Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
  
We meet at 11:05 in the Bamford Room (TLS 171B)
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We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
  
== Theme and Schedule for Fall 2018 ==
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== Theme and Schedule for Fall 2019 ==
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!
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=== Aug. 31 ===
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[https://lukejharmon.github.io/pcm/ We will be reading Luke J. Harmon's book on comparative phylogenetic methods]
Planning meeting (no readings)
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=== Sep. 7 ===
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Students registered for the course shall pick one chapter of the book to elaborate on, either by choosing and assigning a paper relevant to the chapter, or by bringing in their own project/data to present.
  
Conflicts between the results of morphological and molecular datasets in squamate reptiles.
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==August 30==
 +
Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting
  
Paper and supplemental files:
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==September 6==
https://dropbox.uconn.edu/dropbox?n=PhylogIguniaRootProblem18.zip&p=Wzhn6V64Bz4T9W7qH
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Discussion of chapter 2 - Fitting Statistical Models to Data, [http://phytools.org/mexico2018/ex/2/Intro-to-phylogenies.html Introduction to phylogenies in R]
  
Discussion led by Jack Phillips
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==September 13==
 +
Discussion of chapter 3 - Introduction to Brownian Motion
  
jackson.phillips@uconn.edu
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==September 20==
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Discussion of chapter 4 - Fitting Brownian Motion
  
=== Sep. 14 ===
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==September 27==
 +
Discussion of chapter 5 - Multivariate Brownian Motion
  
Diler and Eric discuss [https://doi.org/10.1093/sysbio/syy019 The Biogeography of Deep Time Reticulation]
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==October 4==
 +
Discussion of chapter 6 - Beyond Brownian Motion<br>[https://github.com/kevinliam/Miscellaneous/blob/master/add_tree_info.zip Kevin shows us how to add images to plotted trees in R]
  
=== Sep. 21 ===
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==October 11==
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Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova
  
Diler discusses [https://doi.org/10.1371/journal.pgen.1005896 Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting]
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==October 18==
 +
Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova
  
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.
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==October 25==
 +
Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan
  
=== Sep. 28  ===
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==November 1==
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Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch
  
Katie discusses [https://doi.org/10.1093/sysbio/syy023 HyDe: A Python Package for Genome-Scale Hybridization Detection]
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==November 8==
 +
Discussion of chapter 11 - Fitting birth-death models — Tanner Matson
  
=== Oct. 5 ===
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==November 15==
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Discussion of chapter 12 - Beyond birth-death models - Katie Taylor
  
Kevin discusses [https://doi.org/10.1093/sysbio/syy046 Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors]
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==November 22==
 +
Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes
  
=== Oct. 12 ===
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==December 6==
 
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Discussion of chapter 14 - Summary
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]
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=== Oct. 19 ===
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Eric discusses [https://doi.org/10.1093/sysbio/syy043 Analyzing Contentious Relationships and Outlier Genes in Phylogenomics]
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=== Oct. 26 ===
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Katie and Diler give practice ESA talks
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=== Nov. 2 ===
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Tanner discusses [https://doi.org/10.1093/sysbio/syw072 Species Distributions, Quantum Theory, and the Enhancement of Biodiversity Measures]
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=== Nov. 9  ===
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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] 
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=== Nov. 16 ===
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Grab bag of Next-Gen methods for phylogenetics:
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Chris
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Diler 
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Elizabeth [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/1755-0998.12566  RADcap: sequence capture of dual‐digest RADseq libraries]
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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]
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Jack
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Katie
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Kevin
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Paul
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Tanner
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=== Nov. 23 ===
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'''THANKSGIVING BREAK! WOO!'''
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=== Nov. 30 ===
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=== Dec. 7 ===
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== Information for discussion leaders ==
 
== Information for discussion leaders ==
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== Past Seminars ==
 
== Past Seminars ==
 +
* [[Systematics Seminar Spring 2019|Spring 2019]]
 +
* [[Systematics Seminar Fall 2018|Fall 2018]]
 
* [[Systematics Seminar Spring 2018|Spring 2018]]
 
* [[Systematics Seminar Spring 2018|Spring 2018]]
 
* [[Systematics Seminar Fall 2017|Fall 2017]]
 
* [[Systematics Seminar Fall 2017|Fall 2017]]

Latest revision as of 17:47, 25 October 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 Fall 2019

We will be reading Luke J. Harmon's book on comparative phylogenetic methods

Students registered for the course shall pick one chapter of the book to elaborate on, either by choosing and assigning a paper relevant to the chapter, or by bringing in their own project/data to present.

August 30

Discussion of chapter 1 - A Macroevolutionary Research Program, an organizational meeting

September 6

Discussion of chapter 2 - Fitting Statistical Models to Data, Introduction to phylogenies in R

September 13

Discussion of chapter 3 - Introduction to Brownian Motion

September 20

Discussion of chapter 4 - Fitting Brownian Motion

September 27

Discussion of chapter 5 - Multivariate Brownian Motion

October 4

Discussion of chapter 6 - Beyond Brownian Motion
Kevin shows us how to add images to plotted trees in R

October 11

Discussion of chapter 7 - Models of discrete character evolution — Lisa Terlova

October 18

Discussion of chapter 8 - Fitting models of discrete character evolution — Lisa Terlova

October 25

Discussion of chapter 9 - Beyond the Mk model - Kevin Keegan

November 1

Discussion of chapter 10 - Introduction to birth-death models — Zach Muscavitch

November 8

Discussion of chapter 11 - Fitting birth-death models — Tanner Matson

November 15

Discussion of chapter 12 - Beyond birth-death models - Katie Taylor

November 22

Discussion of chapter 13 - Characters and diversification rates - Amanda Hewes

December 6

Discussion of chapter 14 - Summary

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