Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
For the Spring 2012 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 3-4pm'''
+
Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
  
=== Monday, 23 January 2012 ===
+
== Schedule for Fall 2017 ==
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:
+
=== Sep. 4 ===
:{{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]
+
Labor day holiday (no meeting)
  
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).
+
=== Sep. 11 ===
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]
+
Paul and Suman will lead the discussion of the paper:
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_200x216402.png large_200x216402.png]
+
  
The links below are images of the same two datasets, but wrapped to 1000 pixels wide for easier viewing:
+
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]
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_50930sites.png small_50930sites.png]
+
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_216402sites.png large_216402sites.png]
+
  
=== Monday, 30 January 2012 ===
+
=== Sep. 18 ===
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fučíková will lead a discussion on the following shakeup in the green plant tree:
+
Noah Reid will lead discussion on this paper today:
:{{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.
+
  
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.
+
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.
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed.png S10897_trimmed.png]
+
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full.png S10897_full.png]
+
  
The same as above, but wrapped to 1000 pixels wide (easier to see):
+
https://www.nature.com/articles/s41559-017-0126
:[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 ===
+
We’ll be particularly interested in comparing it to this past Monday’s paper:
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.
+
  
:{{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
+
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.
  
=== Monday, 13 February 2012 ===
+
https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
Brigette Zacharczenko will discuss some of the challenges of lepidoptera systematics.
+
:{{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)?
+
  
=== Monday, 20 February 2012 ===
+
=== Sep. 25 ===
Emily Ellis
+
:{{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
+
  
=== Monday, 27 February 2012 ===
+
Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:
Beth Timpe
+
  
:{{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''
+
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]
  
=== Monday, 5 March 2012 ===
+
=== Oct. 2 ===
Ursula King
+
:{{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)
+
  
=== Monday, 12 March 2012 ===
+
Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf
'''SPRING BREAK''' - no meeting this week
+
  
=== Monday, 19 March 2012 ===
+
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
Lily Lewis
+
:{{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).
+
  
:{{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.
+
=== Oct. 9 ===
 +
Seminar canceled for today
  
=== Monday, 26 March 2012 ===
+
=== Oct. 16 ===
Geert Goemans and Ben Price
+
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.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moulton%20et%20al%202010.pdf}}Moulton et al 2010.pdf
+
'''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]
:{{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
+
  
=== Monday, 2 April 2012 ===
+
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).
Veronica Bueno
+
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.
:{{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
+
[https://doi.org/10.1007/978-81-322-2235-4_2 DOI:10.1007/978-81-322-2235-4_2]
  
=== Monday, 9 April 2012 ===
+
=== Oct. 23 ===
Timothy Moore
+
Diler Haji will lead us in a discussion of the paper below:
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Barrkman%20et%20al%202007.pdf}}Barrkman et al 2007.pdf
+
  
=== Monday, 16 April 2012 ===
+
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]
Erica Lasek-Nesselquist will lead discussion on the following paper:
+
Philippe, H, H. Brinkmann, DV Lavrov, DTJ Littlewood, M Manuel, G Wörheide and D. Baurain. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biology 9(3): e1000602.
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/pbio.1000602.pdf}}pbio.1000602.pdf
+
  
=== Monday, 23 April 2012 ⇐ ===
+
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.
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/>
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Sanderson%20et%20al.%202010.pdf}}Sanderson et al. 2010.pdf
+
  
== Past Systematics Seminars ==
+
=== 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. [https://doi.org/10.1093/sysbio/syw022 doi:10.1093/sysbio/syw022]
 +
 
 +
=== Nov. 6  ===
 +
 
 +
Paul Lewis will lead discussion of:
 +
 
 +
[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.]
 +
 
 +
=== Nov. 13  (today) ===
 +
 
 +
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. [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])
 +
 
 +
=== 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. [http://dx.doi.org/10.1111/j.1365-2052.2008.01810.x doi: 10.1111/j.1365-2052.2008.01810.x]
 +
 
 +
Happy Thanksgiving!
 +
 
 +
=== Nov. 27 ===
 +
 
 +
=== 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:
 +
<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]]
 
* [[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 12:59, 13 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 (today)

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

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