

Cadena, C. D., Zapata, F., & Jiménez, I. (2017). Issues and Perspectives in Species Delimitation using Phenotypic Data—Atlantean Evolution in Darwin’s Finches. Systematic Biology. DOI 10.1093/sysbio/syx071

Oct. 2

Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf

Ziheng Yang; The BPP program for species tree estimation and species delimitation, Current Zoology, Volume 61, Issue 5, 1 October 2015, Pages 854–865, https://doi.org/10.1093/czoolo/61.5.854

Oct. 9

Seminar canceled for today

Oct. 16

Bernard Goffinet will lead the discussion using a study led by Nicholas Magain as part of his Ph.D. at Duke, which deals with species complexes in lichenized fungi. He compares multiple species delimitations in two complexes.

Magain, N., et al. In press. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. Molecular Phylogenetics and Evolution. DOI:10.1016/j.ympev.2017.08.013

Also, for those interested, here is a review of species delimitation methods (in 2015). Note: those on the Systematics-L list received a PDF of this paper (see instructions at the top of this page if you are not currently enrolled in this list and would like to be). Leavitt, SD, CS Moreau, and HT Lumbsch. 2015. The Dynamic Discipline of Species 2 Delimitation: Progress Toward Effectively Recognizing Species Boundaries in Natural Populations. Chapter 2 in DK Upreti et al. (eds.), Recent Advances in Lichenology, Springer India. DOI:10.1007/978-81-322-2235-4_2

Oct. 23

Diler Haji will lead us in a discussion of the paper below:

Ferla, MP, J Cameron Thrash, SJ Giovannoni, and WM Patrick. 2013. New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability. PLoS One 8(12): e83383. doi 10.1371/journal.pone.0083383

The central question for this week is: What exactly is a species of Hodgkinia? Hodgkinia is a cicada-specific alphaproteobacterial endosymbiont within the Rhizobiales that can be more than 20% divergent across its genome and still be considered Hodgkinia. This is a paper looking at alphaproteobacterial phylogeny and the placement of a rhizobiales bacterium.

Oct. 30

Kevin Keegan will lead discussion of:

Beaulieu, Jeremy M., and Brian C. O’Meara 2016 Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction. Systematic Biology 65(4): 583–601. doi:10.1093/sysbio/syw022

Nov. 6

Paul Lewis will lead discussion of:

Allman, E. S., Kubatko, L. S., & Rhodes, J. A. (2017). Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data. Systematic Biology, 66(4), 620–636.

Nov. 13

Lee Deininger will lead discussion of:

Hadfield, JD, BR Krasnov, R Poulin, and S Nakagawa. 2014. A tale of two phylogenies: comparative analyses of ecological interactions. The American Naturalist 183(2):174-187. doi: 10.1086/674445 (supplementary material at doi: 10.5061/dryad.jf3tj)

Nov. 20

Everyone should contemplate:

Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ. 2009. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim Genet. 2009 Apr;40(2):134-41. doi: 10.1111/j.1365-2052.2008.01810.x

Happy Thanksgiving!

Nov. 27 (next meeting)

Dec. 4

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