Difference between revisions of "Systematics Seminar"
From EEBedia
| Line 4: | Line 4: | ||
== Meeting time and place == | == Meeting time and place == | ||
| − | + | We are meeting this semester in the Bamford Room (TLS 171) '''Fridays from 2-3pm'''. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays. | |
== Theme for Spring Semester 2008 == | == Theme for Spring Semester 2008 == | ||
| − | + | The theme this semester is '''Tree Thinking'''. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these: | |
* can you ever say that a clade is basal? | * can you ever say that a clade is basal? | ||
* do non-uniform clade priors make sense? | * do non-uniform clade priors make sense? | ||
| Line 22: | Line 22: | ||
Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''. | Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word ''basal''. | ||
| − | :'''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/ | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Crisp_Cook_2005_TREE_20_122-128.pdf}} '''Crisp, M. D., and L. G. Cook'''. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149. |
| − | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Krell_Cranston_2004_SystEntomol_29_279-281.pdf}} '''Krell, F.-T., and P. S. Cranston'''. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281. | |
| − | === | + | === Friday, February 1, 2008 === |
| − | Discussion leader: | + | Discussion leader: Frank Smith |
| + | |||
| + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/deQueiroz_2007_SystBiol_56_956-974.pdf}} '''de Queiroz, K.''' 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974. | ||
| + | |||
| + | de Queiroz considers how to define names for clades, and discusses tree terms such as ''crown group'', ''stem lineage'', etc. | ||
| − | === | + | === Friday, February 8, 2008 === |
Discussion leader: | Discussion leader: | ||
Change meeting time (EEB Dept. Seminar conflicts)? | Change meeting time (EEB Dept. Seminar conflicts)? | ||
| − | === | + | === Friday, February 15, 2008 === |
Discussion leader: | Discussion leader: | ||
Change meeting time (EEB Dept. Seminar conflicts)? | Change meeting time (EEB Dept. Seminar conflicts)? | ||
| − | === | + | === Friday, February 22, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, February 26, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, February 29, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, March 7, 2008 === |
No meeting (Spring Break) | No meeting (Spring Break) | ||
| − | === | + | === Friday, March 14, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, March 21, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, March 28, 2008 === |
| − | + | ||
| − | + | ||
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, April 4, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, April 11, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, April 18, 2008 === |
Discussion leader: | Discussion leader: | ||
| − | === | + | === Friday, April 25, 2008 === |
Discussion leader: | Discussion leader: | ||
| Line 76: | Line 78: | ||
=== Tree terms === | === Tree terms === | ||
| − | Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Wilkinson_McInerney_Hirt_Foster_Embley_2007_TREE_22_114-115.pdf}} '''Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley'''. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22:114-115. |
| − | + | ||
=== Necessity of unequal split priors: undesirable? === | === Necessity of unequal split priors: undesirable? === | ||
| Line 83: | Line 84: | ||
The Velasco response in combination with one of the other two would make for an interesting discussion. | The Velasco response in combination with one of the other two would make for an interesting discussion. | ||
| − | : | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Pickett_Randle_2005_MPE_203-211.pdf}} '''Pickett. K. M., and C. P. Randle'''. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211. |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Steel_Pickett_2006_MPE_39_585-586.pdf}} '''Steel, M., and K. M. Pickett'''. 2006. On the impossibility of uniform priors on clades MPE 39:585-586. | |
| − | : | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Velasco_2007_MPE_45_748-749.pdf}} '''Velasco, J. D.''' 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749. |
=== Using fossils in dating lineages === | === Using fossils in dating lineages === | ||
| Line 99: | Line 94: | ||
Among other things, this paper explains why fossils cannot indicate actual branching dates. | Among other things, this paper explains why fossils cannot indicate actual branching dates. | ||
| − | :Donoghue, P. C. J., and M. J. Benton. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431 | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Donoghue_Benton_2007_TREE_22_389-440.pdf}} Donoghue, P. C. J., and M. J. Benton. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431. |
=== Signature of adaptive radiations === | === Signature of adaptive radiations === | ||
| Line 105: | Line 100: | ||
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic. | Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic. | ||
| − | : | + | :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Whitfield_Lockhart_2007_TREE_22_258-265.pdf}} Whitfield, J. B., and P. J. Lockhart. 2007. Deciphering ancient rapid radiations. TREE 22:258-265. |
[[#top|Back to top]] | [[#top|Back to top]] | ||
Revision as of 19:55, 24 January 2008
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.
