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 171B) Tuesdays 4-5pm'''.  
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Every Friday at 11 am in the Bamford Room (TLS 171b).
  
== Theme for Fall Semester 2009 ==
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== Schedule for Spring 2018 ==
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=== Jan. 26 ===
This semester we will focus on speciation and hybridization, then transition into phylogeography/ historical biogeography. Random papers/ themes, however, are welcomed.
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We will begin with an overview of comparative methods:
  
== Schedule for Fall Semester 2009 ==
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Cornwell W, Nakagawa S. 2017. Phylogenetic comparative methods. Curr Biol. 27(9):R333-R336. [https://doi.org/10.1016/j.cub.2017.03.049 doi: 10.1016/j.cub.2017.03.049]
'''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]. If you want to upload a PDF file for an upcoming discussion, use the [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html Systematics Seminar PDF upload form]. Uploading PDFs requires the same user name and password as viewing PDFs.
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=== Tuesday, September 8th, 2009: ===
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=== Feb. 2 (next meeting) ===
Discussion leader: [[Elizabeth Wade]]
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Peter Turchin will be our guest to lead discussion of this paper:
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bossu_Near_2009_SysBio.pdf}}Bossu_Near_2009_SysBio.pdf
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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]
  
=== Tuesday, September 15th, 2009 ===
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=== Feb. 9 ===
  
Discussion Leader: Elizabeth Timpe
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Noah Reid will lead a discussion of "Positive association between population genetic differentiation and speciation rates in New World birds." Proceedings of the National Academy of Sciences 114.24 (2017): 6328-6333. [https://doi.org/10.1073/pnas.1617397114 doi: 10.1073/pnas.1617397114]
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bonett%20and%20Chippindale%202004.pdf}}Bonett and Chippindale 2004.pdf
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=== Feb. 16 ===
  
=== Tuesday, September 22nd, 2009 ===
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=== Feb. 23  ===
  
Discussion leaders: Nic Tippery and Dave Wagner
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=== Mar. 2 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield-etal-2006_Apis-biogeog.pdf}}Whitfield et al. 2006. Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, ''Apis mellifera''. ''Science'' 314: 642-645.
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=== Mar. 9 ===
  
http://www.sciencemag.org/cgi/content/abstract/314/5799/642
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=== Mar. 16 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Albrecht-etal-2007_Dreissena-native.pdf}}Albrecht et al. 2007. Invaders or endemics? Molecular phylogenetics, biogeography and systematics of ''Dreissena'' in the Balkans. ''Freshwater Biology'' 52: 1525-1536.
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===Mar. 23 ===
  
http://www3.interscience.wiley.com/journal/117962459/abstract
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=== Mar. 30 ===
  
=== Tuesday, September 29th, 2009 ===
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=== Apr. 6  ===
  
Discussion leader: Chris Owen
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=== Apr. 13 ===
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Clark_et_al-2008-SystBio.pdf}}Clark_et_al-2008-SystBio.pdf
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=== Apr. 20 ===
  
=== Tuesday, October 6th, 2009 ===
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=== Apr. 27 ===
Discussion leader: Daniel Fan
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We will continue talking about Dispersal-Extinction-Cladogesis (DEC) model this week. In 2005, Ree et al. proposed the initial version of DEC although this approach was not named at that time. In 2008, Ree and Smith developed it and published a paper in Sys. Bio., which might be thought as the second version. The paper we will read is about the third version of DEC, likelihood with fossil, and they call it DEC*.
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== Information for discussion leaders ==
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'''Seminar Format:''' Registered students be prepared to lead discussions, perhaps more than once depending on the number of participants.  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moore_2009_.pdf}}Moore et al. 2009. Incorporating Fossil Data in Biogeographic Inference: A Likelihood Approach.
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=== Tuesday, October 13th, 2009 ===
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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. 
  
Juan Carlos Villarreal
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'''Readings:''' In consultation with the instructors, each leader should assign one primary paper for discussion and up to two other ancillary papers or resources.  The readings should be posted to EEBedia at least 5 days in advance.
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Santos.etal.2009.Plosbiolo.pdf}}Santos.etal.2009.Plosbiolo.pdf
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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:
  
I would recommend to check Figure S6 (supplements are available online).  
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1. If the paper is available online through our library, it is sufficient to create a link to the DOI:
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<nowiki>:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]</nowiki>
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In this case, you need not give all the citation details because the DOI should always be sufficient to find the paper. The colon (:) at the beginning of the link causes the link to be indented an placed on a separate line. Note that the DOI is in the form of a URL, starting with <code><nowiki>http://dx.doi.org/</nowiki></code>. Here is how the above link looks embedded in this EEBedia page:
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:[http://dx.doi.org/10.1093/sysbio/syv041 Doyle et al. 2015. Syst. Biol. 64:824-837.]
  
