PBIO 250 Lecture Notes

James L. Reveal

Norton-Brown Herbarium, University of Maryland

Principles of Plant Taxonomy

Establishment of Characters
similarities vs. dissimilarities
variation in form and function
gross similarities
special creation
fixity of species - see this review covering this subject and the historical steps leading to theories dealing with evolution and speciation
"Animal, Vegetable or Both": Classification of all things
phylogenetic systems of classification
linear sequences vs. branching patterns
See the essay on Systematics and Biological Characteristics by John D. Pinto of the Departament of Entomology at UC Riverside; an excellent summary using insects as examples

hierarchy of categories
categories are comparable to rank
Code determines the hierarchy
ranks and hierarchy derived from the Linnaean method
1 division (Magnoliophyta)
  5 classes (Magnoliopsida)
    19 subclasses (Magnoliidae)
      72 superorders (Magnolianae)
        201 orders (Magnoliales)
          552 families (Magnoliaceae)
ca 13,900 genera (e.g., Magnolia)
ca 255,000 species (e.g., virginiana)

definitions - a useful list of phylogenetic terms from University of California Museum of Paleontology
monophyletic: a taxon derived from one ancestral population
polyphyletic: a taxon derived from two or more ancestral populations; a polyphyletic taxon should be divided into two or more monophyletic taxa
monophyletic categories at all ranks in the hierarchy express evolutionary lineages and relationships
species: the fundamental unit of classification; a species should be separated by distinct morphological differences so that it is possible to distinguish one group of individual plants from all other groups of plants; the concept of "species" cannot be defined in exact terms
Cronquist (1988): "Species are the smallest groups that are consistently and persistently distinct, and distinguished by ordinary means."

1. Cronquist, A. 1988. The evolution and classification of flowering plants, ed. 2. Bronx.

Speciation - see this site for a brief summary; we will do more on this subject when we discuss evolution - see also this site
"A species is what a good taxonomist says it is!"
species: a series of reproductive, or at least potentially interbreeding individuals
reproduction
reproductive strategies
reproductive isolation - Follow the links by clicking on "Next Section"
isolation mechanisms: geographic, seasonal, genetic, physiological or mechanical evolutionary divergence
biological species concept
polyploidy: diploid, tetraploid, octoploid
hybrids and hybridization

amixis: a reproductive cycle which lacks meiosis and fertilization
amphimixis: sexual reproduction when the individual has two parent or biparental reproduction
mixis: same as amphimixis.
apomixis: in general a plant reproducing without sex

infraspecific taxa:

   subspecies: subsp. or ssp.
   variety: var.
   forma: f.

Christian H. Persoon (1761-1836)
Synopsis plantarum (1805-1806)
Harvey Munroe Hall (1874-1932)
The phylogenetic method in taxonomy (1923)
Liberty Hyde Bailey (1858-1954)
variety (var.) vs. cultivar (cv.)
learn more about the horticultural rank of cv.
Merritt Lyndon Fernald (1873-1950)
F. Raymond Fosberg (1908-1993)
Arthur Cronquist
incipient species
subspecies: morphological and geographical distinct units that interbreed along a narrow band of contact
variety: either morphologically or geographically distinct units or only weakly distinct with a greater area of overlap
varieties may be grouped into subspecies - subspecies that in their totality are markedly distinct geographically and morphologically
genus: an inclusive category whose species have more characters in common with each other than with species of other genera in the same family; a genus must be a monophyletic lineage of related species having a common ancestry from a taxon - extant or not - that is equivalent to the rank of genus
tradition
Robert M. King (1930- )
Harold Robinson (1932- )
Eupatorium

1. King, R.M. & H. Robinson. 1987. The genera of the Eupatorieae (Asteraceae). Mem. Syst. Bot. 22: 1-581.

Verbenaceae and Lamiaceae
Solanaceae and Scrophulariaceae
Liliaceae

characters
typological concept
characters are features or attributes that can be observed and used in a comparative fashion. Most characters are morphological. A character is an attribute but is not comparable unless that character is divided into character states
presence vs. absence
numerical terms vs. descriptive terms
numerical are quantitative characters
descriptive are qualitative characters
objective vs. subjective observations
diagnostic vs. key characters
constant characters are synthetic characters
"good" characters are genetically fixed, largely unaffected by the environment and relatively constant throughout the population vegetative characters
reproductive characters
for an interesting historical essay on this subject in general, and specifically as it applies to mammals, see Revolution and Evolution in Taxonomy: Mammalian classification before and after Darwin by David Polly

