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'''
 
  
=== Monday, 23 January 2012 ===
+
We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
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:
+
:{{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]
+
  
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).
+
== Theme and Schedule for Spring 2019 ==
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]
+
TBD
:[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:
+
=== Jan. 25 ===
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_50930sites.png small_50930sites.png]
+
(no meeting)
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_216402sites.png large_216402sites.png]
+
=== Feb. 1 ===
 +
Kevin and Katie discuss [https://doi.org/10.1093/sysbio/syz002 Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited]
  
=== Monday, 30 January 2012 ===
+
=== Feb. 8 ===
Continuing on the phylogenomic theme, Louise Lewis and Karolina Fučíková will lead a discussion on the following shakeup in the green plant tree:
+
:{{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.
+
Katie delves into [https://doi.org/10.1093/sysbio/syz004 OSF-Builder: A new tool for constructing and representing evolutionary histories involving introgression]
:[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):
+
=== Feb. 15 ===
:[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 ===
+
RADseq: What the heck is it good for anyways?
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
+
*Katie talks mitogenome extraction from RADseq data.<br/>
 +
*Tanner ponders RADseq for his PhD.<br/>
 +
*Kevin and Dave entertain Sanger vs. RADseq for a beginning grad student in a far-away land
  
=== Monday, 13 February 2012 ===
+
[https://dx.doi.org/10.1038%2Fnrg.2015.28 A refresher on RADseq]
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 ===
+
=== Feb. 22  ===
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 ===
+
Tanner discusses [https://doi.org/10.1093/sysbio/syz011 Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies]
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''
+
=== Mar. 1 ===
  
=== Monday, 5 March 2012  ===
+
Kevin discusses [https://doi.org/10.1016/j.ympev.2019.01.024 Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants]
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 ===
+
=== Mar. 8 ===
'''SPRING BREAK''' - no meeting this week
+
Alex discusses [https://doi.org/10.1093/sysbio/syz011 A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error]
  
=== Monday, 19 March 2012 ===
+
We will be meeting in TLS313 so that Janine can regale use with specimens.
Lily Lewis
+
  
=== Monday, 26 March 2012 ===
+
=== Mar. 15 ===
Geert Goemans and Ben Price
+
Diler discusses [https://doi.org/10.1038/s41467-019-08809-7 Hybridization is a recurrent evolutionary stimulus in wild yeast speciation]
  
=== Monday, 2 April 2012 ===
+
=== Mar. 22 ===
Veronica Bueno
+
  
=== Monday, 9 April 2012 ===
+
SPRING BREAK (no meeting)
Timothy Moore
+
  
=== Monday, 16 April 2012 ===
+
=== Mar. 29 ===
 +
Katie discusses [https://doi.org/10.1038/s41467-019-08621-3 Polygyny is linked to accelerated birdsong evolution but not to larger song repertoires]
  
=== Monday, 23 April 2012 ===
+
=== Apr. 5  ===
 +
Mark discusses [https://doi.org/10.1093/sysbio/syy013 Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?]
  
== Past Systematics Seminars ==
+
=== Apr. 12 ===
 +
 
 +
Jack leads the defense of his masters' thesis
 +
 
 +
=== Apr. 19 ===
 +
 
 +
Diler talks about alignment-free phylogenetic reconstruction
 +
 
 +
=== Apr. 26 ===
 +
Kevin and Katie discuss [https://doi.org/10.1086/703055 Revisiting a Key Innovation in Evolutionary Biology:Felsenstein’s“Phylogenies and the Comparative Method]
 +
 
 +
=== May 5 ===
 +
 
 +
== 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 2018|Fall 2018]]
 +
* [[Systematics Seminar Spring 2018|Spring 2018]]
 +
* [[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 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 15:19, 24 April 2019

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

We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).

Theme and Schedule for Spring 2019

TBD

Jan. 25

(no meeting)

Feb. 1

Kevin and Katie discuss Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited

Feb. 8

Katie delves into OSF-Builder: A new tool for constructing and representing evolutionary histories involving introgression

Feb. 15

RADseq: What the heck is it good for anyways?

  • Katie talks mitogenome extraction from RADseq data.
  • Tanner ponders RADseq for his PhD.
  • Kevin and Dave entertain Sanger vs. RADseq for a beginning grad student in a far-away land

A refresher on RADseq

Feb. 22

Tanner discusses Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies

Mar. 1

Kevin discusses Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

Mar. 8

Alex discusses A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error

We will be meeting in TLS313 so that Janine can regale use with specimens.

Mar. 15

Diler discusses Hybridization is a recurrent evolutionary stimulus in wild yeast speciation

Mar. 22

SPRING BREAK (no meeting)

Mar. 29

Katie discusses Polygyny is linked to accelerated birdsong evolution but not to larger song repertoires

Apr. 5

Mark discusses Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

Apr. 12

Jack leads the defense of his masters' thesis

Apr. 19

Diler talks about alignment-free phylogenetic reconstruction

Apr. 26

Kevin and Katie discuss Revisiting a Key Innovation in Evolutionary Biology:Felsenstein’s“Phylogenies and the Comparative Method

May 5

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