Principles and Methods of Systematic Biology (EEB 5347)

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[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]
 
[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]
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[[Image:AMNH2011_roof.jpg|right|''2011 Class on top of the AMNH'']]
 +
 
<span style="font-size: large">Fall 2011<br/>
 
<span style="font-size: large">Fall 2011<br/>
  
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!style="background:#00B7EB;" width="275"|Lab
 
!style="background:#00B7EB;" width="275"|Lab
 
|-  
 
|-  
| Aug 29 ||Class canceled due to hurricane Irene<br/><!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Rules%20of%20Pronunciation%20Sci.%20Name.PDF}}Rules of Pronunciation Sci.Name.pdf-->
+
| Aug 29 ||Class canceled due to Hurricane Irene<br/><!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Rules%20of%20Pronunciation%20Sci.%20Name.PDF}}Rules of Pronunciation Sci.Name.pdf-->
 
|| || rowspan="3"| Lecture instead of lab this week
 
|| || rowspan="3"| Lecture instead of lab this week
 
|-
 
|-
| Aug 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)
+
| Aug 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional)
 
|-
 
|-
| Sept 2 ||The many roles of biological systematics & collections tour<!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||<!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf-->
+
| Sept 2 ||The many roles of biological systematics & collections tour <!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf
 
|-
 
|-
<!--| Sept 7 No class ||No class ||No class || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library Level 2 electronic classroom, across the lobby from the stairs and elevators'''
+
| Sept 5 ||Labor Day No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 '''
 
|-
 
|-
|Sept 9 || Species definitions & intermediacy{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I.ppt}}Species.ppt || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf (For 09/16)
+
|Sept 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf ||
 
|-
 
|-
|Sept 11 Lab ||Lab ||Lab
+
|Sept 9 || Meet in library || Meet in library
 
|-
 
|-
|Sept 14 Lab ||Lab ||Lab || rowspan="3"| Taxonomic resoursces: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''
+
|Sept 12  || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Sept 16 || Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf
+
|Sept 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf ||
|| {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18)
+
<!--Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18) -->
 
|-
 
|-
|Sept 18 || Subspecies and geographic variation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202009.ppt}}Subspecies 2009.ppt||
+
|Sept 16 || lab || lab
 
