Difference between revisions of "Systematics Seminar"
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| − | This is the home page of the UConn EEB department's Systematics Seminar. 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. | + | 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. |
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]] | [[Systematics Listserv|Click here for information about joining and using the Systematics email list]] | ||
== 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 === |
| − | + | At this meeting we will discuss possible themes for this semester's seminar: | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | == | + | === Monday, 2 September 2013 === |
| − | + | Labor Day, no meeting | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | === | + | === Monday, 9 September 2013 === |
| + | Elizabeth Jockusch will lead the discussion this week. | ||
| − | + | We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment. | |
| − | + | <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 === |
| − | + | 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: |
| + | :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] | ||
| + | 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 === |
| + | 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] | |
| − | + | :Paul's handout on calculating internode certainty measure [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/internode-certainty.pdf link] | |
| − | + | ||
| − | === | + | === Monday, 30 September 2013 === |
| + | 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 | ||
| − | === | + | === Monday, 07 October 2013 === |
| + | Veronica Bueno will lead the discussion this week. | ||
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Fujisawa%2C%20Barraclough_2013_Delimiting%20Species%20Using%20Single-Locus%20Data%20and%20the%20Generalized%20Mixed%20Yule%20Coalescent%20Approach%20A%20Revised%20Metho.pdf}}Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf | ||
| − | === | + | === Monday, 14 October 2013 === |
| − | + | Paul Lewis will lead the discussion. | |
| − | + | Main paper for discussion: | |
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Proceedings%20of%20the%20National%20Academy%20of%20Sciences%202010%20Yang.pdf}} Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269. | ||
| − | + | Optional followup paper describing improvements in technical details: | |
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Genetics%202013%20Rannala.pdf}} Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253. | ||
| − | === | + | === Monday, 21 October 2013 === |
| + | Simona Augyte will lead the discussion this week. | ||
| − | === | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Syst%20Biol-2012-Moalic-127-37.pdf}}Syst Biol-2012-Moalic-127-37.pdf |
| + | |||
| + | === Monday, 28 October 2013 === | ||
| + | Paul Lewis will lead the discussion this week. | ||
| + | |||
| + | :[http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/62/1/50.full.pdf link] Goremykin et al. 2013. The evolutionary root of flowering plants. Systematic Biology 62(1): 50-61 | ||
| + | |||
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/gorymykin_etal_2013_systbiol_62_50-61.key.pdf}} Paul's handout | ||
| + | |||
| + | === Monday, 4 November 2013 === | ||
| + | There are two things to do to prepare for this week: | ||
| + | <ul> | ||
| + | <li> Come up with an example of speciation that does not follow the classic bifurcating tree structure.</li> | ||
| + | <li>Read this article <br> | ||
| + | [http://ezproxy.lib.uconn.edu/login?url=http://sysbio.oxfordjournals.org/content/62/3/479.long link] Mindell, D. 2013. The Tree of Life: Metaphor, Model, and Heuristic Device. Syst. Biol. 62:479-489.</li> | ||
| + | </ul> | ||
| + | |||
| + | === Monday, 11 November 2013 === | ||
| + | Paper for this week: | ||
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/SystematicBiology2013-Leache.pdf}} Leaché A.D., Harris R.B., Rannala B., Yang Z. 2013. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology. doi:10.1093/sysbio/syt049 (Advance Access, August 13, 2013) | ||
| + | |||
| + | === Monday, 18 November 2013 === | ||
| + | Veronica Bueno will lead the discussion this week. Zhang et al., 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. doi:10.1093/bioinformatics/btt499 | ||
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Bioinformatics-2013-Zhang-2869-76.pdf}}Bioinformatics-2013-Zhang-2869-76.pdf | ||
| + | |||
| + | === Monday, 2 December 2013=== | ||
| + | Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading. <br> | ||
| + | {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/BIN%20paper.pdf}}A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System <br> | ||
| + | {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/geography_barcoding.pdf}}The Effect of Geographical Scale of Sampling on DNA Barcoding | ||
== Past Systematics Seminars == | == Past Systematics Seminars == | ||
