Biology 427 Plant Systematics course outline by Levone

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									                         Biology 427 – Taxonomy of Vascular Plants
                                        Spring 2008

Instructor information
Simon Malcomber, Ph.D.
Office: MLSC 202
Office phone: 562-985-4814
Departmental fax: 562-985-8878
E-mail: smalcomb@csulb.edu
Office hours: Tuesday 9:00-10:00 a.m., Thursday 1:00-2:00 p.m. or by appointment. Please e-
        mail to set up an appointment
Website: http://beachboard.csulb.edu. All course materials will be posted online.

Course information
Prerequisites: Bio 211A & B (or equivalent), with a grade C or better
Meeting time and place: Lecture MW 1:00-1:50 p.m., Lab MW 2:00-4:45 p.m, PH1-209.
Format: Lecture/discussion, Lab. Group discussions of papers from the primary literature.

Course Description: Principles and methods of plant systematics, including phylogenetics,
      different types of systematic data, evolutionary history and diversification of plants.
      Emphasis in the laboratory will be on retrieving and analyzing systematic data, using
      phylogenetic methods, and identifying native and introduced plants of Southern
      California.

Goals of course:
   To introduce you to the science and methods of plant systematics
   To provide an overview of plant diversity
   To give you the necessary tools to conduct a plant systematics project
   To introduce you to the plants and communities of Southern California and emphasize
      the characters that identify them
   To teach you to think critically about systematic data in particular and scientific data in
      general
   To consider the implications of systematic data for other biological disciplines

Required texts (both available in University bookstore)
Simpson, MG. 2006. Plant Systematics. Elsevier Inc, Burlington MA
Harris, JG. and Harris-Woolf, M. Plant Identification Terminology: An Illustrated Glossary, ed. 2,
        Spring Lake Publishing

In addition to these textbooks, there will be readings from the primary literature. PDFs of these
papers will be posted on the course website.

Recommended text
Hickman, JC. (ed). 1993. The Jepson Manual: Higher Plants of California, University of
        California Press, Berkeley
        This is THE authoritative source on native plants in California and is highly
recommended. However, aside from the key to the major groups of plants (which will be
distributed in class), all keys and descriptions are available online at
http://ucjeps.berkeley.edu/interchange.html. Fifteen hard copies are available for consultation in
the lab sessions and for short-term loan (see below). Web site addresses of other useful
resources will be discussed in class and posted on the course web site.

Essential supplies (available in University bookstore)
Large 3-ring notebook for course materials distributed in class or printed from the class
        Beachboard site
10X hand lens
Metric rule, 15 cm long
Small field notebook (for taking notes on field trips)
Small collecting book (to record locality information and descriptions of plant characters (e.g.
        colors) that will not be preserved after drying)
128 MB (or larger) USB flash drive (to access and store information on your plant systematics
        project)

Useful field equipment and other materials
Sturdy gardening trowel
Pruning clippers (I prefer Felco #2, but that's just me)
Plastic collecting bags

Plant presses: These will be provided on loan from the Department of Biological Sciences for
the semester. Each must be returned, or replaced, before the final grade will be released, or
withdrawal form is signed.

Beachboard: This is a university system-wide web site for course use. In order to access
Beachboard you must have a CSULB email account. If you do not have such an account, you
must get on line at http://www.csulb.edu/namemaster, or contact the computer helpdesk at
helpdesk@csulb.edu, or http://helpdesk.csulb.edu, or phone 562-985-4959. You can activate
and access Beachboard once you have an account at http://beachboard.csulb.edu

Use of classroom references: Fifteen copies of the Jepson Manual are available for use in lab
to supplement on-line materials. Students will be able to sign out these copies for short-term
use, on condition that the borrowed copies are returned to the instructor prior to the next class
period (i.e. return before Wednesday 1:00 pm if borrowed Monday - Tuesday; return before
Monday 1:00 pm if borrowed Wednesday – Friday of the previous week). Borrowed copies
must be returned or replaced before a final grade will be released or withdrawal form will be
signed.
        Other reference materials are either University-owned or Dr. Malcomber’s personal
copies. These materials are present for student use in the classroom and are never to be
removed (no matter how cool they might be).

