Difference between revisions of "Seminar in Comparative Biology"

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[[Image:ComparativeMethod.png|200px|right]]Fall 2007 Instructor of Record: [mailto:schlicht@uconn.edu Carl Schlichting]
+
[[Image:ComparativeMethod.png|200px|right]]Spring 2018 Instructor of Record: [mailto:schlicht@uconn.edu Carl Schlichting]
  
This is the home page of the UConn EEB department's Seminar in Comparative Biology. This (Fall 2007) semester, we are meeting each '''Monday''' at '''11:30am''' in the [[Bamford Conference Room]] in the [[Torrey Life Science]] building.
+
This is the home page of the UConn EEB department's Seminar in Comparative Biology on '''The Evolution of Phenotypic Plasticity'''. This (Spring 2018) semester, we are meeting each '''Wednesday''' at '''10:00am''' in the [[Bamford Conference Room]] in the [[Torrey Life Science]] building.
  
== Possible papers for discussion ==
+
== Possible topics for discussion ==
 +
Maladaptive plasticity
  
A separate EEBedia page, [[Comparative Biology Papers]], has been created for listing possible papers for discussion. Feel free to add to it!
+
Genetic assimilation/accommodation
  
== Schedule for Fall Semester 2007 ==
+
Costs of Plasticity
  
The papers for discussion are available as PDF files, but to keep us from getting into hot water with the journals involved, a '''username''' and '''password''' are required for access. If you have forgotten the username/password, please contact [http://hydrodictyon.eeb.uconn.edu/eebwww/people/person.php?uniqueID=plewis Paul Lewis].
+
Transgenerational plasticity & epigenetic marking
  
Note: in addition to this web site, we will be using the Systematics Listserv for communication because this seminar is taking the place of the [[Systematics Seminar]] this semester.
+
Genetic control of plastic responses
  
[[Systematics Listserv|Click here for information about joining and using the Systematics email list]]
+
Integration of plastic responses
  
To upload a pdf use [http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/upload.html this form] (username/password required)
+
Hidden reaction norms/cryptic genetic variation
  
=== August 29, 2007 ===
+
:Organizational meeting, Bamford Conference Room, 4pm
+
  
=== September 10, 2007 ===
+
== Schedule ==
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Felsenstein_1985_AmNat_125_1-15.pdf}} Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/FelsensteinContrasts.pdf}}  Paul's notes explaining Felsenstein's paper in greater detail for those interested. The original has been updated to reflect some suggestions made by Eric Schultz and an explanation of why branch lengths should be lengthened to accommodate uncertainty in character values at interior nodes of the tree.
+
The papers for discussion are available either online (through the library or journals) or as a pdf in the UConn Dropbox if not available online
  
=== September 17, 2007 ===
+
=== January 24, 2018 ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Westoby_Harvey_etal.pdf}} The following eight papers have been bundled into one PDF:
+
:Organizational meeting, Bamford Conference Room, 10am
  
:Westoby, M., M. R. Leishman and J. M. Lord. 1995. On misinterpreting the 'phylogenetic correction'. ''Journal of Ecology'' 83: 531-534.
+
=== January 31, 2018  ===
 +
:'''Costs of Plasticity''',  Annette Evans
 +
Reading for discussion:
 +
[http://dx.doi.org/10.1016/S0169-5347(97)01274-3 DeWitta et al 1998, Costs and Limits of Phenotypic Plasticity]
  
:Harvey, P.H., A. F. Read and S. Nee. 1995. Why ecologists need to be phylogenetically challenged. ''Journal of Ecology'' 83: 535-536.
+
Optional 2nd reading:  
 +
[http://dx.doi.org/10.1038/hdy.2015.8 Murren et al 2015 Contraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity]
  
:Westoby, M., M. R. Leishman and J. M. Lord. 1995. Further remarks on phylogenetic correction. ''Journal of Ecology'' 83: 727-730.
+
=== February 7, 2018  ===
 +
:'''Costs of Plasticity''',    Carl Schlichting
 +
''Readings for discussion'':
  
