Biol. 403/L  Plant Morphology as taught by Paul Wilson

Liverwort Goals
(1) To survey the major groups of land plants, (2) to study plant life cycles and reproductive biology, (3) to learn the methods used by comparative biologists, (4) to abstract science out of popular botany literature, and (5) to look at a lot of beautiful plants.

Prerequisite
BIOL 106 and 106L are prerequisites for this course. If you feel rusty, you should re-read your 106 text concerning (1) meiosis and fertilization, (2) plant life cycles, and (3) major groups of plants.  Although I will review quickly before extending my treatment of these topics, having the 106 coverage fresh in your mind will make the rest of the class much less frustrating. There's no reason to start of behind!

Readings
We will start with a book, Robin Kimmerer’s Gathering Moss. And as the semester progresses, we will move on to articles from the primary literature. For the book, I am asking that you abstract this science out of the reading for each chapter.  In other words, for each chapter or group of chapters, you will write a paragraph or so about the scientific content of the chapter.  For the technical articles, you will not write an abstract but instead write a question or comment about the reading. Whatever the reading, each week, you should bring something written down for me and hand it in before the discussion.Moss

Packet
You will have to purchase a course packet that has diagrams and brief summaries of the lectures.  The life cycle diagrams were given to me by Dennis Walker from whom I took plant morphology.  They were drawn over several years by several of his students whose names I don’t know but who I acknowledge in their anonymity.  My views on land plants and comparative biology have been greatly influenced by M. Mesler, D. Norris, D. Walker, E. Voss, K. Omland, and M. Donoghue, each of whom would have a right to feel some ownership if they were to read my lecture notes.

Videos
I have a set of videos that I’m hoping we will have time to watch.  This will usually be at the end of the day, and they don’t go with any particular lecture.  They’re pretty good.  Please take them seriously.

Supplemental text
Some of you may want to study a textbook.  I suggest Michael Simpson’s Plant Systematics.

Tests
About half of each test will be a mixture of practical information from the labs like identifying plants and organs, definitional and short answer questions about the vocabulary.  The other half will be essay questions about the readings, the lectures, and systematic methodology. Study sheets will be provided.  There will be three such exams during the semester, and there will be a cumulative final, which will be heavy on life cycles and knowing the diversity of land plants.

Paper
You will write a 2500 word paper. It will be reviewed. And you will revise (probably extensively). There will be more about this later, but basically it is an overview of an evolutionary radiation of some plants (often a genus or family) and the variety of modes of life they have adopted.

Oral presentations
It is said that one learns best from teaching.  So, at the end of the term, we will have a symposium in which each student gives a talk.

Grading
Each of the four exams, the paper including its revision, and the talk with its handout will count as 1/8th of your grade (totaling 6/8ths).  An additional 1/8th will be for your abstracting of the books and the discussion questions.  The last 1/8th will be for attendance, punctuality (be there at 1:00), and participation (this means being prepared and actively discussing the readings). Grades will be issued with +, no sign, or - to show fine distinctions in performance. I won’t say now exactly what the grade cut-offs will be, but past experience suggests that the A-/B+ line is 90%, the B-/C+ line is about 75%, and the C-/D+ line is about 55%.