Field trips
     Field experience is an important aspect of plant systematics, so several field trips are
        scheduled. Students are expected to attend one of three weekend trips offered on
        March 22, April 11-13 (a three day trip with the Entomology course) and April 27 to
        observe different plant communities in the mountains surrounding greater Los Angeles.
        Two class-time field trips are scheduled to a local coastal area (March 3) and Rancho
        Santa Ana botanic garden (a botanic garden specializing in native Californian plants,
        March 26).
     Plant collecting will be permitted on all weekend field trips and the in-class field trip on
        March 3. NO collecting is permitted on the field trip to Ranch Santa Ana botanic garden
        on March 26.
      For legal reasons, participation in field trips is REQUIRED, and only persons formally
       enrolled in the course may participate.
      Due to unpredictable weather, actual dates of field trips may vary from those specified in
       this syllabus. Updates will be posted on Beachboard so check the class website if you
       have questions.
      As discussed in the safety overview, make sure you are prepared and dress
       appropriately when going in the field. This includes having sunscreen and sufficient
       water available, wearing a hat and sturdy sneakers or hiking boots. No flip-flops will be
       allowed. If you are susceptible to poison oak or other irritants consider wearing long
       pants and long sleeved shirt, and bring appropriate medication to treat affected areas.

Grading. Your grade will be determined by the points you earn in the various components of the
course:

       Midterm 1                                                           200
       Class discussion (5 X 10 points)                                     50
       Plant systematics project paper (180) and presentation (10)         190
       Class and lab quizzes (Best 6 X 15)                                  90
       Collection (90) and notebook (30)                                   120
       Plant identification practicum                                      200
       Final paper                                                         150

       Total                                                               1000

Grading Scale (if necessary, this scale will be curved)

                      900-1000                      A
                      800-890                       B
                      700-790                       C
                      600-690                       D
                      less than 600                 F

Midterm exam (200 points) Exam format will be a combination of short answer and essay
questions. Midterm exam on March 3 will cover materials up to and including February
27. A study guide including all of the questions that will appear on the midterm (and several
others) will be posted on or before February 25.

Class discussion (50 points) We will have a total of five class discussions on various aspects
of plant systematics and evolution (see syllabus). 10 points will be awarded for participating
(asking a question, responding to a question, making a comment about the paper) in each
discussion. NO makeup discussions will be given

Plant systematics project (190 points) Projects will be conducted in groups of 3-4 and will be
based on a Californian native plant species collected on our class field trip to the Palos Verdes
Pensinsula Land Conservancy on February 27.
    The project will present a systematic analysis of your plant species in question
       emphasizing nomenclature, conservation, morphological evolution and/or biogeography.
    The laboratory component of this project will entail DNA extraction, PCR amplification
       and PCR purification followed by a bioinformatics analysis using your new DNA
       sequence to estimate a phylogeny.
      Powerpoint summaries of your analyses will be presented in groups to the rest of the
       class on April 16. Although the projects will be conducted in groups, you are all
       required to submit a scientific paper comprising an abstract (200 words), introduction
       (including a brief discussion of taxonomic history, key morphological characters,
       ecology, and conservation status), methods (describing the collection, PCR amplification
       and phylogenetic analysis), results and discussion.
      When writing your paper emphasize how you can use your phylogeny to investigate
       the evolution of your species and relatives after conducting an extensive literature
       search. Particulars on how to conduct this literature survey will be posted online, but
       each person will be expected to use online resources (google, google scholar, web of
       science, etc) plus other resources at CSULB and local libraries (e.g. UC-Irvine) to
       conduct the survey. A word of warning, I do not consider some questionable citations to
       web pages that you’ve found from a few minutes of google-ing an extensive literature
       survey!
      Your individual paper is due on April 18 at 5:00 PM via TurnItIn on Beachboard. The
       paper should be no more than 15 double space pages in length, plus figures and
       references. Time will be allotted in labs 12-20 to work on this project.