:Fitter, A. H. 1995. Interpreting quantitative and qualitative characteristics in comparative analyses. ''Journal of Ecology'' 83: 730.
+
[http://dx.doi.org/10.1038/hdy.2015.8 Murren et al 2015 Contraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity]
  
:Ackerly, D. D. and M. J. Donoghue. 1995. Phylogeny and ecology reconsidered. ''Journal of Ecology'' 83: 730-733.
+
[http://www.genetics.org/content/177/2/937 Maughan et al 2007 The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis]
  
:Harvey, P.H., A. F. Read and S. Nee. 1995. Further remarks on the role of phylogeny in comparative ecology. ''Journal of Ecology'' 83: 733-734.
 
  
:Rees, M. 1995. EC-PC comparative analyses? ''Journal of Ecology'' 83: 891-892.   
+
''To discuss during seminar'':
  
:Westoby, M., M. R. Leishman and J. M. Lord. 1995. Issues of interpretation after relating comparative datasets to phylogeny. ''Journal of Ecology'' 83: 892-893.  
+
Schlichting, C. D., J. R. Auld, H. S. Callahan, C. K. Ghalambor, C. A. Handelsman, M. A. Heskel, . . . C. J. Murren. unpub. Detecting Costs of Phenotypic Plasticity.
 +
[https://dropbox.uconn.edu/dropbox?n=Schlichting%20et%20al%20Detecting%20costs%20of%20plasticity.docx&p=LR5G3WlhVqjvd4Yjq]
  
=== September 24, 2007 ===
+
=== February 14, 2018  ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/garlandetal1992.pdf}} Garland, T. Jr., P. H. Harvey, A. R. Ives.  1992.  Procedures for the analysis of comparative data using phylogenetically independent contrasts.  Systematic Biology 41: 18-32.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/EEB485refs.pdf}} Some additional references suggested by Jones, Schultz and Schlichting
+
:'''Epigenetics and Plasticity''',  Lauren Stanley
  
=== October 1, 2007 ===
+
Readings:  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Caro_etal.pdf}}Caro, T. M., C. M. Graham, C. J. Stoner, and M. M. Flores. 2003. Correlates of horn and antler shape in bovids and cervids. Behav. Ecol. Sociobiol. 55:32-41.
+
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/PDTREE_Mesquite-1.pdf}} PDTREE_Mesquite-1.pdf
+
1. [http://onlinelibrary.wiley.com/doi/10.1111/mec.14213/full Hales et al. 2017 Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia]
  
=== October 8, 2007 ===
+
2. [http://onlinelibrary.wiley.com/doi/10.1111/nph.14495/full Auge et al. 2017 Adjusting phenotypes via within- and across-generational plasticity]
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Cavender-Bares%202004%20AmNat.pdf}} Cavender-Bares, J., D. D. Ackerly, D. A. Baum, and F. A. Bazzaz. 2004 American Naturalist 163(6): 823-843.
+
  
=== October 15, 2007 ===
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Phillimore%20et%20al%20Am%20Nat%2006.pdf}}  Phillimore, A. B., R. P. Freckleton, C. D. L. Orme and I. P. F. Owens. 2006. Ecology predicts large-scale patterns of phylogenetic diversification in birds. American Naturalist 168: 220-229.
 
  
=== October 22, 2007 ===
+
=== February 21, 2018  ===
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/Hulsey%20et%20al%20PRSB%2007.pdf}} Hulsey, C. D., M. C. Mims and J. T. Streelman. 2007. Do constructional constraints influence cichlid craniofacial diversification? Proceedings of the Royal Society London B 274: 1867-1875.
+
 
 +
:'''Maladaptive Plasticity''', Eileen Schaub
 +
 
 +
1. [http://dx.doi.org/10.1038/nature15256 Ghalambor et al 2015 Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature]
 +
 
 +
2. [https://link.springer.com/content/pdf/10.1051/forest:2008004.pdf Sánchez-Gómez 2007 Functional traits and plasticity linked to seedlings’ performance under shade and drought in Mediterranean woody species]
 +
 