http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1000056;jsessionid=697A5A8835708B33E83085CE4729FB59
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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):
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<nowiki>:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.]</nowiki>
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In this case, you should provide a full citation to the paper for the benefit of those that visit the site long after the dropbox link has expired; however, the full details need not be part of the link text. Here is what this kind of link looks like embedded in this EEBedia page:
  
The next paper is optional. It talks about priors for molecular dating analyses. Simon Ho has published a more recent paper on the topic, this is shorter/simpler.
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:[https://dropbox.uconn.edu/dropbox?n=SystBiol-2015-Doyle-824-37.pdf&p=ELPFIc5NtO3c4V44Ls Doyle et al. 2015.] Full citation: Vinson P. Doyle, Randee E. Young, Gavin J. P. Naylor, and Jeremy M. Brown. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology 64 (5): 824-837. doi:10.1093/sysbio/syv041
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/ho.2007.j.avianbiol..pdf}}ho.2007.j.avianbiol..pdf
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If you have ancillary papers, upload those to the dropbox individually and create separate links.  
  
=== Tuesday, October 20th, 2009 ===
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Finally, send a note to the [[Systematics Listserv]] letting everyone know that a paper is available.
Discussion Leader: Roberta
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{{pdf|http://www.bioone.org/doi/abs/10.1111/j.1558-5646.2008.00566.x}}
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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.  
Hurt et al. 2009 A MULTILOCUS TEST OF SIMULTANEOUS DIVERGENCE ACROSS THE ISTHMUS OF PANAMA USING SNAPPING SHRIMP IN THE GENUS ALPHEUS
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=== Tuesday, October 27th, 2009 ===
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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.
Discussion leader: Geert Goemans
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Himes%20et%20al%202008.pdf}}Himes et al 2008.pdf
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=== Tuesday, November 3rd, 2009 ===
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Prepare 3-5 questions that you expect will spur discussion. Ideally, you would distribute questions a day or two before our class meeting.
Discussion leader: Nic Tippery
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Nielsen-Beaumont-2009_phylogeog.pdf}}Nielsen, R. and M. A. Beaumont. 2009. Statistical inferences in phylogeography. Molecular Ecology 18: 1034-1047.
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http://www3.interscience.wiley.com/journal/121681049/abstract?CRETRY=1&SRETRY=0
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=== Tuesday, November 10th, 2009 ===
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'''Projector:'''
Discussion Leader: Beth Wade
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The Bamford room has joined the modern world--you should just need to plug in your computer or USB key to project.
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Lemmon%20Lemmon%202008%20Phylomapper.pdf}}Lemmon Lemmon 2008 Phylomapper.pdf
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=== Tuesday, November 17th, 2009 ===
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== Past Seminars ==
Discussion leader: Karolina Fučíková
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* [[Systematics Seminar Fall 2017|Fall 2017]]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PNAS%20Brawley%202009.pdf}} Brawley et al. 2009.pdf
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* [[Systematics Seminar Fall 2014|Fall 2014]]
 
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* [[Systematics Seminar Fall 2013|Fall 2013]]
=== Tuesday, December 1st, 2009 ===
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* [[Systematics Seminar Spring 2012|Spring 2012]]
Discussion Leader: Dave Wagner
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* [[Systematics Seminar Fall 2011|Fall 2011]]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/McKenna%20and%20Farrell.pdf}}McKenna and Farrell.pdf
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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]]
=== Tuesday, December 8th, 2009 ===
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* [[Systematics Seminar Spring 2010|Spring 2010]]
Discussion Leader: Chris Owen
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* [[Systematics Seminar Fall 2009|Fall 2009]]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Moore%20%26%20Donoghue%202009.pdf}}Moore & Donoghue 2009.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Supplementary%20Material.pdf}}Supplementary Material.pdf
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[[#top|Back to top]]
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== Past Systematics Seminars ==
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* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Fall 2008|Fall 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]
 
* [[Systematics Seminar Spring 2008|Spring 2008]]

Revision as of 13:26, 6 February 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

Feb. 23

Mar. 2

Mar. 9

Mar. 16

Mar. 23

Mar. 30

Apr. 6

Apr. 13

Apr. 20

Apr. 27

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