|-
 
|-
|Sept 21 ||Variation within a genotype: ontogeny & phenotypic plasticity{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific%20Variation%202009.pdf}}Infrasubspecific Variation 2009.pdf || || rowspan="3"| Alpha Taxonomy<br/>Tiger Beetle Exercise<br/>Mesquite Morphological Matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf
+
|Sept 19 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202011.pdf}}Subspecies 2011.pdf || || rowspan="3"| Intro to Mesquite and Morphological Matrices '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Sept 21 || Infrapopulation variation (lecture sent via email) ||
 +
|-
 +
|Sept 23 || lab || lab
 +
|-
 +
|Sept 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202011.pdf}}Higher Categories 2011.pdf || || rowspan="3"| Keys, species descriptions, and cybertaxonomy '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Sept 28 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inferencev2_2011.pdf}}Intro to phylogenetic inference ||
 +
|-
 +
|Sept 30 || lab || lab
 +
|-
 +
|Oct 3 || Trees and characters; types of dendrograms;<br/>rooting and polarization ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf<br/>(only read chapter 2)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf || rowspan="3"| Manipulating molecular characters with Mesquite<br/>and a BLAST tutorial '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Oct 5 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_1%202011.pdf}}Characters_1 2011.pdf ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf
 +
|-
 +
|Oct 7 || lab || lab
 +
|-
 +
|Oct 10 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202011.pdf}}Multivariate Methods 2011.pdf || || rowspan="3"| Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Oct 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf
 +
|-
 +
|Oct 14 || lab || lab
 +
|-
 +
|Oct 17 || Midterm exam ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PageHolmesChptr5.pdf}}PageHolmesChptr5.pdf|| rowspan="3"| Parsimony with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Oct 19 ||Midterm Review ||
 +
|-
 +
|Oct 21 || lab || lab
 +
|-
 +
|Oct 24 ||lab ||lab || rowspan="3"| PAUP*: tree searches and tree statistics<br/>'''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Oct 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202011.pdf}}Reliability 2011.pdf||
 +
|-
 +
|Oct 28 || No Lab/AMNH & Bronx Zoo Trip || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lewis_2001-TREE-16-1.30-37.pdf}}Lewis_2001_TREE.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Holder%26Lewis2003NatRevGen.pdf}}Holder&Lewis2003_NatRevGen.pdf
 +
|-
 +
|Oct 31 ||lab ||lab || rowspan="3"| Model comparison with Modeltest '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Nov 2 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Guest Lecture Paul Lewis ||
 +
|-
 +
|Nov 4 ||  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis ||
 +
|-
 +
|Nov 7 || Data partitions; consensus; comparing tree topologies<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202011.pdf}}Consensus 2011.pdf || || rowspan="3"| Maximum likelihood and Bayesian inference '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Nov 9 || Guest lecture by Don Les:<br/>Molecular systematics in plants(lecture too big, so I emailed it to you) ||
 +
|-
 +
|Nov 11 || lab || lab
 +
|-
 +
|Nov 14 || Guest lecture by Chris Simon:<br/>Molecular systematics in animals<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CSimon%20Lecture-How%20Molecules%20Evolve.%20Parts%20I%20%26%20II.pdf}}CSimon Lecture.pdf|| || rowspan="3"| COI Barcoding and analyzing your own data sets '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Nov 16 || lab || lab
 +
|-
 +
|Nov 18 || Procedural flow chart for phylogenetic analysis; DNA barcoding<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes%2018%20Nov%20%5BCompatibility%20Mode%5D.pdf}}DNA Barcodes 18 Nov 2011.pdf
 +
||
 +
|-
 +
|Nov 21 || Thanksgiving recess || || rowspan="3"| Thanksgiving recess '''DO NOT Meet in McCarthy Room'''
 +
|-
 +
|Nov 23 || Thanksgiving recess ||
 +
|-
 +
|Nov 25 || Thanksgiving recess||
 +
|-
 +
|Nov 28 || Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202011%20final.pdf}}Nomenclature 2011 final.pdf|| || rowspan="3"| Mesquite and R: Ancestral states and character correlation '''(Meet in McCarthy Room, 4th floor TLS)'''
 +
|-
 +
|Nov 30 || Nomenclature; phylocode ||
 +
|-
 +
|Dec 2 || lab || lab
 +
|-
 +
|Dec 5 ||Patterns and process<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20Two.pdf}}Patterns and Processes 2011 Two.pdf || || rowspan="3"| No lab this week '''DO NOT Meet in McCarthy Room'''
 +
|-
 +
|Dec 7 || Taxonomic collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections%202011.pdf}}Importance of Collections 2011.pdf ||
 +
|-
 +
|Dec 9 || Biodiversity Crisis and Future of Systematics<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Biodiversity%20Crisis%20and%20Future%20of%20Systematics.pdf}}Biodiversity Crisis and Future of Systematics.pdf ||
 +
|-
 +
<!--|Sept 21 ||Variation within a genotype: ontogeny & phenotypic plasticity{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific%20Variation%202009.pdf}}Infrasubspecific Variation 2009.pdf || || rowspan="3"| Alpha Taxonomy<br/>Tiger Beetle Exercise<br/>Mesquite Morphological Matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf
 
|-
 
|-
 
|Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)
 
|Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)
Line 52: Line 127:
 
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools
 
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools
 
|-
 
|-
|Sept 30 ||Trees and characters:  types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf||
+
|Sept 30 ||Trees and characters:  types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf ||
 
|-
 
|-
 
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)
 
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)
Line 106: Line 181:
 
|Dec 4 ||Lab ||
 
|Dec 4 ||Lab ||
 
|-
 
|-
|Dec 7 ||Special topic: Taxonomic Collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab
+
|Dec 7 ||Special topic: Taxonomic collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab
 
|-
 
|-
|Dec 9 ||Special topic:  Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202009%20Class%20Version.pdf}}Patterns and Processes.pdf||
+
|Dec 9 ||Special topic:  Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20Two.pdf}}Patterns and Processes 2011 Two.pdf||
 
|-
 
|-
|Dec 11 ||Conservation, Systematics, and looking ahead<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}Looking Ahead 2009.pdf||
+
|Dec 11 ||Special topic: Biodiversity crisis and future of systematics<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}||
 
|}-->
 
|}-->
 
<br/>
 
<br/>
Line 125: Line 200:
 
=='''Grading'''==
 
=='''Grading'''==
 
{| border="1" cellpadding="1"
 