 +
 
 +
=== March 21, 2018  ===
 +
:'''Hidden Reaction Norms and Cryptic Genetic Variation'''  -  Chris Nadeau
 +
 
 +
''Background Readings'':
 +
 
 +
1. [http://onlinelibrary.wiley.com/doi/10.1196/annals.1438.010/abstract Schlichting. 2008. Hidden reaction norms, cryptic genetic variation, and evolvability]
 +
 
 +
2. [https://www.sciencedirect.com/science/article/pii/S0169534710001059 Pfenning et al. 2010. Phenotypic plasticity's impacts on diversification and speciation]
 +
 
 +
''Reading for Discussion'':
 +
 
 +
1. [http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01195.x/full McGuigan et al. 2010. Cryptic genetic variation and body size evolution in threespine stickleback]
 +
 
 +
 
 +
=== March 28, 2018  ===
 +
 
 +
:'''Plasticity's Role in Adaptation to New Environments: A Look into Climate Change''',  Tanisha Williams
 +
 
 +
''Background Readings'':
 +
 
 +
1. [https://ac.els-cdn.com/S1360138510001986/1-s2.0-S1360138510001986-main.pdf?_tid=fd5845fd-2a98-40b8-9838-60f40be69491&acdnat=1520006246_6c2e0d291d432482aea3ea10baa1aa07 Nicotra et al. 2010 Plant phenotypic plasticity in a changing climate] 
 +
 
 +
2. [http://onlinelibrary.wiley.com/doi/10.1111/eva.12137/epdf Merilä and Hendry 2013 Climate change, adaptation, and phenotypic plasticity: the problem and the evidence]
 +
 
 +
 
 +
''Reading for Discussion'':
 +
 
 +
1. [http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12762/epdf Münzbergová et al. 2017 Genetic differentiation and plasticity interact along temperature and precipitation gradients to determine plant performance under climate change]
 +
 
 +
 
 +
=== April 4, 2018  ===
 +
 
 +
:'''Plasticity and Evolution of Trait Integration/Covariation'''  -  Kristen Nolting
 +
 
 +
''Reading for Discussion'':
 +
 
 +
[https://onlinelibrary.wiley.com/doi/epdf/10.1111/jeb.12839 Plasticity and evolution in correlated suites of traits ]
 +
 
 +
 
 +
=== April 11, 2018  ===
 +
 
 +
 
 +
=== April 18, 2018  ===
 +
:'''Evolution of phenotypic plasticity in extreme environments'''  -  Austin Spence
 +
 
 +
''Reading for Discussion'':
 +
 
 +
[http://rstb.royalsocietypublishing.org/content/372/1723/20160138 Evolution of phenotypic plasticity in extreme environments ]
 +
 
 +
 
 +
=== April 25, 2018  ===
 +
 
 +
:'''Empirical field experiments of phenotypic responses to climate change''' - Sam Apgar
 +
 
 +
''Reading for Discussion'':
 +
 
 +
http://science.sciencemag.org/content/sci/320/5877/800.full.pdf
 +
 
 +
''Background Reading'':
 +
 
 +
https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.12112
 +
 
 +
 
 +
===, 2018 ===
 +
:'''Plasticity & Microenvironment''',   Timothy Moore, James Mickley
 +
 
 +
 
 +
== Information for discussion leaders ==
 +
'''Seminar Format:''' Registered students will 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 shutting down 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 Plasticity seminar list letting everyone know that a paper is available.
 +
 
 +
'''Introductory Presentation:''' Introduce your topic with a 10- to 15-minute presentation (Powerpoint or Keynote encouraged).  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 "Expectations" at https://elphick.lab.uconn.edu/eeb-5370-current-topics-in-conservation-biology/.   Prepare several 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.
 +
 
  
=== October 29, 2007 ===
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematicsseminar/restricted/for_29_October.pdf}}  Preparing for 29 October session.
 