Class and lab quizzes (90 points) Ten class and lab quizzes will be given throughout the
semester, based on materials in lecture, lab or assigned readings since the last quiz. Each quiz
will be worth a total of 15 points and your best 5 quizzes from the semester will be used and
weighted accordingly to calculate your class/lab quiz score. NO makeup quizzes will be
given.

Plant collection (120 points): Each student is required to submit a collection of 30 different
NATIVE Californian species (these are listed in BOLD TYPE in the Jepson manual).
Detailed collection and field notebook specifications will be posted on Beachboard. Grade for
collection will be based on the quality of the plant collection (i.e. how well it is presented and
preserved, whether the specimen is fertile), field notes and whether the collection is correctly
identified. Each plant specimen must be accompanied by a piece of paper summarizing how
the plant was keyed out from the Jepson (be warned, if the key requires information on flowers,
your specimen should have flowers….). No credit will be given to sterile (i.e. no flowers or fruits)
plant collections.

Plant identification practicum (200): A selection of herbarium and fresh specimens of plants
you have identified in lab during the semester will be presented in a plant identification
practicum on May 14. The class will be split into two sections and the two lab exams will last 1
hour and 45 minutes each. Copies of the Jepson manual will be available for consultation, but
no other notes will be permitted.

Final paper (150 points): Your final paper will be in a take-home format answering a question
that aims to synthesize presented materials on plant evolution, plus other additional materials
you can find from independent literature searches. The question will be posted on BeachBoard
by May 11. Final exam essays will be checked for plagiarism via TurnItIn.com and must be
uploaded by 2:30 PM on May 19.
Course policies
    Students are expected to uphold CSULB’s standards of academic honesty in all exams
      and assignments (see the Course catalog, pay particular reference to the section on
      plagiarism on pages 55-56).
    Regular attendance is expected. No credit will be given for missed discussions or
      quizzes
    Class begins promptly at 1:00 pm. Please arrive punctually for the start of the lectures.
      The midterm exam will be taken in class, beginning promptly at 1:00 pm. Use of books,
      notes or other external resources (text messaging, copying from your classmate, etc.) is
      not permitted.
    You are responsible for all course announcements, assignments, handouts, etc. even if
      you are late or absent, as well as all course-related materials on Beachboard. You
      should check Beachboard regularly.
    University safety protocols will be presented at the beginning of the semester. You must
      practice appropriate safety at all times in the lab. ALL food and drink are prohibited in
      the lab (this includes chewing gum).
    Efforts will be made to accommodate special needs, but it is up to the student to inform
      the instructor as early in the semester as possible so that I can make special
      arrangements.
    Withdrawal policy will be posted in the lab, but some important dates and points to
      remember:

01/27- 02/10/08, WITHDRAWALS DURING THE FIRST TWO WEEKS OF INSTRUCTION
       Students may withdraw during this period and the course will not appear on their
       permanent records. NOTE: THIS WITHDRAWAL OPTION BOTH BEGINS AND
       ENDS ON SUNDAY.
02/11 - 04/25/08, WITHDRAWALS AFTER THE FIRST TWO WEEKS OF INSTRUCTION AND
       PRIOR TO THE FINAL THREE WEEKS OF INSTRUCTION
       C. During this period of time, withdrawals are permissible only for serious and
       compelling reasons. Written approval must be obtained from both the Instructor
       and Department Chair.
04/26-05/16/08, WITHDRAWALS DURING THE FINAL THREE WEEKS OF INSTRUCTION
    Withdrawals during the final three weeks of instruction are not permitted except in
       cases such as accident or serious illness where the circumstances causing the
       withdrawal are clearly beyond the student's control and the assignment of an
       Incomplete is not practical. Written approval must be obtained from the Instructor,
       the Department Chair, and the Dean

