Difference between revisions of "Systematics Seminar"

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== Meeting time and place ==
 
== Meeting time and place ==
For the Fall 2013 semester, we are meeting in the '''Bamford Room (TLS 171B) Mondays 2-3pm'''
 
  
=== Monday, 26 August 2013 ===
+
We meet at 11:05 in the Bamford Room (TLS 171B)
At this meeting we will discuss possible themes for this semester's seminar:
+
  
=== Monday, 2 September 2013 ===
+
== Theme and Schedule for Fall 2018 ==
Labor Day, no meeting
+
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!
  
=== Monday, 9 September 2013 ===
+
=== Aug. 31 ===
Elizabeth Jockusch will lead the discussion this week.
+
Planning meeting (no readings)
  
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.
+
=== Sep. 7 ===
<ul>
+
<li>Lemmon AR, Emme SA, Lemmon EM. 2012.  Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. [http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/61/5/727.long link]</li>
+
</ul>
+
  
=== Monday, 16 September 2013 ===
+
Conflicts between the results of morphological and molecular datasets in squamate reptiles.
Lily Lewis will lead the discussion this week
+
  
Since cichlids came up last week, it may be fun to read a cichlid RAD-seq paper:
+
Paper and supplemental files:
:Wagner et al. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology 22(3):787-798 [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12023/full link]
+
https://dropbox.uconn.edu/dropbox?n=PhylogIguniaRootProblem18.zip&p=Wzhn6V64Bz4T9W7qH
Here is a link to a supplementary paper folks may be interested in for an overview of the applications of RAD-sequencing (or at least those conceived of thus far):
+
:Davey, J. W., and M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9(5-6):416-423 [http://ezproxy.lib.uconn.edu/login?url=http://bfg.oxfordjournals.org/content/9/5-6/416 link]
+
Here is a link to a protocol for RAD-seq library prep, just in case anyone is interested:
+
:Etter, P. Sequenced RAD markers for rapid SNP disovery and genetic mapping. [http://ezproxy.lib.uconn.edu/login?url=https://www.wiki.ed.ac.uk/download/attachments/68630442/sequenced+RAD-Tag+protocol-version+2.doc?version=1 link]
+
Finally, here is a PowerPoint concatenation of a few figures from various papers laying out how the RAD-seq process works. This may be a helpful supplement for understanding the methods in the cichlid paper [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/RAD-seq_Compiled-Figues.ppt link]
+
  
=== Monday, 23 September 2013 ===
+
Discussion led by Jack Phillips
Paul Lewis will lead the discussion this week.
+
  
:Salichos L., and Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497:327–331. [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SalichosRokas2013.pdf link]
+
jackson.phillips@uconn.edu
  
:Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link]
+
=== Sep. 14 ===
  
=== Monday, 30 September 2013 ===
+
Diler and Eric discuss [https://doi.org/10.1093/sysbio/syy019 The Biogeography of Deep Time Reticulation]
Brigette Zacharczenko will lead the discussion this week.<br>
+
:Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2013-Adams-181-92.pdf}}Link
+
  
== Past Systematics Seminars ==
+
=== Sep. 21 ===
 +
 
 +
Diler discusses [https://doi.org/10.1371/journal.pgen.1005896 Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting]
 +
 
 +
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.
 +
 
 +
=== Sep. 28  ===
 +
 
 +
Katie discusses [https://doi.org/10.1093/sysbio/syy023 HyDe: A Python Package for Genome-Scale Hybridization Detection]
 +
 
 +
=== Oct. 5 ===
 +
 
 +
Kevin discusses [https://doi.org/10.1093/sysbio/syy046 Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors]
 +
 
 +
=== Oct. 12 ===
 +
 
 +
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]
 +
 
 +
=== Oct. 19 ===
 +
 
 +
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 [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171053] GBS  Genotyping-by-sequencing.
 +
 
 +
Kevin [https://doi.org/10.1093/sysbio/sys049 Anchored hybrid enrichment for massively high-throughput phylogenomics]
 +
 
 +
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]
 +
 
 +
Dave [https://doi.org/10.1093/sysbio/sys004 Ultraconserved elements anchor thousandsof genetic markers spanning multiple evolutionary timescales]
 +
 
 +
====Further Reading====
 +
 
 +
[https://www.molecularecologist.com/2015/12/comparing-your-options-for-phylogenomic-data/ Molecular Ecologist has multiple posts on Next-Gen methods]
 +
 
 +
[https://www.taylorfrancis.com/books/9781482235357 Phylogenomic Data Acquisition (Jennings 2016)]
 +
 
 +
=== Nov. 23 ===
 +
 
 +
'''THANKSGIVING BREAK! WOO!'''
 +
 
 +
=== Nov. 30 ===
 +
 
 +
====Grab bag of Next-Gen methods for phylogenetics (continued):====
 +
 
 +
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]
 +
 
 +
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]
 +
 
 +
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]
 +
 
 +
=== 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 Spring 2012|Spring 2012]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]
 
* [[Systematics Seminar Fall 2011|Fall 2011]]

Latest revision as of 14:44, 30 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 [1] GBS Genotyping-by-sequencing.

Kevin Anchored hybrid enrichment for massively high-throughput phylogenomics

Tanner Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits

Dave Ultraconserved elements anchor thousandsof genetic markers spanning multiple evolutionary timescales

Further Reading

Molecular Ecologist has multiple posts on Next-Gen methods

Phylogenomic Data Acquisition (Jennings 2016)

Nov. 23

THANKSGIVING BREAK! WOO!

Nov. 30

Grab bag of Next-Gen methods for phylogenetics (continued):

Elizabeth RADcap: sequence capture of dual‐digest RADseq libraries

Eric HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

Diler Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms

Katie HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA

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