Schedule of topics (subject to change)
29 Jan - Land plant overview (handout 1). Tour greenhouse and plant organs in lab.
31 Jan - Learn how to map characters on a phylogeny (2).
5 Feb - Lecture on bryophyte ecology (3). Discuss Kimmerer pp. 1-34
7 Feb - Learn how to infer phylogenies (4). Discuss Kimmerer pp. 35-51
12 Feb - Field trip to Walker Ranch (upstream from Placerita Canyon) weather permitting; meet at van 1:00.
14 Feb - Meiosis and fertilization (5). Bryophyte reproductive biology (6). Look at sex organs.
19 Feb - Species boundaries (7). Discuss Kimmerer pp. 62-99
21 Feb - Learn local bryophytes. Write Key (8). Discuss pp. Kimmerer 111-124
26 Feb - Learn local bryophytes. Discuss pp. Kimmerer 141-150, 156-162
28 Feb - Test 1 (bryophytes)
5 Mar - Pteridophyte life cycles (9). Greenhouse ferns, Lycopods, Equisetum, Psilotum. Discuss Des Marais et al. 2003
7 Mar - Lecture on allopolyploidy in pteridophytes (10). Do exercise with Polystichum to study hybrid inference (11).
12 March - Lecture on fern diversity. Greenhouse work (12). Discuss Werth & Whidham 1991
14 Mar - Phenetics above the species level using chielanthoid ferns (13)
Saturday 17 Mar - field trip to Cold Creek to study ferns, etc. (If weather bad, this will be on 24th instead)
19 Mar – Learn local pteridophytes. Discuss Schneider et al. 2004
21 Mar – Scanning electron microscopy. Data in Systematics (14). Discuss Guo et al 2003
26 Mar - no class in lieu of field trip time
28 Mar - no class in lieu of field trip time
SPRING BREAK
9 April – PAPERS DUE. Review pteridophytes.
11 April – Test 2 (pteridophytes)
16 April - Lecture introducing seed life cycles. Look at gymnosperm sex organs (15). Discuss Chaw et al. 2000
18 April - Lecture on angiosperm life cycle (16). Study slides of lily gametophytes and seeds.
23 April - Some important families of angiosperms (17). Study flower parts variously modified
25 April - adaptive correlation (18). Pollination and fruit dispersal (19). Discuss Armbruster 2002
30 April –Write key to conifers of the San Gabriel Mountains. Discuss Donaldson 1997
2 May – no class in lieu of field trip time
Saturday 5 May - field trip to San Gabriel Mts. IT MAY BE COLD; DRESS IN LAYERS
7 May – REVISIONS OF PAPERS DUE. The analyses of clines (20)
9 May – Students give talks on major groups of plants I
14 May - Students give talks on major groups of plants II. Then I sum up class.
16 May - Test 3 (seed plants)
21 May 12:45-2:45 - Final (=Test 4)

Biology Department Withdrawal Policy—Unrestricted class withdrawals are permitted only until the end of the third week.  Thereafter, requests to withdraw will be honored only when a verifiable serious and compelling reason exists and when there is no viable alternative to withdrawal.  Poor performance is not an acceptable reason for dropping a class; in fact, you must be passing in order to withdraw.  During the last three weeks of class, withdrawals will not be approved except when a student is withdrawing from all classes for verifiable medical reasons.

Cheating—Cheating on tests—for instance, by looking at someone else's paper or looking at your notes—is completely unacceptable.  Don't do it, not even just a little bit in the spur of the moment.  Go out of your way to not be tempted and to not tempt anyone else.  Plagiarism is a form of cheating. Every sentence in your paper must be in your own words, and each piece of factual content must come with a reference to a scholarly publication (not a website). If you do cheat, you will be punished as per university policy (see Catalog).


Paper Assignment
I'm open to suggestions about your topic, but you need to clear it with me early in the semester. You should get cracking on this if for no other reason than that you will probably have to interlibrary loan some of the references. Below are some ideas as starting points. As soon as you have selected a topic, email me, and I'll show the topic has been taken so no one else can choose that topic.

Once you have chosen a topic, go to scholar.google.com and browse abstracts. You may also want to read a textbook account if you are working on a special group that shows up in textbooks. Just spend a couple of hours. Get together a list of (say) 5 references that you'll need and indicate if you have them or if you need to order/find them. Email me this list. Order stuff from interlibrary loan a.s.a.p.

Stand-Up  Talk
Each of you will give a talk and make a 1-page handout that outlines the take-home message and facts that you want others to learn. You may use the back side of the paper for figures if you wish. The talks should be from 15-30 minutes; I am flexible on this, so that exact timing is not important, but time yourself when you practice. You should know about how long it will take when you stand up in front of the class. Most of you will want to present in Powerpoint, although if you wish, you may lecture using only the board or no visual aids (and I would respect you for it). If you are to use Powerpoint, bring your talk on a CD or memory stick, and be sure it shows up well on a PC (not just a Mac). Error on the side of being too dramatic and choreographed. If you wish to change your topic from what you wrote on, fine, but clear the new one with me. This talk and the handout are equal in credit to an exam. Take this assignment is seriously, and you will raise your grade, which I know a lot of you are concerned about.