| + | * [[Systematics Seminar Spring 2012|Spring 2012]] | ||
| + | * [[Systematics Seminar Fall 2011|Fall 2011]] | ||
| + | * [http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography Spring 2011] (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester) | ||
| + | * [[Systematics Seminar Fall 2010|Fall 2010]] | ||
| + | * [[Systematics Seminar Spring 2010|Spring 2010]] | ||
| + | * [[Systematics Seminar Fall 2009|Fall 2009]] | ||
| + | * [[Systematics Seminar Fall 2008|Fall 2008]] | ||
| + | * [[Systematics Seminar Spring 2008|Spring 2008]] | ||
* [[Systematics Seminar Fall 2007|Fall 2007]] | * [[Systematics Seminar Fall 2007|Fall 2007]] | ||
* [[Systematics Seminar Spring 2007|Spring 2007]] | * [[Systematics Seminar Spring 2007|Spring 2007]] | ||
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* [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004] | * [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/SystSemFall2004.html Fall 2004] | ||
* [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004] | * [http://hydrodictyon.eeb.uconn.edu/courses/phylomath/ Spring 2004] | ||
| − | |||
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| − | |||
[[Category:EEB Seminars]] | [[Category:EEB Seminars]] | ||
Revision as of 18:37, 28 November 2013
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
Contents
- 1 Meeting time and place
- 1.1 Monday, 26 August 2013
- 1.2 Monday, 2 September 2013
- 1.3 Monday, 9 September 2013
- 1.4 Monday, 16 September 2013
- 1.5 Monday, 23 September 2013
- 1.6 Monday, 30 September 2013
- 1.7 Monday, 07 October 2013
- 1.8 Monday, 14 October 2013
- 1.9 Monday, 21 October 2013
- 1.10 Monday, 28 October 2013
- 1.11 Monday, 4 November 2013
- 1.12 Monday, 11 November 2013
- 1.13 Monday, 18 November 2013
- 1.14 Monday, 2 December 2013
- 2 Past Systematics Seminars
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
At this meeting we will discuss possible themes for this semester's seminar:
Monday, 2 September 2013
Labor Day, no meeting
Monday, 9 September 2013
Elizabeth Jockusch will lead the discussion this week.
We will follow up on Emily Lemmon's visit by discussing her methods paper on anchored enrichment.
- Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61(5):727-44. link
Monday, 16 September 2013
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:
- 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 link
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 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. 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 link
Monday, 23 September 2013
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. link
- Paul's handout on calculating internode certainty measure link
Monday, 30 September 2013
Brigette Zacharczenko will lead the discussion this week.
- Adams, 2013. Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood
Link
Monday, 07 October 2013
Veronica Bueno will lead the discussion this week.
- Fujisawa, Barraclough_2013_Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach A Revised Metho.pdf
Monday, 14 October 2013
Paul Lewis will lead the discussion.
Main paper for discussion:
- Yang Z., and Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 107:9264–9269.
Optional followup paper describing improvements in technical details:
- Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194:245–253.
Monday, 21 October 2013
Simona Augyte will lead the discussion this week.
- Syst Biol-2012-Moalic-127-37.pdf
Monday, 28 October 2013
Paul Lewis will lead the discussion this week.
- link Goremykin et al. 2013. The evolutionary root of flowering plants. Systematic Biology 62(1): 50-61
- Paul's handout
Monday, 4 November 2013
There are two things to do to prepare for this week:
- Come up with an example of speciation that does not follow the classic bifurcating tree structure.
- Read this article
link Mindell, D. 2013. The Tree of Life: Metaphor, Model, and Heuristic Device. Syst. Biol. 62:479-489.
Monday, 11 November 2013
Paper for this week:
- Leaché A.D., Harris R.B., Rannala B., Yang Z. 2013. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology. doi:10.1093/sysbio/syt049 (Advance Access, August 13, 2013)
Monday, 18 November 2013
Veronica Bueno will lead the discussion this week. Zhang et al., 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. doi:10.1093/bioinformatics/btt499
- Bioinformatics-2013-Zhang-2869-76.pdf
Monday, 2 December 2013
Brigette and Dave will lead the discussion this week on DNA barcoding. The second paper is optional reading.
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
The Effect of Geographical Scale of Sampling on DNA Barcoding
Past Systematics Seminars
- Spring 2012
- Fall 2011
- Spring 2011 (we joined Kent Holsinger's seminar on Statistical Phylogeography this semester)
- Fall 2010
- Spring 2010
- Fall 2009
- Fall 2008
- Spring 2008
- Fall 2007
- Spring 2007
- Fall 2006
- Spring 2005
- Fall 2004
- Spring 2004