Click here for information about joining and using the Systematics email list
Meeting time and place
We are meeting this semester in the Bamford Room (TLS 171) Fridays from 2-3pm. Let's try to get started on time, as another group is meeting in the Bamford Room starting at 3pm on Fridays.
Theme for Spring Semester 2008
The theme this semester is Tree Thinking. David Baum (Univ. Wisconsin, Madison) is writing a book on Tree Thinking and has agreed to let us read the chapters he has written in return for some constructive criticism. Baum's book will be supplemented with some thought-provoking and heated-debate-generating papers on subjects such as these:
- can you ever say that a clade is basal?
- do non-uniform clade priors make sense?
- what can and can't fossils say about node age
- when gene trees and species trees are both right, but different
- the signature of an adaptive radiation
Some suggested papers are listed below the schedule in the section entitled Some possibilities.
Schedule for Spring Semester 2008
Note: the papers linked here require a user name and password to access. If you have forgotten the user name and/or password, contact Paul Lewis.
Tuesday, January 22, 2008: Basal clades
Discussion leader: Paul Lewis
Two of our Tuesday time slots this semester will be taken over by departmental seminars, so rather than waste the first time slot with an organizational meeting, let's get right into things with a consideration of the meaning of the word basal.
Crisp, M. D., and L. G. Cook. 2005. Do early branching lineages signify ancestral traits? TREE 20(3):105-149.- Krell, F.-T., and P. S. Cranston. 2004. Which side of the tree is more basal? Systematic Entomology 29:279-281.
Friday, February 1, 2008
Discussion leader: Frank Smith
- de Queiroz, K. 2007. Toward an integrated system of clade names. Syst. Biol. 56:956-974.
de Queiroz considers how to define names for clades, and discusses tree terms such as crown group, stem lineage, etc.
Friday, February 8, 2008
Discussion leader: Change meeting time (EEB Dept. Seminar conflicts)?
Friday, February 15, 2008
Discussion leader: Change meeting time (EEB Dept. Seminar conflicts)?
Friday, February 22, 2008
Discussion leader:
Friday, February 26, 2008
Discussion leader:
Friday, February 29, 2008
Discussion leader:
Friday, March 7, 2008
No meeting (Spring Break)
Friday, March 14, 2008
Discussion leader:
Friday, March 21, 2008
Discussion leader:
Friday, March 28, 2008
Discussion leader:
Friday, April 4, 2008
Discussion leader:
Friday, April 11, 2008
Discussion leader:
Friday, April 18, 2008
Discussion leader:
Friday, April 25, 2008
Discussion leader:
Some possibilities
Feel free to expand this list, and there is of course no requirement that papers for discussion be chosen from this list. To upload a PDF (and receive a free email describing how to make a link to it here), click this link to the upload form. You will need to know the username and password to upload a PDF (same combination needed to download PDFs from this web site).
Tree terms
- Wilkinson, M., J. O. McInerney, R. P. Hirt, P. G. Foster and T. M. Embley. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. TREE 22:114-115.
Necessity of unequal split priors: undesirable?
The Velasco response in combination with one of the other two would make for an interesting discussion.
- Pickett. K. M., and C. P. Randle. 2005. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. MPE 34: 203-211.
- Steel, M., and K. M. Pickett. 2006. On the impossibility of uniform priors on clades MPE 39:585-586.
- Velasco, J. D. 2007. Why non-uniform priors on clades are both unavoidable and unobjectionable. MPE 45:748-749.
Using fossils in dating lineages
Among other things, this paper explains why fossils cannot indicate actual branching dates.
- Donoghue, P. C. J., and M. J. Benton. 2007. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. TREE 22:424-431.
Signature of adaptive radiations
Discusses problems (lineage sorting) associated with, and methods for dealing with, adaptive radiations. May be too far from the topic.
- Whitfield, J. B., and P. J. Lockhart. 2007. Deciphering ancient rapid radiations. TREE 22:258-265.