      Make-up exams will only be scheduled for valid medical or personal reasons. Please
       contact me as soon as possible if you are unable to attend any of the exam dates. No
       makeup lecture or laboratory quizzes will be scheduled. Lecture quizzes will be given at
       1:00. Any student more than 5 minutes late will NOT be allowed to take that day’s quiz.
      Incompletes in the course will only be granted in accordance with University policy (in
       Course catalog)
      Any assignment submitted late will incur an automatic 10% score reduction for each day.
      Students may always review their exams outside of class during scheduled office hours
       or by appointment with the instructor. Any challenge of the scoring of a particular exam
       must be made within three weeks of the scores being posted.
                             BIOLOGY 427 SCHEDULE – 2008

Wk Date                 Topics
1    January 28
              Lecture Course outline. Why study plants? What is systematics?
                        (Simpson 3-16)
                  Lab Safety overview; Introduction to resources
Learning the tools: Field and Lab techniques
2    January 30
              Lecture Plant Morphology I: Overview of plant morphology
                        (Simpson 348-361)
                  Lab Plant morphology I: Habit, roots, stems, buds, and leaves
3    February 4
              Lecture Plant Morphology II: Floral morphology
                        (Simpson 364-382, 465-468)
                        Quiz #1
                  Lab Plant morphology II: Flowers, floral formulae
4    February 6
              Lecture Plant Morphology III: Fruit morphology
                        (Simpson 382-389)
                  Lab Plant Morphology III: Fruit types
5    February 11
              Lecture Phylogenetics I: What are phylogenetic trees? How do you
                        read them? How to choose the best one for your needs?
                        (Simpson 17-47)
                        Quiz #2
                  Lab Computer exercise: Learning to use phylogenetic software I
6    February 13
              Lecture Phylogenetics II: Molecular characters. How well supported is
                        your phylogenetic tree?
                        (Simpson 477-491)
                  Lab Computer exercise: Finding DNA sequences in GenBank,
                        aligning the sequences, and making phylogenetic trees
7    February 18
              Lecture Phylogenetics III: The power of modeling - different ways to
                        generate and choose phylogenetic trees
                        (Simpson 36, other reading TBA)
                        Quiz # 3
                  Lab Computer exercise: Maximum Likelihood and Bayesian
                        methods
8    February 20
              Lecture How to make a classification from a phylogenetic tree; History
                        of systematics; Nomenclature
                        (Simpson 501-515; Beachboard Judd et al. 33-38, 42-52)
                  Lab Class exercise: Integrating phylogenetics and classification
9    February 25
              Lecture The Californian Perspective: Flora and plant communities.
                        (Beachboard: Munz 1947, Holland and Keil, 1995)
                        Quiz # 4
                  Lab Making plant specimens
                        (Simpson 517-524)
                        Presses issued for individual plant collections
10   February 27        Field trip to Palos Verdes Peninsula Land Conservancy
                        Collection of herbarium vouchers and plant materials in
                        silica gel for DNA analysis
11   March 3            Midterm

