Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
  
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We meet at 11:05 in the Bamford Room (TLS 171B)
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We meet at 2 PM in TBD.
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== Theme and Schedule for Fall 2018 ==
 
== Theme and Schedule for Fall 2018 ==
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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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TBD
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=== Aug. 31 ===
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Planning meeting (no readings)
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=== Sep. 7 ===
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Conflicts between the results of morphological and molecular datasets in squamate reptiles.
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Paper and supplemental files:
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https://dropbox.uconn.edu/dropbox?n=PhylogIguniaRootProblem18.zip&p=Wzhn6V64Bz4T9W7qH
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Discussion led by Jack Phillips
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jackson.phillips@uconn.edu
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=== Sep. 14 ===
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Diler and Eric discuss [https://doi.org/10.1093/sysbio/syy019 The Biogeography of Deep Time Reticulation]
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=== Sep. 21 ===
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Diler discusses [https://doi.org/10.1371/journal.pgen.1005896 Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting]
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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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=== Sep. 28  ===
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Katie discusses [https://doi.org/10.1093/sysbio/syy023 HyDe: A Python Package for Genome-Scale Hybridization Detection]
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=== Jan. 25 ===
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(no meeting)
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=== Feb. 1 ===
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[https://doi.org/10.1093/sysbio/syz002 Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited]
  
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=== Oct. 5 ===
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=== Feb. 8 ===
  
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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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=== Oct. 12 ===
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=== Feb. 15 ===
  
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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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=== Feb. 22  ===
  
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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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=== Mar. 1 ===
  
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Katie and Diler give practice ESA talks
 
  
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=== Nov. 2 ===
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=== Mar. 8 ===
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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 [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171053] GBS  Genotyping-by-sequencing.
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=== Mar. 15 ===
  
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Kevin [https://doi.org/10.1093/sysbio/sys049 Anchored hybrid enrichment for massively high-throughput phylogenomics]
 
  
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Tanner [https://www.biorxiv.org/content/early/2018/05/30/333799 Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits]
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=== Mar. 22 ===
  
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Dave [https://doi.org/10.1093/sysbio/sys004 Ultraconserved elements anchor thousandsof genetic markers spanning multiple evolutionary timescales]
 
  
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====Further Reading====
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=== Mar. 29 ===
  
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[https://www.molecularecologist.com/2015/12/comparing-your-options-for-phylogenomic-data/ Molecular Ecologist has multiple posts on Next-Gen methods]
 
  
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[https://www.taylorfrancis.com/books/9781482235357 Phylogenomic Data Acquisition (Jennings 2016)]
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=== Apr. 5  ===
  
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=== Nov. 23 ===
 
  
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'''THANKSGIVING BREAK! WOO!'''
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=== Apr. 12 ===
  
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=== Nov. 30 ===
 
  
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====Grab bag of Next-Gen methods for phylogenetics (continued):====
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=== Apr. 19 ===
  
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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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Diler [https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12905 Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms]
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=== Apr. 26 ===
  
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Katie [https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12785 HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA]
 
  
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=== Dec. 7 ===
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=== May 5 ===
  
 
== Information for discussion leaders ==
 
== Information for discussion leaders ==

Revision as of 19:34, 30 January 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 at 2 PM in TBD.

Theme and Schedule for Fall 2018

TBD

Jan. 25

(no meeting)

Feb. 1

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

Feb. 8

Feb. 15

Feb. 22

Mar. 1

Mar. 8

Mar. 15

Mar. 22

Mar. 29

Apr. 5

Apr. 12

Apr. 19

Apr. 26

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

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