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 at 11:05 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 Fall 2018 ==
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_200x50930.png small_200x50930.png]
+
We will largely be discussing papers on character mapping, reticulation, and biogeography+dating. Any students that would like to sign up to present a practice talk or talk through ideas related to their research are encouraged to do so!
:[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:
+
=== Aug. 31 ===
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/small_50930sites.png small_50930sites.png]
+
Planning meeting (no readings)
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/large_216402sites.png large_216402sites.png]
+
  
=== Monday, 30 January 2012 ===
+
=== Sep. 7 ===
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.
+
Conflicts between the results of morphological and molecular datasets in squamate reptiles.  
:[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):
+
Paper and supplemental files:
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_trimmed_wrap.png S10897_trimmed_wrap.png]
+
https://dropbox.uconn.edu/dropbox?n=PhylogIguniaRootProblem18.zip&p=Wzhn6V64Bz4T9W7qH
:[http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/S10897_full_wrap.png S10897_full_wrap.png]
+
  
=== Monday, 6 February 2012 ===
+
Discussion led by Jack Phillips
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
+
jackson.phillips@uconn.edu
  
=== Monday, 13 February 2012 ===
+
=== Sep. 14 ===
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 ===
+
Diler and Eric discuss [https://doi.org/10.1093/sysbio/syy019 The Biogeography of Deep Time Reticulation]
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 ===
+
=== Sep. 21 ===
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''
+
Diler discusses [https://doi.org/10.1371/journal.pgen.1005896 Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting]
  
=== Monday, 5 March 2012  ===
+
Watch Cecile Ané's [https://www.youtube.com/watch?v=PF4j_JOQP0c PhyloSeminar] and check out her [http://www.stat.wisc.edu/~ane/PhyloNetworks/MBL2018-networkmodels.pdf slides] from the 2018 Molecular Evolution Workshop at Woods Hole for more information on phylogenetic networks.
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 ===
+
=== Sep. 28  ===
'''SPRING BREAK''' - no meeting this week
+
  
=== Monday, 19 March 2012 ===
+
Katie discusses [https://doi.org/10.1093/sysbio/syy023 HyDe: A Python Package for Genome-Scale Hybridization Detection]
Lily Lewis
+
  
=== Monday, 26 March 2012 ===
+
=== Oct. 5 ===
Geert Goemans and Ben Price
+
  
=== Monday, 2 April 2012 ===
+
Kevin discusses [https://doi.org/10.1093/sysbio/syy046 Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors]
Veronica Bueno
+
  
=== Monday, 9 April 2012 ===
+
=== Oct. 12 ===
Timothy Moore
+
  
=== Monday, 16 April 2012 ===
+
Diler discusses [https://doi.org/10.1111/jbi.13173 Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection]
  
=== Monday, 23 April 2012 ===
+
=== Oct. 19 ===
  
== Past Systematics Seminars ==
+
Eric discusses [https://doi.org/10.1093/sysbio/syy043 Analyzing Contentious Relationships and Outlier Genes in Phylogenomics]
 +
 
 +
=== Oct. 26 ===
 +
 
 +
Katie and Diler give practice ESA talks
 +
 
 +
=== Nov. 2 ===
 +
Tanner discusses [https://doi.org/10.1093/sysbio/syw072 Species Distributions, Quantum Theory, and the Enhancement of Biodiversity Measures]
 +
 
 +
=== Nov. 9  ===
 +
Katie discusses [https://academic.oup.com/sysbio/article/67/6/925/4971555 Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus] 
 +
=== Nov. 16 ===
 +
Grab bag of Next-Gen methods for phylogenetics:
 +
 
 +
Chris
 +
 
 +
Diler 
 +
 
 +
Elizabeth [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/1755-0998.12566  RADcap: sequence capture of dual‐digest RADseq libraries]
 +
 
 +
Eric: [http://ezproxy.lib.uconn.edu/login?url=https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12783 HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing]
 +
 
 +
Jack
 +
 
 +
Katie
 +
 
 +
Kevin
 +
 
 +
Paul
 +
 
 +
Tanner
 +
 
 +
=== Nov. 23 ===
 +
 
 +
'''THANKSGIVING BREAK! WOO!'''
 +
 
 +
=== Nov. 30 ===
 +
 
 +
=== Dec. 7 ===
 +
 
 +
== 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 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 22:12, 13 November 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

We meet at 11:05 in the Bamford Room (TLS 171B)

Theme and Schedule for Fall 2018

We will largely be discussing papers on character mapping, reticulation, and biogeography+dating. Any students that would like to sign up to present a practice talk or talk through ideas related to their research are encouraged to do so!

Aug. 31

Planning meeting (no readings)

Sep. 7

Conflicts between the results of morphological and molecular datasets in squamate reptiles.

Paper and supplemental files: https://dropbox.uconn.edu/dropbox?n=PhylogIguniaRootProblem18.zip&p=Wzhn6V64Bz4T9W7qH

Discussion led by Jack Phillips

jackson.phillips@uconn.edu

Sep. 14

Diler and Eric discuss The Biogeography of Deep Time Reticulation

Sep. 21

Diler discusses Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

Watch Cecile Ané's PhyloSeminar and check out her slides from the 2018 Molecular Evolution Workshop at Woods Hole for more information on phylogenetic networks.

Sep. 28

Katie discusses HyDe: A Python Package for Genome-Scale Hybridization Detection

Oct. 5

Kevin discusses Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors

Oct. 12

Diler discusses Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection

Oct. 19

Eric discusses Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Oct. 26

Katie and Diler give practice ESA talks

Nov. 2

Tanner discusses Species Distributions, Quantum Theory, and the Enhancement of Biodiversity Measures

Nov. 9

Katie discusses Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus

Nov. 16

Grab bag of Next-Gen methods for phylogenetics:

Chris

Diler

Elizabeth RADcap: sequence capture of dual‐digest RADseq libraries

Eric: HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

Jack

Katie

Kevin

Paul

Tanner

Nov. 23

THANKSGIVING BREAK! WOO!

Nov. 30

Dec. 7

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