Study Sheet for Test 1:
Expect essays or short answer questions on lectures on
    bryophyte ecology
    bryophyte reproduction
    character mapping
    inferring phylogenies
    species boundaries
    writing keys
Be able to sketch bryophyte life cycles, labeling structures, and identifying polidy.
There will also be some vocabulary (e.g. distinguish homology from homoplasy).

Bryophyte
    Liverworts
        Jungermaniales: Porella
        Metzgeriales: Pellia, Fossombronia
        Marchantiales: Marchantia, Asterella, Targionia, Riccia
    Hornwort
        Anthoceros
    Mosses
        Sphagnum
        Andraea
        Polytrichum
       True mosses: Fissidens, Dicranum, Syntrichia, Scleropodium, Didymodon,
            Bryum, Funaria, Timmiella, Wissia, Grimmia, Anacolia,
            Orthotrichum, Dendroalsia, Fabronia
Tracheophyte = vascular plant
Pteridophyte
    Lycophytes
        Lycopodium, Sellaginella, Isoetes
    Equisetum
    Psilotum
    Ferns
Spermatophyte = seed plant
    Cycad
    Gingko biloba
    Conifers
    Gnetales
        Gnetum
        Ephedra
        Welwitschia
    Angiosperm = flowering plant
sporophyte
sporangium (often called "capsule")
sporocyte
spore
protonemata
gametophyte
gametangium (plural gametangia)
antheridium (plural antheridia)
sperm
archegonium (plural archegonia)
egg
zygote, embryo
diploid, haploid
meiosis, fertilization (syngamy)
mitosis
gemma (plural gemmae)
thallus
archegoniaphore, antheridiophore
elater
leaf insertion: succubus, incubus, transverse
complicate bilobed
seta
capsule (sporangium)
peristome
operculum,
calyptra (N)
stem, leaf, rhizoid
leptoides, hydroids
perigonium (male head)
perichaetium (female head)
paraphyses
archegonium: venter, neck, canal cells
monoicous, dioicous
monoecious, dioecious
apocarpous, pleurocarpous
poikilohydric/homeohydric
epiphytic
saxicolous
xerophytic (xeric)
mesophytic (mesic)
entomophilous
phylogeny
cladistic, phyletic, phenetic
monophyletic, paraphyletic, polyphyletic
sister group, outgroup
rooting
parsimony
branch & bound
homology, homoplasy
convergence, reversal, analogy
synapomorphy
synplesiomorphy
autapomorphy
character evolution, character mapping
MacClade, PAUP*
bootstrap
species concepts:  biological, phylogenetic
biosystematics; alpha taxonomy
gap
rank
splitters, lumpers


Study Sheet for Test 2

Expect questions on the pteridophyte life cycles, allopolyploidy and hybrid inference, fern phylogeny, classification and phenetics, and various types of data used in systematics.

This test is only mildly cumulative: you need to know stuff we see on the second field trip whether it’s a bryophyte, a pteridophyte, or a seed plant, you need to be able to know what an alpha taxonomist is.

There will questions from the readings of the technical articles.

Lycophytes
    Lycopodium, Sellaginella, Isoetes
Equisetum subg. Hippochaete, Equisteum
Psilotum
Ophioglossales
Marattiales
Osmundales
Hymenophyllales
Gleicheniales
Schizaeales
Salviniales: Marsilea, Salvinia, Azolla
Cyatheales: Cyathea, Dixsonia
Polypodiales
    Pteridium
    Adiantum, Aspidotis, Cheilanthes, Pellaea, Pentagramma
    Asplenium
    Blechnum, Woodwardia
    Dryopteris, Polystichum, Rumohra
    Nephrolepis
    Davallia
    Polypodium, Platycerium