Useful tools in systematic studies

• (1) anatomy: 1800s
  
• (2) chromosome numbers: 1920's
  
• (3) comparative garden studies: 1940's
  
• (4) palynology: 1950's
  
• (5) phenetics: 1960's
  
• (6) biochemical systematics: 1970's
  
• (7) cladistics: 1980's
  
• (8) chloroplast DNA and RNA: 1990's

Schools of Classification
see the brief overview from a "creation science" group
pre-Darwinian: natural system
polythetic: placing together organisms that have the greatest number of shared characters with no one character essential for membership - systems of Ray
monothetic: establishing groups based on a unique often pre-determined set of features arranged in a rigid and successively logical series of divisions - systems of Linnaeus principles of angiosperm phylogeny: read What is Phylogeny by David and Wayne Maddison at the University of Arizona
classification established on examination of contemporary plants, the existing fossil record and a correlation of characters based on a series of established evolutionary trends in the flowering plants
three schools or approaches to constructing classification schemes; each seeks natural (rather than artificial) and objective (rather than subjective) classifications

1. EVOLUTIONARY: Groups are constructed by emphasizing relationships based on the perceived decent of the group by the author of the system of classification following a series of preconceived phylogenetic assumptions or dicta.

1. Hooker, J.D. 1873. "Appendix. On the classification of plants by the natural method, with an analysis of their classes, cohorts, and orders, as arranged in this work" p. 985-1023. In: E. Le Maout & J. Decaisne, A general system of botany, transl. by F.H. Hooker. London.
   
2. Prantl, K.A.E. 1874. Lehrbuch der Botanik. Leipzig.
3. Eichler, A.W. 1883. Syllabus der Vorlesungen über Phanerogamenkunde, 3rd ed. Berlin.
   
4. Engler, H.G.A. & K.A.E. Prantl. 1892. Syllabus der Vorlesungen über specielle und medicinisch-pharmaceutische Botanik. Berlin.
   
5. ----. 1898. Syllabus der Pflanzenfamilien. Berlin.
   
6. Bessey, C.E. 1915. The phylogenetic taxonomy of vascular plants. Ann. Missouri Bot. Gard. 2: 109-164.

Besseyan principles

• 1. woody to non-woody; perennial to annual; terrestrial to aquatic or epiphytic, saprophytic and parasitic conditions
• 2. cylindric to scattered vascular bundle(s)
• 3. alternate leaves to opposite or whorled; simple leaves to compound leaves
• 4. bisexual flowers to unisexual in most instances
• 5. perianth parts many and spirally arranged to few and whorled with actinomorphic (regular) to zygomorphic (irregular) flowers
• 6. separate perianth parts, poorly differentiated in to sepals and petals, to fused perianth parts, sharply differentiated; petalous to apetalous
• 7. many separate stamens to few united stamens
• 8. hypogyny to perigyny and epigyny (e.g. superior to inferior)
• 9. numerous and separate carpels to few and fused carpels
• 10. pollen grains with one pore to grains with two or more pores
• 11. small embryo in abundant endosperm in arillate seeds to large embryo without endosperm in non-arillate seeds
• 12. axile placentation to free-central placentation
• 13. single fruits to aggregate fruits; capsules to drupe or berry
• 14. pro-anthocyanin compounds to anthocyanin compounds

In summary: angiosperm evolution has been one of reduction in number, fusion and specialization of parts coupled with changes in symmetry justification: evolution is the cause of a natural system of classification; natural classification will represent the hierarchy of evolution. Classifications are based on features that seem to reflect common ancestry.
methods:

(1) describe organisms in terms of shared characters;
(2) make groupings using the features that seem most appropriate. This requires detailed knowledge of the biology of the taxa involved;
(3) arrange groups hierarchically;
(4) produce a formal classification, dividing the hierarchy into groups and naming them. Monophyletic groups are preferred but exceptions are made.

2. NATURAL: A system of classification which utilizes all attributes under consideration and therefore is broadly useful with phylogeny being only one criterion used to establish the system. Nonetheless, related groups must be clearly and closely associated.

1. Huxley, J. (ed.). 1940. The new systematics. Oxford.
   
2. Mayr, E. 1942. Systematics and the origin of species from the viewpoint of a zoologist. New York.
   
3. --. 1957. The species problem. Washington, D.C.
   
4. --. 1969. Principles of systematic zoology. New York.
   
5. Simpson, G.G. 1961. Principles of animal taxonomy. New York.
   
6. Benson, L.H. 1962. Plant taxonomy: Methods and principles. New York.
   
7. Davis, P.H. & V.H. Heywood. 1963. Principles of angiosperm taxonomy. New York.
   
8. Porter, C.L. 1959. Taxonomy of flowering plants. San Francisco.
   
9. Solbrig, O.T. 1970. Principles and methods of plant biosystematics. Toronto.
   
10. Radford, A.E., W.C. Dickison, J.R. Massey & C.R. Bell. 1974. Vascular plant systematics. New York.

phenetics
see this overview of numerical taxonomy compare with the overview of cladistics and a justification for evolutionary classification

1. Adanson, M. 1763. Familles des plantes. Paris.

Charles Michener
Robert Sokal (1926- )
Peter H. A. Sneath

1. Sokal, R. & P.H.A. Sneath. 1963. Principles of numerical taxonomy. San Francisco.
   
2. Heywood, V.H. & J. McNeill (eds.). 1964. Phenetic and phylogenetic classification. London.
   
3. Sneath, P.H.A. & R. Sokal 1973. Numerical taxonomy: The principles and practice of numerical classification. San Francisco.
   