 
__NOEDITSECTION__
 
__NOEDITSECTION__
  
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Latest revision as of 22:07, 22 April 2018

ComparativeMethod.png
Spring 2018 Instructor of Record: Carl Schlichting

This is the home page of the UConn EEB department's Seminar in Comparative Biology on The Evolution of Phenotypic Plasticity. This (Spring 2018) semester, we are meeting each Wednesday at 10:00am in the Bamford Conference Room in the Torrey Life Science building.

Possible topics for discussion

Maladaptive plasticity

Genetic assimilation/accommodation

Costs of Plasticity

Transgenerational plasticity & epigenetic marking

Genetic control of plastic responses

Integration of plastic responses

Hidden reaction norms/cryptic genetic variation

Schedule

The papers for discussion are available either online (through the library or journals) or as a pdf in the UConn Dropbox if not available online

January 24, 2018

Organizational meeting, Bamford Conference Room, 10am

January 31, 2018

Costs of Plasticity, Annette Evans

Reading for discussion: DeWitta et al 1998, Costs and Limits of Phenotypic Plasticity

Optional 2nd reading: Murren et al 2015 Contraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

February 7, 2018

Costs of Plasticity, Carl Schlichting

Readings for discussion:

Murren et al 2015 Contraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

Maughan et al 2007 The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis


To discuss during seminar:

Schlichting, C. D., J. R. Auld, H. S. Callahan, C. K. Ghalambor, C. A. Handelsman, M. A. Heskel, . . . C. J. Murren. unpub. Detecting Costs of Phenotypic Plasticity. [1]

February 14, 2018

Epigenetics and Plasticity, Lauren Stanley

Readings:

1. Hales et al. 2017 Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia

2. Auge et al. 2017 Adjusting phenotypes via within- and across-generational plasticity


February 21, 2018

Maladaptive Plasticity, Eileen Schaub

1. Ghalambor et al 2015 Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature

2. Sánchez-Gómez 2007 Functional traits and plasticity linked to seedlings’ performance under shade and drought in Mediterranean woody species


March 21, 2018

Hidden Reaction Norms and Cryptic Genetic Variation - Chris Nadeau

Background Readings:

1. Schlichting. 2008. Hidden reaction norms, cryptic genetic variation, and evolvability

2. Pfenning et al. 2010. Phenotypic plasticity's impacts on diversification and speciation

Reading for Discussion:

1. McGuigan et al. 2010. Cryptic genetic variation and body size evolution in threespine stickleback


March 28, 2018

Plasticity's Role in Adaptation to New Environments: A Look into Climate Change, Tanisha Williams

Background Readings:

1. Nicotra et al. 2010 Plant phenotypic plasticity in a changing climate

2. Merilä and Hendry 2013 Climate change, adaptation, and phenotypic plasticity: the problem and the evidence


Reading for Discussion:

1. Münzbergová et al. 2017 Genetic differentiation and plasticity interact along temperature and precipitation gradients to determine plant performance under climate change


April 4, 2018

Plasticity and Evolution of Trait Integration/Covariation - Kristen Nolting

Reading for Discussion:

Plasticity and evolution in correlated suites of traits


April 11, 2018

April 18, 2018

Evolution of phenotypic plasticity in extreme environments - Austin Spence

Reading for Discussion:

Evolution of phenotypic plasticity in extreme environments


April 25, 2018

Empirical field experiments of phenotypic responses to climate change - Sam Apgar

Reading for Discussion:

http://science.sciencemag.org/content/sci/320/5877/800.full.pdf

Background Reading:

https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.12112


, 2018

Plasticity & Microenvironment, Timothy Moore, James Mickley


Information for discussion leaders

Seminar Format: Registered students will 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 shutting down 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 Plasticity seminar list letting everyone know that a paper is available.

Introductory Presentation: Introduce your topic with a 10- to 15-minute presentation (Powerpoint or Keynote encouraged). 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 "Expectations" at https://elphick.lab.uconn.edu/eeb-5370-current-topics-in-conservation-biology/. Prepare several 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.