Biol 317: Plant Classification & Identification
Summer 2011
Instructor: Valerie Soza
Office: 408 Hitchcock
Office hours: by appointment
Email: [email protected]
Course website: http://courses.washington.edu/bot113/summer/2011
TA: Pat Lu-Irving
Peer TAs:
Willie Foster, Shula Harkavy, Michelle Mark
Handouts
Course information sheet Syllabus Reading assignments online
Medicinal Herb Garden project
Lab exercises for this week available in lab
Nomenclature
Why naming is important?
George
http://popular-cartoon.blogspot.com/2011/02/george-of-jungle.html
Nomenclature
Why naming is important?
George
George Bush
http://en.wikipedia.org/wiki/George_H._W._Bush
Nomenclature
Why naming is important?
George
George Bush
George W. Bush
George W. Bush, Jr.
http://en.wikipedia.org/wiki/George_W._Bush
Nomenclature
Problems with common names
No rules for usage!
One kind of plant will have many different common names.
The same common name may be associated with many
different plant species.
potato = Solanum tuberosum, Dioscorea
bulbifera, Apios americana, Dioscorea batatas,
Solanopteris bifrons, Plectranthus rotundifolius,
Allium cepa, Gastrodia sesamoides, Ipomoea
batatas, Solanum macranthum, Ipomoea
pandurata, Solanum jasminoides, Dioscorea
esculenta (Mabberley 1997)
http://tombutton.users.btopenworld.com/potato_1.jpg
Early Attempts at Formal Nomenclature
1700s:
Very specific, descriptive names
Up to a dozen Latin adjectives
Example:
http://en.wikipedia.org/wiki/Rosa_canina
Early scientific names for the common wild briar rose
Rosa sylvestris inodora seu canina ( odorless woodland dog rose )
Rosa sylvestris alba cum rubore, folio glabro
( pinkish white woodland rose with hairless leaves )
Linnaeus System Species Plantarum (1753)
Carl von Linné or Carolus Linnaeus
Binomial nomenclature
Genus + species names = scientific name
e.g., Homo sapiens, Solanum tuberosum
or Homo sapiens, Solanum tuberosum
Carolus Linnaeus, detail of a portrait by
Alexander Roslin, 1775; in the Svenska
Porträttarkivet, Stockholm.
Hierarchical system
Kingdom
Phylum
Class Order
Family Genus
Species
Plantae
Magnoliophyta Magnoliopsida
Solanales Solanaceae
Solanum
Solanum tuberosum L.
Hierarchical system
Kingdom
Phylum
Class Order
Family Genus
Species
Plantae
Magnoliophyta Magnoliopsida
Solanales Solanaceae
Solanum
Solanum tuberosum L.
Flexible system
Kingdom
Phylum
Class
Subclass
Order
Family Subfamily Tribe
Genus Species
Subspecies
Plantae
Magnoliophyta Magnoliopsida
Asteridae
Solanales Solanaceae
Solanoideae
Solaneae
Solanum
Solanum tuberosum L.
S. tuberosum ssp. andigena
Classification
What is Classification?
The sorting of things into groups and the assigning of names to
those groups.
Biological science - The grouping of organisms into categories
based on shared characteristics or traits.
Why is this important?
Dealing with large amounts of information.
Understanding and communication about the natural world.
Power of prediction.
To make sense of comparative studies…
prevents comparing apples to oranges Classification is the way we communicate about biological
diversity!
How do we classify organisms?
Group organisms based on how alike they
appear… Linnaeus Sexual System:
Used the presence or absence and number
of sexual parts as the basis for
classification. -24 classes for all plants, on the basis
of stamens. -Classes into orders on the basis of styles in each flower.
http://www.robinsonlibrary.com/science/natural/biography/graphics/linnaeus3.gif
How do we classify organisms?
Group organisms based on how alike they appear…
Today, scientists use:
1. 
2. 
3. 
4.
Visible morphology - structures
Anatomy – internal or microscopic structures
Chemicals – presence/absence, pigments, toxins, etc.
Genetics – chromosome, DNA similarity
Linnaeus’ Classification
Species Plantarum (1753) 100 years before anyone had heard of the idea of evolution.
At the time, people thought species were static or unchanging.
Linnaeus system was artificial. Artificial classification - with no regard for evolutionary
relationships. (e.g., any classification of things other than living things would have to be
artificial). Natural Classification
Charles Darwin (1859 – On the Origin of Species) was the first to suggest that
any classification of life should be genealogical and would naturally be
hierarchical.
Charles Darwin (1859)
http://universe-review.ca/I10-70-Darwin.jpg
Haekel s tree of life (1866)
http://plus.maths.org/issue46/features/phylogenetics/Haeckel.png
Systematics as a process
Since Darwin, scientists have placed more and more emphasis on
developing natural classification systems that reflect the
evolutionary relationships of a group of organisms.
Systematics = the study of biological diversity and its evolutionary
history. Basic activities include classification and naming
(taxonomy). Just like any other kinds of science, systematics is a process.
The goal to classify life based on its evolutionary history is an
ongoing process. As a result, our classifications are dynamic…
Classifications are dynamic…
http://www.wpclipart.com/food/fruit/tomato/tomato.png
Before:
Lycopersicon esculentum Now:
Solanum lycopersicum
(Spooner et al., 1993)
Phylogenetic Classification
A good classification system should have power of prediction.
Ever since Darwin, the goal of classification has been a natural
classification that reflects evolutionary relationships. Phylogeny = the pattern of evolutionary relationships among
species; a branching evolutionary tree of life.