4. Felsenstein, J. (ed.). 1983. Numerical taxonomy. Berlin.

justification: repeatability and objectivity. Subjectivity is eliminated through the selection of a large number of characters and constructing a classification by means of a hierarchic, multivariate statistic. The resulting classification is based on overall similarity.
methods:

(1) describe organism using their many features and treat the characters equally
(2) record all features in the form of a data matrix;
(3) calculate similarities between pairs of taxa;
(4) group taxa based on overall similarity;
(5) name the groups.

phenetics claims to be highly predictive and allows the maximum of generalizations to be made from its generated scheme of classification. Note that all characters are phenotypic and all are of equal weight.

3. CLADISTICS: the organization of data based on perceived similarities for the purpose of obtaining a system of classification. The goal is to produce objective and repeatable branching diagrams depicting hypothecial evolutionary histories.
Introduction to cladistics from the University of California Museum of Paleotology - be sure to follow the links to the methodology, the implications of the methodology, and the need for cladistical studies.
What is phylogeny? by David Joyce - follow the links.
Macroevolutionary patterns and phylogeny by Barry Sinervo - REQUIRED READING
Willi Hennig (1913-1989)
Warren H. Wagner, Jr. (1920- )
groundplan/divergence method (1950)

1. Funk, V.A. & D.R. Brooks. 1981. Advances in cladistics. New York.
   
2. Funk, V.A. & M. Donoghue. 1996+. Cladistic literature: http://www.utexas.edu/depts/systbiol/info/cladliterature.html
   
3. Hennig, W. 1966. Phylogenetic systematics (trans. D.D. Davis & R. Zangerl). Urbana.
   Kluge, A.G. & J.S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1-32.
   
4. Nelson, G.J. 1971. "Cladism" as a philosophy of classification. Syst. Zool. 20: 373-384.
   
5. -- 1972. Phylogenetic relationship and classification. Syst. Zool. 21: 227-231.
   
6. -- 1973. Classification as an expression of phylogenetic relationships. Syst. Zool. 22: 344-359.
   
7. Wagner, W.H. 1980. Origin and philosophy of the groundplan-divergence method of cladistics. Syst. Bot. 5: 173-193.
   
8. Wiley, E.O. 1981. Phylogenetics: The theory and practice of phylogenetic systematics. New York.

justification: the branching hierarchy of phylogeny is the only natural hierarchy suited to classification. This branching pattern is unique and unambiguous. Classifications are based on recentcy of common ancestry.
methods:

(1) identify and record features;
(2) shared features are identified and are used to sort the taxa into groups;
(3) construct a cladogram and select one using parsimony;
(4) interpret the cladogram(s);
(5) produce a formal classification by naming groups.

Definitions:
See this list of definitions

analogous trait: states of a character shared through adaptations
autapomorphy: an uniquely-derived character
clade: a group.
cladogram: a branching diagram reflective of evolution.
dendrogram: a branching diagram.
hierarchy: a system of groups within groups, generally with the levels ranked according to their inclusiveness.
homologous trait: states of a character derived from an ancestral state; shared by decent.
homoplasy: possession by two or more groups of a similar trait or character not derived by the groups from a common ancestor; embraces convergencies.
monophyletic: a group which includes an ancestor and all of its descendants.
paraphyletic: a group which includes an ancestor and some but not all of its descendants.
parsimony: the principle of invoking the minimal number of evolutionary changes to infer phylogenetic relationships.
plesiomorphy: a primitive character relative to the group being studied.
polarity: the direction of an evolutionary trend as determined from outgroup comparisons, paleotology and ontogeny.
polyphyletic: a group in which the most recent common ancestor is assigned to some other group and not to the group itself; a group consisting of descendants from more than one ancestor.
polythetic: taxa based on a mosaic of characters, no character in isolation being diagnostic for all members.
symplesiomorphy: a shared, evolutionarily primitive or ancestral character; it can not be used to define a group.
synapomorphy: a shared, evolutionarily derived character; it can be used to define a group or clade.
transformation series: the evolutionary history of a character.
monophyletic groups recognized by uniquely derived characters; i.e., synapomorphies.
synapomorphies are shared, uniquely derived characters while sympleisomorphies are shared, primitive character-states.

