Principles and Methods of Systematic Biology (EEB 5347) - Revision history

DaveWagner at 21:28, 10 December 2011

2011-12-10T21:28:25Z

DaveWagner at 22:54, 9 December 2011

2011-12-09T22:54:37Z

DaveWagner at 22:48, 9 December 2011

2011-12-09T22:48:10Z

DaveWagner at 21:40, 9 December 2011

2011-12-09T21:40:04Z

DaveWagner at 22:38, 7 December 2011

2011-12-07T22:38:55Z

DaveWagner at 22:11, 7 December 2011

2011-12-07T22:11:37Z

PaulLewis at 15:06, 4 November 2011

2011-11-04T15:06:53Z

PaulLewis at 13:17, 3 November 2011

2011-11-03T13:17:12Z

ChrisOwen at 18:20, 31 October 2011

2011-10-31T18:20:58Z

ChrisOwen at 16:26, 27 October 2011

2011-10-27T16:26:26Z

@@ Line 107: / Line 107: @@
 |Nov 25 || Thanksgiving recess||
 |-
-|Nov 28 || Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202011%20I%20%26%20II.pdf}}Nomenclature 2011 I & II.pdf|| || rowspan="3"| Mesquite and R: Ancestral states and character correlation '''(Meet in McCarthy Room, 4th floor TLS)'''
+|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 ||

@@ Line 113: / Line 113: @@
 |Dec 2 || lab || lab
 |-
-|Dec 5 ||Patterns and process  || || rowspan="3"| No lab this week '''DO NOT Meet in McCarthy Room'''
+|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 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 and future of systematics  ||
+|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

@@ Line 115: / Line 115: @@
 |Dec 5 ||Patterns and process  || || 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 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 and future of systematics  ||

@@ Line 181: / Line 181: @@
 |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/>

← Older revision		Revision as of 22:38, 7 December 2011
Line 1:		Line 1:
	[[Image:AMNH2009.jpg\|right\|''2009 Class on top of the AMNH'']]		[[Image:AMNH2009.jpg\|right\|''2009 Class on top of the AMNH'']]
		+	[[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/>

@@ Line 56: / Line 56: @@
 |Sept 30 || lab || lab
 |-
-|Oct 3 || ||{{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 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
@@ Line 68: / Line 68: @@
 |Oct 14 || lab || lab
 |-
-|Oct 17 || ||{{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 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 || ||
+|Oct 19 ||Midterm Review ||
 |-
 |Oct 21 || lab || lab
 |-
-|Oct 24 || |||| rowspan="3"| AMNH and Bronx Zoo Trip
+|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 || {{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 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)'''
@@ Line 85: / Line 85: @@
 |-
 |Nov 4 ||  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis ||
 |-
 <!--|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

@@ Line 82: / Line 82: @@
 |Oct 31 ||lab ||lab || rowspan="3"| Model comparison with Modeltest '''(Meet in McCarthy Room, 4th floor TLS)'''
 |-
-|Nov 2 || Guest Lecture Paul Lewis|| {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Likelihood_2Nov2011.pdf
+|Nov 2 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Guest Lecture Paul Lewis ||
 |-
-|Nov 4 || Guest Lecture Paul Lewis ||
+|Nov 4 ||  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis ||
 |-
 <!--|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