Today our goal is phylogenetic classification = a hierarchical
ordering of taxa according to phylogenetic relationships consisting
of a nested set of ever more inclusive groups.
Phylogeny
Phylogeny is often presented as a diagram (a phylogenetic tree).
http://media-2.web.britannica.com/eb-media/98/5598-004.gif
http://www.sp.uconn.edu/~terry/DHE/Mione1.jpg
Phylogenetic tree
Ingroup
Outgroup
Group 2
H
F E D
G
Group 1
C
B
A
Terminal branch
Node = most recent
common ancestor
Internal branch = ancestral species
Root = common ancestor
time
Ingroup = the study group.
Sister group = the group that is most closely related to the ingroup; closest outgroup.
Outgroup = a more distantly related group. The tree thinking challenge Sister relationships are reciprocal relationships!
(Baum et al. 2005)
Topology = pattern of branching of a phylogenetic tree.
The tree thinking challenge cont. (Baum et al. 2005)
The tree thinking challenge cont. (Baum et al. 2005)
Monophyletic groups
H
G
F E D
C
B
A
Monophyletic group (or clade) = a group composed of a
common ancestor and all of its descendents. [mono = one, phylum = tribe]
Paraphyletic groups
H
G
F E D
C
B
A
Paraphyletic group = a group containing a common ancestor
and some, but not all, of its descendents. [para = near, not quite , phylum = tribe]
Polyphyletic groups
H
G
F E D
C
B
A
Polyphyletic group = a group that does not include the common
ancestor of its members.
[poly = many, phylum = tribe]
Phylogenetic classification
Phylogenetic classification = a hierarchical ordering of
taxa according to phylogenetic relationships consisting of
a nested set of ever more inclusive groups. Or, in a more concise way, the use of phylogeny to
produce the classification taxon (plural – taxa) = any named group at any
hierarchical level (could be a species, genus, family, etc.).
Goal of phylogenetic classification: recognize
monophyletic groups only!
In other words, identify a nested, hierarchical set of
monophyletic groups. Phylogenetic classification
http://www.wpclipart.com/food/fruit/tomato/tomato.png
Before:
Lycopersicon esculentum Now:
Solanum lycopersicum
(Spooner et al., 1993)
Phylogenetic
classification has
more power of
prediction
Phylogenetic reconstruction
Phylogenetic reconstruction (cladistics) in systematics = the
process by which we determine or estimate relationships (from
the present diversity to the pattern of evolutionary relationships). It’s a hypothetical reconstruction of the sequence of evolutionary
events.
Phylogenetic hypotheses are subject to further evaluation when
new data become available. BUT HOW DO WE RECONSTRUCT PHYLOGENY?
Phylogenetic reconstruction
We look for comparable similarities (characters).
The characters which naturalists consider as showing true
affinity between any two or more species, are those which
have been inherited from a common parent, all true
classification being genealogical. (Charles Darwin 1859)
Character = a variable trait of an organism or group.
Character states = alternate forms of a character.
Homology
Homology = similarity due to inheritance of a feature from a common ancestor. A character that arose with the evolution of a group and is shared
due to common ancestry is homologous.
Homologous character: wing of all birds.
Non-homologous character: wing of birds, bats, and insects.
Two components of homology: When we talk about homology as evidence for relationship, we
must refer both to a trait (character) and a group of organisms. Synapomorphy
Synapomorphy = shared, derived character.
(from Gr. syn—together (shared) + apo—away + morph—form)
A character in two or more groups that can be traced back to
the same feature in the common ancestor of those groups,
and not found in other organisms.
Synapomorphies diagnose monophyletic groups.
Example: feathers on birds.
Symplesiomorphy
Symplesiomorphy = shared, ancestral character. (from Gr. syn—together (shared) + plesio—near + morph—form)
An ancestral trait that is shared by two or more modern groups
and can be traced back to their common ancestor, but is not
found among all descendants of this ancestor.
Symplesiomorphies diagnose paraphyletic groups.
Example: keratin scales on reptiles.
Convergent character
Convergent character is NOT homologous!
(from Latin: con—together + vergere—to incline together) A trait due to evolution in parallel in two different organisms,
i.e., convergent evolution or parallel evolution, and not due to
common ancestry.
Convergent characters diagnose polyphyletic groups.
Example: wings on birds, bats, and insects.
Determining whether a character is derived or ancestral
Polarity = direction of evolutionary change.
Most commonly used method to determine polarity:
Outgroup comparison = inference from distribution of
character states in sister group. For a variable character with two or more states, the state
occurring in the outgroup is ancestral. Phylogenetic reconstruction = grouping species by shared
derived states of characters.
Phylogenetic reconstruction from characters
Parsimony = the principle that the explanation requiring the least
change is preferred.
Characters
a
b
c
0
0
0
0
1
0
1
0
1
1
1
1
Taxa
outgrp
1
2
3
out
1
2
3
1
3
b
b
a
4 steps
out
a
c
b
5 steps
2
c
a
c
out
1
2
b
a
3
c
b
6 steps
a
c
Sources of character data
Actual phylogenetic inferences often use many taxa and a
large number of characters.
Sources of data = any comparative data.
morphology
cytology
behavior
DNA sequences
etc.
Inferring phylogenies using DNA sequences
Real example with DNA
sequence data (nucleotide sites).
Green plants
Green plants
Land plants
Tracheophytes (vascular plants)
Seed plants
Ferns
Lycophytes
Hornworts
Mosses
Green algae
Liverworts
Bryophytes
Gymnosperms
Angiosperms
Conifers
(Stefanovic et al. 1998)