Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
For the Fall 2013 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
+
Every Friday at 11 am in the Bamford Room (TLS 171b).
  
=== Monday, 26 August 2013 ===
+
== Schedule for Spring 2018 ==
At this meeting we will discuss possible themes for this semester's seminar:
+
=== Jan. 26 ===
 +
We will begin with an overview of comparative methods:
  
=== Monday, 2 September 2013 ===
+
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]
Labor Day, no meeting
+
  
=== Monday, 9 September 2013 ===
+
=== Feb. 2 (next meeting) ===
Elizabeth Jockusch will lead the discussion this week.
+
Peter Turchin will be our guest to lead discussion of this paper:
  
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. 
+
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]
<ul>
+
<li>Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. [http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/61/5/727.long link]</li>
+
</ul>
+
  
=== Monday, 16 September 2013 ===
+
=== Feb. 9 ===
Lily Lewis will lead the discussion this week
+
  
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
+
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]
:Wagner et al. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology 22(3):787-798 [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12023/full link]
+
Here is a link to a supplementary paper folks may be interested in for an overview of the applications of RAD-sequencing (or at least those conceived of thus far):
+
:Davey, J. W., and M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9(5-6):416-423 [http://ezproxy.lib.uconn.edu/login?url=http://bfg.oxfordjournals.org/content/9/5-6/416 link]
+
Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
+
:Etter, P. Sequenced RAD markers for rapid SNP disovery and genetic mapping. [http://ezproxy.lib.uconn.edu/login?url=https://www.wiki.ed.ac.uk/download/attachments/68630442/sequenced+RAD-Tag+protocol-version+2.doc?version=1 link]
+
Finally, here is a PowerPoint concatenation of a few figures from various papers laying out how the RAD-seq process works. This may be a helpful supplement for understanding the methods in the cichlid paper [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
+
  
=== Monday, 23 September 2013 ===
+
=== Feb. 16 ===
Paul Lewis will lead the discussion this week.
+
Suman gives a job talk!
  
:Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
+
=== Feb. 23  ===
 +
Attend PhyloSeminar by Josef Uyeda:[https://www.youtube.com/watch?v=uzHz5jk_L7w On the need for phylogenetic history]
  
:Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
+
=== Mar. 2 ===
 +
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]
  
=== Monday, 30 September 2013 ===
+
=== Mar. 9 ===
Brigette Zacharczenko will lead the discussion this week.<br>
+
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)]
:Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2013-Adams-181-92.pdf}}Link
+
  
=== Monday, 07 October 2013 ===
+
=== Mar. 16 ===
Veronica Bueno will lead the discussion this week.
+
SPRING BREAK WOO!
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Fujisawa%2C%20Barraclough_2013_Delimiting%20Species%20Using%20Single-Locus%20Data%20and%20the%20Generalized%20Mixed%20Yule%20Coalescent%20Approach%20A%20Revised%20Metho.pdf}}Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf
+
  
=== Monday, 14 October 2013 ===
+
===Mar. 23 ===
Paul Lewis will lead the discussion.
+
Katie discusses [https://doi.org/10.1093/sysbio/syy014 When Darwin’s Special Difficulty Promotes Diversification in Insects]
  
Main paper for discussion:
+
=== Mar. 30 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Proceedings%20of%20the%20National%20Academy%20of%20Sciences%202010%20Yang.pdf}} Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.
+
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)
  
Optional followup paper describing improvements in technical details:
+
=== Apr. 6  ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genetics%202013%20Rannala.pdf}} Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.
+
Eric discusses [https://doi.org/10.1093/sysbio/syx074 The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates]
  
=== Monday, 21 October 2013 ===
+
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]
Simona Augyte will lead the discussion this week.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2012-Moalic-127-37.pdf}}Syst Biol-2012-Moalic-127-37.pdf
+
=== Apr. 13 ===
 +
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
  
 +
in preparation for Michael Landis' visit May 4th
  
== Past Systematics Seminars ==
+
=== 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"
 +
 
 +
Sign up here to talk to him:  http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Seminar_speaker_sign-up#Friday.2C_May_4th.2C_2018
 +
 
 +
== 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 2017|Fall 2017]]
 +
* [[Systematics Seminar Fall 2014|Fall 2014]]
 +
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]

Latest revision as of 00:18, 1 May 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"

Sign up here to talk to him: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Seminar_speaker_sign-up#Friday.2C_May_4th.2C_2018

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