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).
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Every Friday at 11 am in the Bamford Room (TLS 171b).
  
== Schedule for Fall 2017 ==
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== Schedule for Spring 2018 ==
=== Sep. 4 ===
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=== Jan. 26 ===
Labor day holiday (no meeting)
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We will begin with an overview of comparative methods:
  
=== Sep. 11 ===
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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]
Paul and Suman will lead the discussion of the paper:
+
  
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]
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=== Feb. 2 (next meeting) ===
 +
Peter Turchin will be our guest to lead discussion of this paper:
  
=== Sep. 18 ===
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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]
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.
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=== Feb. 9 ===
  
https://www.nature.com/articles/s41559-017-0126
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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]
  
We’ll be particularly interested in comparing it to this past Monday’s paper:
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=== Feb. 16 ===
 +
Suman gives a job talk!
  
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.
+
=== Feb. 23  ===
 +
Attend PhyloSeminar by Josef Uyeda:[https://www.youtube.com/watch?v=uzHz5jk_L7w On the need for phylogenetic history]
  
https://academic.oup.com/sysbio/article-abstract/66/4/517/2950896
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=== 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]
  
=== Sep. 25 ===
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=== Mar. 9 ===
 +
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)]
  
Katie Taylor will lead a discussion of this (very) recent species delimitation paper in Systematic Biology:
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=== Mar. 16 ===
 +
SPRING BREAK WOO!
  
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]
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===Mar. 23 ===
 +
Katie discusses [https://doi.org/10.1093/sysbio/syy014 When Darwin’s Special Difficulty Promotes Diversification in Insects]
  
=== Oct. ===
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=== Mar. 30 ===
 +
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)
  
Charlie Delavoi will lead a discussion on the BPP process for species delimitation: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf
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=== Apr. 6  ===
 +
Eric discusses [https://doi.org/10.1093/sysbio/syx074 The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates]
  
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
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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]
  
=== Oct. 9 ===
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=== Apr. 13 ===
Seminar canceled for today
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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
  
=== Oct. 16 ===
+
in preparation for Michael Landis' visit May 4th
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]
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=== 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
  
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).
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=== May 4th ===
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.
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[https://doi.org/10.1007/978-81-322-2235-4_2 DOI:10.1007/978-81-322-2235-4_2]
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+
=== Oct. 23 ===
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Diler Haji will lead us in a discussion of the paper below:
+
 
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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]
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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.
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=== Oct. 30 ===
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Kevin Keegan will lead discussion of:
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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]
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+
=== Nov. 6  ===
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Paul Lewis will lead discussion of:
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[http://doi.org/10.1093/sysbio/syw103 Allman, E. S., Kubatko, L. S., & Rhodes, J. A. (2017). Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data. Systematic Biology, 66(4), 620–636.]
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+
=== Nov. 13  ===
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Lee Deininger will lead discussion of:
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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])
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+
=== Nov. 20 ===
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Everyone should contemplate:
+
 
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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. [http://dx.doi.org/10.1111/j.1365-2052.2008.01810.x doi: 10.1111/j.1365-2052.2008.01810.x]
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Happy Thanksgiving!
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=== Nov. 27 (next meeting) ===
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Let's discuss this one on Monday:
+
 
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O'Leary, MA, et al. 2017. Crowds replicate performance of scientific experts scoring phylogenetic matrices of phenotypes. Systematic Biology (advance access). [http://doi.org/10.1093/sysbio/syx052 DOI:10.1093/sysbio/syx052]
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=== Dec. 4 ===
+
  
 +
Michael Landis, Postdoctoral Research Associate, Yale University will present his work on "Dating the silversword radiation using Hawaiian paleogeography"
  
 
== Information for discussion leaders ==
 
== Information for discussion leaders ==
Line 127: Line 95:
  
 
== Past Seminars ==
 
== Past Seminars ==
 +
* [[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]]

Revision as of 23:52, 17 April 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"

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