{| border="1" cellpadding="1"
| Lab and take home exercises || 20% || 100 pts
+
| Lab and take home exercises || 20% || 200 pts
 
|-
 
|-
| Midterm || 20% || 100 pts
+
| Midterm || 20% || 200 pts
 
|-
 
|-
| Term paper || 25% || 115 pts
+
| Term paper || 22% || 220 pts
 
|-
 
|-
| Nomenclature exercise || 2% || 10 pts
+
| Nomenclature exercise || 1% || 10 pts
 
|-
 
|-
| Final || 35% || 175 pts
+
| Participation || 2% || 20 pts
 
|-
 
|-
| '''Total''' || '''100%''' || '''500 pts'''
+
| Final || 35% || 350 pts
 +
|-
 +
| '''Total''' || '''100%''' || '''1000 pts'''
 
|}
 
|}
 
<br/>
 
<br/>
 
=='''Term paper'''==
 
=='''Term paper'''==
 
Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review
 
Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://researchfunding.duke.edu/detail.asp?OppID=587 htm
+
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm
 +
<br/>
 +
=='''Funding sources for taxonomy and biodiversity'''==
 +
Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies.  It was created in 2010, so most sources are up to date.<br/>
 +
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf
 
<br/>
 
<br/>
 
=='''Important dates'''==
 
=='''Important dates'''==
 
<span style="font-size: large">
 
<span style="font-size: large">
 
7 October, 2011: conference; topic selection<br/>
 
7 October, 2011: conference; topic selection<br/>
 +
17 October, 2011: midterm<br/>
 
21 October, 2011: outline with 5+ references<br/>
 
21 October, 2011: outline with 5+ references<br/>
 
18 November, 2011: first draft due<br/>
 
18 November, 2011: first draft due<br/>
 
2 December, 2011: paper due<br/>
 
2 December, 2011: paper due<br/>
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]

Revision as of 17:28, 10 December 2011

2009 Class on top of the AMNH
2011 Class on top of the AMNH

Fall 2011

Lecture MW 9:00-10:30, Lab F 9:00-10:30

Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours as available
email: david.wagner'at'uconn.edu

Graduate Teaching Assistant: Chris Owen
Office hours: BioPharm 325 Wednesdays 10:30-11:30 or by appointment
Phone: 486-6650
email: christopher.l.owen'at'uconn.edu

Contents

Textbook and readings

There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Many readings will be available as pdfs, downloadable from the course website. Others, available in hard copy only, will be on reserve in the departmental office (TLS 312) in the filing cabinet next to the window. You are free to check out copy #2 for 3 hours; copy #1 should stay in the office, i.e., so one is always there for others to photocopy.