significant publications

1. Rieseberg, L.H. & L. Brouillet. 1994. Are many plant species paraphyletic? Taxon 43: 21-32.

assumptions:

ontogenetic and outgroup
ancestral states and derived states
primitive or advanced features or characters
outgroup comparisons
primitive characters are more inclusive
advanced characters are less inclusive

subgroups are defined by shared characters and distinguished by unshared or unique characters
cladistics requires character evaluation and characters may be weighted
directionality
principle of parsimony
parsimony demands acceptance of the hypothesis that requires the fewest number of character state changes
the most acceptable hypothesis is therefore the most parsimoniest

Biogeography

For a review of the biomes of North America, see the PBIO 100 notes
patterns of distribution
classification depends on the evolutionary development of the taxon, its relationship to current environmental conditions, and its distribution both past and present
Alexander von Humboldt (1769-1859)
Aimé Bonpland (1773-1858)
Essai sur la géographie des plants (1806)
life zones and altitudinal zonation
a good overall review in note format
sympatric: same general geographic range
allopatric: ranges do not overlap
disjunct: widely separated populations
continental drift and information on how it relates to biogeography
plate tectonics with some additional details on the earth and its interior
a rather simplified view of plate tectonics in several pages
Pangaea
Gondwanaland
Laurasia
endemism and endemic
Death Valley; southern Utah; central Texas; central Florida
insular endemism
Hawaii, Galapagos, Canary island
shale barren endemics
adaptive radiation relative to climate, space and source of material
vicariant biogeography is concerned with discovering the commonality of the observed distribution patterns shown by unrelated taxa which suggests a common and simultaneous process
vicariance; vicariant: one species replaced by a similar closely related one in separate geographic or ecological areas
vicariance events: extinction or some type of disruption resulting in the fragmentation of a widely dispersed species such as continental drift, mountain building, climatic change or any other kind of geographic or environmental
reproductive isolation reinforced by disjunction
five basic historical biogeographic methods

• dispersalism: dispersals from centers of origin
  
• phylogenetic: rates of progression and deviation
  
• panbiogeography: plotting individual patters of distributions to elucidate general patterns
  
• cladistic: correlation between taxonomic and area relationships parsimony analysis of endemicity: areas defined by shared taxa

significant literature

1. Axelius, B. 1991. Areas of distribution and areas of endemism. Cladistics 7: 197-199.
   
2. Bremer, K. 1992. Ancestral areas: A cladistic reinterpretation of the center of origin concept. Syst. Biol. 4: 436-445.
   
3. Cracraft, J. 1982. Geographic differentiation, cladistics, and vicariance biogeography: Reconstructing the tempo and mode of evolution. Amer. Zool. 22: 411-424.
   
4. Harold, A.S. & R.D. Mooi. 1994. Areas of endemism: Definition and recognition criteria. Syst. Biol. 43: 261-266.
   
5. Henderson, I.M. 1991. Biogeography without area? Austral. Syst. Bot. 4: 59-71.
   
6. Humphries, C.J. 1992. "Cladistic biogeography," pp. 137-159. In: P.L. Forey et al. (eds.), Cladistics: A practi-cal course in systematics. Oxford.
   
7. -- & L.R. Parenti. 1986. Cladistic biogeography. Oxford.
   
8. Mayden, R.L. 1991. The wilderness of panbiogeography: A synthesis of space, time, and form? Syst. Zool. 40: 503-519.
   
9. Morrone, J.J. 1994. On the identification of areas of endemism. Syst. Biol. 43: 438-441.
   
10. -- & J.V. Crisci. 1995. Historical biogeography: Introduction to methods. Ann. Rev. Ecol. Syst. 26: 373-401.
    
11. Nelson, G.J. & N.I. Platnick. 1981. Systematics and biogeography: Cladistics and vicariance. New York.
    
12. -- & D.E. Rosen (eds.). 1981. Vicariance biogeography. New York.
    
13. Ronquist, F. 1994. Ancestral areas and parsimony. Syst. Biol. 43: 267-274.
    
14. Rosen, D.E. 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27: 159-188.
    
15. Wiley, E.O. 1988. Vicariance biogeography. Ann. Rev. Ecol. Syst. 19: 513-542.

• long-distance dispersal (LDD)

1. Van der Pijl. 1972. Principles of dispersal in higher plants, ed. 2. New York.

catastrophic selection and sympatric speciation
parallelism: gross similarities in related taxa
convergence: similarities in unrelated taxa
adaption
Mediterranean vegetation
Cactaceae and Euphorbiaceae
vegetative convergence

1. Brown, J.H. & A.C. Gibson. 1983. Biogeography. St. Louis.
   
2. Myers, A.A. & P.S. Giller. 1988. Analytical biogeography. An integrated approach to the study of animal and plant distribution. London.

Sites of Interest
Course syllabus on ecology and evolutionary biology by Sinervo & Potts at UC Santa Cruz

Last revised: 21 Jan 1999