Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
Every Monday (except Labor Day, Sep. 4) at 3pm in the Bamford Room (TLS 171b).
 
  
== Schedule for Fall 2017 ==
+
We meet on Fridays at 2 PM in the Bamford Room (TLS 171b).
=== Sep. 4 ===
+
Labor day holiday (no meeting)
+
  
=== Sep. 11 ===
+
== Theme and Schedule for Spring 2019 ==
Paul and Suman will lead the discussion of the paper:
+
TBD
  
Brown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66(4): 517-530. [https://doi.org/10.1093/sysbio/syw101 doi:10.1093/sysbio/syw101]
+
=== Jan. 25 ===
 +
(no meeting)
 +
=== 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]
  
=== Sep. 18 ===
+
=== Feb. 8 ===
Noah Reid will lead discussion on this paper today:
+
  
Shen, Xing-Xing, Chris Todd Hittinger, and Antonis Rokas. "Contentious relationships in phylogenomic studies can be driven by a handful of genes." Nature Ecology & Evolution 1 (2017): 0126.
+
Katie delves into [https://doi.org/10.1093/sysbio/syz004 OSF-Builder: A new tool for constructing and representing evolutionary histories involving introgression]
  
https://www.nature.com/articles/s41559-017-0126
+
=== Feb. 15 ===
  
We’ll be particularly interested in comparing it to this past Monday’s paper:
+
RADseq: What the heck is it good for anyways?
  
Brown, Jeremy M., and Robert C. Thomson. "Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses." Systematic biology 66.4 (2016): 517-530.
+
*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
  
https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
+
[https://dx.doi.org/10.1038%2Fnrg.2015.28 A refresher on RADseq]
  
=== Sep. 25 ===
+
=== Feb. 22  ===
  
Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:
+
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]
  
Cadena, C. D., Zapata, F., & Jiménez, I. (2017). Issues and Perspectives in Species Delimitation using Phenotypic Data—Atlantean Evolution in Darwin’s Finches. Systematic Biology. [http://doi.org/10.1093/sysbio/syx071 DOI 10.1093/sysbio/syx071]
+
=== Mar. 1 ===
  
=== Oct. 2  ===
+
Kevin discusses [https://doi.org/10.1016/j.ympev.2019.01.024 Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants]
  
Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf
+
=== Mar. 8 ===
 +
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]
  
Ziheng Yang; The BPP program for species tree estimation and species delimitation, Current Zoology, Volume 61, Issue 5, 1 October 2015, Pages 854–865, https://doi.org/10.1093/czoolo/61.5.854
+
We will be meeting in TLS313 so that Janine can regale use with specimens.
  
=== Oct. 9 ===
+
=== Mar. 15 ===
Seminar canceled for today
+
Diler discusses [https://doi.org/10.1038/s41467-019-08809-7 Hybridization is a recurrent evolutionary stimulus in wild yeast speciation]
  
=== Oct. 16 ===
+
=== Mar. 22 ===
Bernard Goffinet will lead the discussion using a study led by Nicholas Magain as part of his Ph.D. at Duke, which deals with species complexes in lichenized fungi. He compares multiple species delimitations in two complexes.
+
  
'''Magain, N., et al. In press. Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus ''Peltigera'' section ''Polydactylon.'' Molecular Phylogenetics and Evolution.''' [https://doi.org/10.1016/j.ympev.2017.08.013 DOI:10.1016/j.ympev.2017.08.013]
+
SPRING BREAK (no meeting)
  
Also, for those interested, here is a review of species delimitation methods (in 2015). Note: those on the Systematics-L list received a PDF of this paper (see instructions at the top of this page if you are not currently enrolled in this list and would like to be).
+
=== Mar. 29 ===
Leavitt, SD, CS Moreau, and HT Lumbsch. 2015. The Dynamic Discipline of Species 2 Delimitation: Progress Toward Effectively Recognizing Species Boundaries in Natural Populations. Chapter 2 in DK Upreti et al. (eds.), Recent Advances in Lichenology, Springer India.
+
Katie discusses [https://doi.org/10.1038/s41467-019-08621-3 Polygyny is linked to accelerated birdsong evolution but not to larger song repertoires]
[https://doi.org/10.1007/978-81-322-2235-4_2 DOI:10.1007/978-81-322-2235-4_2]
+
  
=== Oct. 23 ===
+
=== Apr. ===
Diler Haji will lead us in a discussion of the paper below:
+
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?]
  
Ferla, MP,  J Cameron Thrash, SJ Giovannoni, and WM Patrick. 2013. New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability. PLoS One 8(12): e83383. [http://dx.doi.org/10.1371/journal.pone.0083383 doi 10.1371/journal.pone.0083383]
+
=== Apr. 12 ===
  
The central question for this week is: What exactly is a species of ''Hodgkinia''? ''Hodgkinia'' is a cicada-specific alphaproteobacterial endosymbiont within the Rhizobiales that can be more than 20% divergent across its genome and still be considered ''Hodgkinia''. This is a paper looking at alphaproteobacterial phylogeny and the placement of a rhizobiales bacterium.
+
Jack leads the defense of his masters' thesis
  
=== Oct. 30  (next meeting) ===
+
=== Apr. 19 ===
  
Kevin Keegan will lead discussion of:
+
Diler talks about alignment-free phylogenetic reconstruction
  
Beaulieu, Jeremy M., and Brian C. O’Meara 2016 Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction. Systematic Biology 65(4): 583–601. [https://doi.org/10.1093/sysbio/syw022 doi:10.1093/sysbio/syw022]
+
=== 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]
=== Nov. 6 ===
+
 
+
Lee Deininger will lead discussion of:
+
 
+
Hadfield, JD, BR Krasnov, R Poulin, and S Nakagawa. 2014. A tale of two phylogenies: comparative analyses of ecological interactions. The American Naturalist 183(2):174-187. [http://dx.doi.org/10.1086/674445 doi: 10.1086/674445] (supplementary material at [http://dx.doi.org/10.5061/dryad.jf3tj doi: 10.5061/dryad.jf3tj])
+
 
+
=== Nov. 13 ===
+
 
+
=== Nov. 20 ===
+
Everyone should contemplate:
+
 
+
Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ. 2009. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo.  Anim Genet. 2009 Apr;40(2):134-41. doi: 10.1111/j.1365-2052.2008.01810.x.
+
 
+
=== Nov. 27 ===
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+
=== Dec. 4 ===
+
  
 +
=== May 5 ===
  
 
== Information for discussion leaders ==
 
== Information for discussion leaders ==
Line 117: Line 102:
  
 
== Past Seminars ==
 
== 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 2014|Fall 2014]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]
 
* [[Systematics Seminar Fall 2013|Fall 2013]]

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