Putting the tools to use
12 March 5
               Lecture Overview of plant evolution: Making the transition to land.
                         (Beachboard: Judd et al. 153-181)
                   Lab DNA extraction and gene amplification via PCR
13 March 10
               Lecture Lycophyte and Pteridophyte morphology and evolution
                         Review midterm exams
                         (Simpson 69-95)
                   Lab Discussion #1: Species bar codes: Marshall. 2005. Will
                         DNA bar codes breathe life into classification? Science
                         307: 1037. Kress et al. 2005. Use of DNA barcodes to
                         identify flowering plants. PNAS 102: 8369-8374
                         Lycophyte and Pteridophyte morphology and identification
                         Systematic projects: Electrophoresis gel to check DNA
                         amplification, PCR purification.
14 March 12
               Lecture Gymnosperms morphology and evolution.
                         (Simpson 97-119)
                         Quiz # 5
                   Lab Gymnosperms morphology and identification.
                         Systematic projects
15 March 17
               Lecture The origin of flowering plants: monocot/dicot versus basal
                         angiosperms/monocots/eudicots; Magnoliids and basal
                         eudicot evolution and morphology
                         (Simpson 121-153)
                         Discussion #2: Extant ferns ancient or recent?
                         (Schneider et al. 2004. Ferns diversified in the shadow of
                         angiosperms. Nature 428: 557)
                   Lab Early diverging angiosperm families, Magnoliid and basal
                         eudicot morphology and identification
                         Systematic projects: Analyze sequence data
16 March 19
               Lecture Core Eudicots I: Caryophyllidae and basal rosidae evolution
                         and morphology.
                         (Simpson 228-249)
                         Quiz 6
                   Lab Caryophyllidae and basal Rosidae morphology and
                         identification
                         Systematic projects
     March 22         Weekend field trip #1
17   March 26
              Lecture Eudicots: Eurosids I evolution and morphology
                      (Simpson 252-289)
                 Lab Morphology and identification of Eurosids
                      Systematic projects
18   March 26         Field trip to Rancho Santa Ana Botanic Garden
     March 31                                  Spring Break
     April 2                                   Spring Break
19   April 7
              Lecture Eudicots: Eurosids II evolution and morphology
                      (Simpson 252-289)
                      Quiz 7
                 Lab Morphology and identification of Eurosids II
                      Systematic projects
20   April 9
              Lecture Eudicots: Asterids I morphology and evolution
                      (Simpson 291-319)
                      Discussion # 3: Evolution of parasitic plants.
                      de Pamphilis, CW et al. 1997. Evolution of plastid gene
                      rps2 in a lineage of hemiparasitic and holoparasitic
                      plants: Many losses of photosynthesis and complex
                      patterns of rate variation PNAS 94: 7367-7372
                      Davis, C. et al 2006. Floral Gigantism in Rafflesiaceae.
                      Nature 315: 1812
                      Eudicots: Asterids I morphology and identification
                      Systematics projects
     April 11-13      Weekend field trip #2 (with Entomology class to regions
                      around -- but not in! -- Joshua Tree National Park)
21   April 14
              Lecture Eudicots: Asterids II morphology and evolution
                      (Simpson 319-325, 331-335)
                 Lab Eudicots: Asterids II morphology and identification
                      ID plant collections
                      Systematic projects
22   April 16         Systematics project: group presentations, question and
                      answer period.
     April 18         Individual systematic project papers due @ 5:00 PM via
                      TurnItIn.com on Beachboard
23   April 21
              Lecture Eudicots: Asteraceae morphology and evolution.
                      (Simpson 325-331)
                 Lab Asteraceae morphology and identification
                      ID plant collections
                      Quiz 8
24   April 23
              Lecture Petaloid monocots I: morphology and evolution.
                      (Simpson 153-184)
                 Lab Petaloid monocots I: morphology and identification
                         ID plant collections
     April 27            Weekend field trip #3
25   April 28
                Lecture Petaloid monocots II: Orchidaceae
                   Lab Petaloid monocots II: Orchidaceae morphology and
                        identification
                        ID plant collections
26   April 30
                Lecture Commelinoid monocots morphology and evolution.
                        (Simpson 184-202)
                   Lab Commelinoid monocots morphology and identification
                        ID plant collections
                        Quiz 9
27   May 5
                Lecture Commelinoid monocots II: Poales
                        (Simpson 203-219)
                   Lab Poales morphology and identification
                        ID plant collections
28   May 7
                Lecture Discussion # 4: Incorporating phylogenies into
                        conservation decisions Forest et al. 2007. Preserving the
                        evolutionary potential of floras in biodiversity hotspots.
                        Nature 445: 757-760
                   Lab ID plant collections, Plant collection (in a large plastic
                        container the specimens pressed and dry, within sheets
                        of newspaper) and collecting book due at 4:00 pm
29   May 12
                Lecture Discussion # 5: The future of systematics
                        Wheeler, Q. 2004. Taxonomic triage and the poverty of
                        phylogeny. Phil. Trans. R. Soc. Lond. B. 2004. 359: 571-
                        583)
                        Quiz 10
                   Lab Review specimens for lab practicum, Question and
                        answer session for final paper
30   May 14
                   Lab   Lab practicum in two sections:
                         Section 1) 1:00-2:45
                         Section 2) 3:00-4:45
     May 21              Final paper due at 2:30 via TurnItIn.com on BeachBoard

								
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