Biol 317: Plant Classification & IdentificationSummer 2011

Instructor: Valerie SozaOffice: 408 Hitchcock

Office hours: by appointmentEmail: vsoza@u.washington.edu

Course website: http://courses.washington.edu/bot113/summer/2011

Peer TAs:Willie Foster, Shula Harkavy, Michelle Mark

TA: Pat Lu-Irving

Course information sheet

Syllabus

Reading assignments online

Medicinal Herb Garden project

Lab exercises for this week available in lab

Handouts

Nomenclature

Why naming is important?

George

http://popular-cartoon.blogspot.com/2011/02/george-of-jungle.html

Why naming is important?

George

George Bush

Nomenclature

http://en.wikipedia.org/wiki/George_H._W._Bush

Why naming is important?

George

George Bush

George W. Bush

George W. Bush, Jr.

Nomenclature

http://en.wikipedia.org/wiki/George_W._Bush

Problems with common names

No rules for usage!

http://tombutton.users.btopenworld.com/potato_1.jpg

The same common name may be associated with many different plant species.

One kind of plant will have many different common names.

“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)

Nomenclature

Early Attempts at Formal Nomenclature

Example:

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”)

1700s:Very specific, descriptive namesUp to a dozen Latin adjectives

http://en.wikipedia.org/wiki/Rosa_canina

Linnaeus System “Species Plantarum” (1753)

Binomial nomenclatureGenus + species names = scientific name

e.g., Homo sapiens, Solanum tuberosumor Homo sapiens, Solanum tuberosum

Carolus Linnaeus, detail of a portrait by Alexander Roslin, 1775; in the Svenska Porträttarkivet, Stockholm.

Carl von Linné or Carolus Linnaeus

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida

Order Solanales

Family Solanaceae

Genus Solanum

Species Solanum tuberosum L.

Hierarchical system

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida

Order Solanales

Family Solanaceae

Genus Solanum

Species Solanum tuberosum L.

Hierarchical system

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida

Subclass Asteridae

Order Solanales

Family Solanaceae

Subfamily Solanoideae

Tribe Solaneae

Genus Solanum

Species Solanum tuberosum L.

Subspecies S. tuberosum ssp. andigena

Flexible system

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!

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.

How do we classify organisms?

http://www.robinsonlibrary.com/science/natural/biography/graphics/linnaeus3.gif

Group organisms based on how alike they appear…

Today, scientists use:

1.  Visible morphology - structures2.  Anatomy – internal or microscopic structures3.  Chemicals – presence/absence, pigments, toxins, etc.4. Genetics – chromosome, DNA similarity

How do we classify organisms?

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).

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.

Natural Classification

Charles Darwin (1859)

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.

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…

Before:Lycopersicon esculentum Now:Solanum lycopersicum

(Spooner et al., 1993)

http://www.wpclipart.com/food/fruit/tomato/tomato.png

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://www.sp.uconn.edu/~terry/DHE/Mione1.jpg

http://media-2.web.britannica.com/eb-media/98/5598-004.gif

Phylogenetic tree

Node = most recent common ancestor

H G F E D C B ATerminal branch

Internal branch = ancestral species

Root = common ancestor

Group 1 Group 2Outgroup

Ingroup

Ingroup = the study group.Sister group = the group that is most closely related to the ingroup; closest outgroup. Outgroup = a more distantly related group.

time

(Baum et al. 2005)

The “tree thinking challenge”

Sister relationships are reciprocal relationships!

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 group = a group containing a common ancestorand some, but not all, of its descendents.

[para = near, “not quite”, phylum = tribe]

H G F E D C B A

Paraphyletic groups

H G F E D C B A

Polyphyletic groups

Polyphyletic group = a group that does not include the common ancestor of its members.

[poly = many, phylum = tribe]

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

Before:Lycopersicon esculentum Now:Solanum lycopersicum

(Spooner et al., 1993)

http://www.wpclipart.com/food/fruit/tomato/tomato.png

Phylogenetic classification has more power of prediction

Phylogenetic classification

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?

“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)

Phylogenetic reconstruction

We look for comparable similarities (characters).

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.

CharactersTaxa a b coutgrp 0 0 01 0 1 02 1 0 13 1 1 1

out 1 2 3

4 steps

acb

b

out 1 23

5 steps

aa c

c

b

out 1 32

6 steps

aa c

cb

b

Phylogenetic reconstruction from characters

Parsimony = the principle that the explanation requiring the least change is preferred.

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 algae”

Green plants

Live

rwor

tsM

osse

sH

ornw

orts

Lyco

phyt

es

Fern

s

Gymnosperms AngiospermsSeed plants

Tracheophytes (vascular plants)Bryophytes

Land plants

Conifers

(Stefanovic et al. 1998)