Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
DaveWagner (Talk | contribs) |
|||
(23 intermediate revisions by 3 users not shown) | |||
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 29: | Line 31: | ||
| 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) | | 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<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 | + | | 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 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 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf || | ||
+ | |- | ||
+ | |Sept 9 || Meet in library || Meet in library | ||
+ | |- | ||
+ | |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 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf || | ||
+ | <!--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 16 || lab || lab | ||
+ | |- | ||
+ | |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 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 | + | |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% | + | |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 || | + | |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 151: | Line 226: | ||
<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 21:28, 10 December 2011
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 | Hubbell.pdf (for Friday) http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday) Mayr&Ashlock1991_pgs1-18.pdf (optional) | |
Sept 2 | The many roles of biological systematics & collections tour | Templeton 1989.pdf De Queiroz 2007.pdf http://en.wikipedia.org/wiki/Species#Definitions_of_species Futuyma_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 | Species I 2011.pdf | ||
Sept 9 | Meet in library | Meet in library | |
Sept 12 | Species II 2011.pdf | Ehrlich&Raven1969.pdf | Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) |
Sept 14 | Species III 2011.pdf | ||
Sept 16 | lab | lab | |
Sept 19 | Subspecies 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 | Higher Categories 2011.pdf | Keys, species descriptions, and cybertaxonomy (Meet in McCarthy Room, 4th floor TLS) | |
Sept 28 | Intro to phylogenetic inference | ||
Sept 30 | lab | lab | |
Oct 3 | Trees and characters; types of dendrograms; rooting and polarization |
Forey et al 1992 Chap2&3.pdf (only read chapter 2) Page & Holmes 1998.pdf |
Manipulating molecular characters with Mesquite and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS) |
Oct 5 | Characters_1 2011.pdf | Krell&Cranston.pdf Felsenstein2004.pdf | |
Oct 7 | lab | lab | |
Oct 10 | Multivariate Methods 2011.pdf | Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS) | |
Oct 12 | Distance Methods 2011.pdf Parsimony 2011.pdf ParsimonyLectureForMidTerm.ppt |
Page&Holmes_Chap6.pdf | |
Oct 14 | lab | lab | |
Oct 17 | Midterm exam | PageHolmesChptr5.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 | Reliability 2011.pdf | ||
Oct 28 | No Lab/AMNH & Bronx Zoo Trip | Lewis_2001_TREE.pdf Holder&Lewis2003_NatRevGen.pdf | |
Oct 31 | lab | lab | Model comparison with Modeltest (Meet in McCarthy Room, 4th floor TLS) |
Nov 2 | Guest Lecture Paul Lewis | ||
Nov 4 | Guest Lecture Paul Lewis | ||
Nov 7 | Data partitions; consensus; comparing tree topologies Consensus 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 CSimon 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 DNA 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 Nomenclature 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 Patterns and Processes 2011 One.pdf Patterns and Processes 2011 Two.pdf |
No lab this week DO NOT Meet in McCarthy Room | |
Dec 7 | Taxonomic collections Importance of Collections 2011.pdf |
||
Dec 9 | Biodiversity Crisis and Future of Systematics Biodiversity Crisis and Future of Systematics.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.
Funding 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