Polystichum dudleyi, P. munitum, P. imbricans, P. scopulinum, P. lemmonii, P. kruckebergi, P. lonchitis, and triploid backcrosses

homosporous, heterosporous
underground gametophytes, epigeous autotrophic ones
microphylls, megaphylls
microspore, megaspore
microgametophyte, megagametophyte
antheridiogens
intragametophytic selfing, intrasporophytic selfing, intersporophytic outcrossing
sorus, indusium, sporangium, annulus
frond, blade, petiole, rachis, penna/ae
palmate, pinnate, pinatifid
phenetics, numerical taxonomy
OTU by CHR matrix
standardized data matrix
distance matrix
cluster diagram versus cladogram
cluster diagram, e.g., UPGMA
ordination, e.g., principle components analysis, non-metric multidimensional scaling
homologous & homeologous chromosomes
reticulate evolution
allopolyploidy, autopolyploid
diploid, triploid, tetraploid, hexaploid
univalent, bivalent chromosome pairing
base chromosome number
gene silencing
speciation by gene silencing versus ‘normal’ means
secondary chemistry
enzyme electrophoresis: allozyme, isozyme
restriction sites
base pair sequences
biosystematics: interfertility, cytology, ecology, biogeography
field guide, manual, flora
review, revision, monograph
SEM, sputter coater

Draft Study Sheet for Test 3
There will be questions about some of the readings since test 2 and the handouts from the student talks.  Study the lecture notes. Know the species of conifers from the trip, and the genera planted around campus.  Know the families of angiosperms and the pollination syndromes. Be able to recognize and interpret any flower, even ones you have not seen before.  Practice on flowers in the garden and greenhouse.

Spermatophyte = seed plant
    Cycadophyta:
        Cycas, Zamia, Macrozamia
    Gingko biloba
    Conifers
        Pinus, Podocarpus, Araucaria, Sequoia, Metasequoia, Calocedrus, Juniperus, Pseudotsuga, Abies, Sequoiadendron, Cedrus, Taxus, Taxodium, Cupressus, Cunninghamia, Cryptomeria, Thuja
    Gnetophyta
        Gnetum (sorry, not in greenhouse)
        Ephedra
        Welwitschia
    Angiosperm = flowering plant (see handout on most important families)
        magnoliids
        paleoherbs
        monocots
        tricolpates (eudicots)

Conifers of the San Gabriel Mountains
    Abies concolor
    Calocedrus decurrens
    Cupressus macrocarpa
    Juniperus californica
    Pinus attenuata (serotinous)
    Pinus contorta ssp. murrayana
    Pinus coulteri
    Pinus jeffreyi
    Pinus lambertiana
    Pinus monophylla
    Pinus ponderosa
    Pseudotsuga macrocarpa
What makes an identification key good or bad?
What makes a classification good or bad?
What makes a phylogeny good or bad?

mega and microstrobili, spores, gametophytes
integument, micropyle, pollination drop
pollen grain, exine, pollen tube
pollination
seed dispersal
saccate and non-saccate pollen
siphonogamy
nucellus
merosity
pollen grain (microgametophyte)
tube cell nucleus, sperm nuclei
embryo sac (megagametophyte)
antipidal cells, synergid cells, egg cell,
polar nuclei
double fertilization
endosperm
adaptive correlations
paired contrasts
in a conifer cone: scale, ovule, bract
calyx:  sepals
corolla:  petals
androecium:  stamen (filament, anther)
gynoecium:  carpels (ovary, style, stigma)
perianth
connation (=coalescence)
adnation
perfect and imperfect
monoecious, dioecious
actinomorphic (radial), zygomorphic (bilateral)
superior, inferior ovary

The cumulative test will stress contrasting the major groups of land plants, methods in comparative biology, and life cycles.  You do not need to review articles that you have already been tested on or incidental genera (i.e., you need to know Lycopodium but not Isothecium).  Everything else on past study lists is fair game.

This course has three content themes:
•What systematists do and why and how.
•The major groups of land plants by gestalt.
•Life cycles and variations in C major.
The test will reflect each one.