Schedule


Supplementary Reading

Day Topics Reading/Assignment Lab
Aug 29 Class canceled due to Hurricane Irene
Lecture instead of lab this week
Aug 31 Organizational meeting, an introduction to biological systematics Pdficon small.gifHubbell.pdf (for Friday)
http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)
Pdficon small.gifMayr&Ashlock1991_pgs1-18.pdf (optional)
Sept 2 The many roles of biological systematics & collections tour Pdficon small.gifTempleton 1989.pdf
Pdficon small.gifDe Queiroz 2007.pdf
http://en.wikipedia.org/wiki/Species#Definitions_of_species
Pdficon small.gifFutuyma_spconcepts_445-451.pdf
Sept 5 Labor Day No class Babbidge Library resources; taxonomic literature Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1
Sept 7 Pdficon small.gifSpecies I 2011.pdf
Sept 9 Meet in library Meet in library
Sept 12 Pdficon small.gifSpecies II 2011.pdf Pdficon small.gifEhrlich&Raven1969.pdf Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS)
Sept 14 Pdficon small.gifSpecies III 2011.pdf
Sept 16 lab lab
Sept 19 Pdficon small.gifSubspecies 2011.pdf Intro to Mesquite and Morphological Matrices (Meet in McCarthy Room, 4th floor TLS)
Sept 21 Infrapopulation variation (lecture sent via email)
Sept 23 lab lab
Sept 26 Pdficon small.gifHigher Categories 2011.pdf Keys, species descriptions, and cybertaxonomy (Meet in McCarthy Room, 4th floor TLS)
Sept 28 Pdficon small.gifIntro to phylogenetic inference
Sept 30 lab lab
Oct 3 Trees and characters; types of dendrograms;
rooting and polarization
Pdficon small.gifForey et al 1992 Chap2&3.pdf
(only read chapter 2)
Pdficon small.gifPage & Holmes 1998.pdf
Manipulating molecular characters with Mesquite
and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS)
Oct 5 Pdficon small.gifCharacters_1 2011.pdf Pdficon small.gifKrell&Cranston.pdf
Pdficon small.gifFelsenstein2004.pdf
Oct 7 lab lab
Oct 10 Pdficon small.gifMultivariate Methods 2011.pdf Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 12 Pdficon small.gifDistance Methods 2011.pdf
Pdficon small.gifParsimony 2011.pdf
Pdficon small.gifParsimonyLectureForMidTerm.ppt
Pdficon small.gifPage&Holmes_Chap6.pdf
Oct 14 lab lab
Oct 17 Midterm exam Pdficon small.gifPageHolmesChptr5.pdf Parsimony with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 19 Midterm Review
Oct 21 lab lab
Oct 24 lab lab PAUP*: tree searches and tree statistics
(Meet in McCarthy Room, 4th floor TLS)
Oct 26 Pdficon small.gifReliability 2011.pdf
Oct 28 No Lab/AMNH & Bronx Zoo Trip Pdficon small.gifLewis_2001_TREE.pdf
Pdficon small.gifHolder&Lewis2003_NatRevGen.pdf
Oct 31 lab lab Model comparison with Modeltest (Meet in McCarthy Room, 4th floor TLS)
Nov 2 Pdficon small.gifGuest Lecture Paul Lewis
Nov 4 Pdficon small.gifGuest Lecture Paul Lewis
Nov 7 Data partitions; consensus; comparing tree topologies
Pdficon small.gifConsensus 2011.pdf
Maximum likelihood and Bayesian inference (Meet in McCarthy Room, 4th floor TLS)
Nov 9 Guest lecture by Don Les:
Molecular systematics in plants(lecture too big, so I emailed it to you)
Nov 11 lab lab
Nov 14 Guest lecture by Chris Simon:
Molecular systematics in animals
Pdficon small.gifCSimon Lecture.pdf
COI Barcoding and analyzing your own data sets (Meet in McCarthy Room, 4th floor TLS)
Nov 16 lab lab
Nov 18 Procedural flow chart for phylogenetic analysis; DNA barcoding
Pdficon small.gifDNA Barcodes 18 Nov 2011.pdf
Nov 21 Thanksgiving recess Thanksgiving recess DO NOT Meet in McCarthy Room
Nov 23 Thanksgiving recess
Nov 25 Thanksgiving recess
Nov 28 Nomenclature
Pdficon small.gifNomenclature 2011 final.pdf
Mesquite and R: Ancestral states and character correlation (Meet in McCarthy Room, 4th floor TLS)
Nov 30 Nomenclature; phylocode
Dec 2 lab lab
Dec 5 Patterns and process
Pdficon small.gifPatterns and Processes 2011 One.pdf
Pdficon small.gifPatterns and Processes 2011 Two.pdf
No lab this week DO NOT Meet in McCarthy Room
Dec 7 Taxonomic collections
Pdficon small.gifImportance of Collections 2011.pdf
Dec 9 Biodiversity Crisis and Future of Systematics
Pdficon small.gifBiodiversity Crisis and Future of Systematics.pdf
Topics Additional Reading
Species as ranked taxa and species concepts Pdficon small.gifApplication of Evolutionary Species concept.pdf Pdficon small.gifSpecies concept for prokaryotes.pdf Pdficon small.gifIs the BSC showing its age?.pdf
Pdficon small.gifImportance of stating species concept for conservation purposes.pdf Pdficon small.gifImpact of species concepts on biodiversity studies.pdf
Pdficon small.gifThe need for specifying species concepts.pdfPdficon small.gifOn the failure of modern species concepts.pdf Pdficon small.gifSpecies as ranked taxa.pdf

Pdficon small.gifDoes the choice of species concept result in an increase in bird species?.pdf Pdficon small.gifMethod for delimiting Cohesion speceis.pdf

DNA Barcodes Pdficon small.gifElias et al. 2007.pdf
Pdficon small.gifJanzen et al 2005.pdf
Pdficon small.gifTen Reasons For Barcoding.pdf
Pdficon small.gifWill & Rubinoff 2004.pdf
Pdficon small.gifHebert and Gregory 2005.pdf
Pdficon small.gifMoritz and Cicero 2004.pdf
Pdficon small.gifHebert et al.2003.pdf
Pdficon small.gifPLoS_Birds_Hebert et al. 2004.pdf

Grading

Lab and take home exercises 20% 200 pts
Midterm 20% 200 pts
Term paper 22% 220 pts
Nomenclature exercise 1% 10 pts
Participation 2% 20 pts
Final 35% 350 pts
Total 100% 1000 pts


Term paper

Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm

Funding sources for taxonomy and biodiversity

Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.
Pdficon small.gifFunding for biodiversity and taxonomy 2010.pdf

Important dates

7 October, 2011: conference; topic selection
17 October, 2011: midterm
21 October, 2011: outline with 5+ references
18 November, 2011: first draft due
2 December, 2011: paper due

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