Phylogeny and the Tree of Life

Chapter 26

BCOR 012

February 4,7, 2011

Systematics: Connecting Classification to Phylogeny

Systematics, Taxonomy, and PhylogenyConstructing cladograms

Phylogenetic Classification Molecular Systematics Parsimony

Outline for February 4,7 2011

Systematics is the study of biological diversity in an evolutionary context. It includes

•speciation•taxonomy •phylogeny.

Taxonomy is the branch of systematics concerned with naming and classification.

• Scientific names are binomials • Example: Acer saccharum

- Acer is the genus name - it is a Latin noun

- saccharum is the specific epithet - it is a Latin adjective

Carolus Linnaeus1707-1778

Biological classifications are hierarchical: each taxonomic group is nested within a more inclusive higher order group.

(Note that only the genus name and specific epithet are italicized.)

Fig. 26-4Species

Canislupus

Pantherapardus

Taxideataxus

Lutra lutra

Canislatrans

Order Family Genus

Carn

ivora

Felidae

Mu

stelidaeC

anidae

Canis

Lu

traT

axideaP

anthera

“Our classificationswill come to be, asfar as they can beso made, genealogies.”

- Charles Darwin, 1859

Phylogeny and Classification

Phylogeny is the study of the pattern of divergence history.

(as opposed to speciation, which addresses process.)

Assembling a phylogeny using cladistics, taxa are associated on the basis of shared evolutionary innovations.

Willi Hennig, 1913 - 1976

Founder of PhylogeneticSystematics

(also called cladistics)

One of the evolutionary innovations shared by birds is the feather …

Homology, the sharing of an innovation (derived character) because of its invention in a common ancestor.

Serial Homology of the Lobster

Figure 34.4b-c  Chordate segmentation

CRUSTACEANS COMPARED - EVOLUTIONARY HOMOLOGY

CRUSTACEANS COMPARED: EVOLUTIONARY TRANSFORMATION

LOBSTERROCK CRAB

Fig. 26-8

Deletion

Insertion

1

2

3

4

Fig. 26-8a

Deletion

Insertion

1

2

Fig. 26-8b

3

4

DNA Evolution: stable and labile characters relate to function.Example: Homeobox genes, which govern variation in serial homologs.

The homeobox (in the gene) codes for a homeodomain (in the protein synthesized from the gene). The homeodomain has a precise three-dimensional structure related to its function.

In evolution, the homeodomain is relatively stable because it has a precise job.

Dm - FruitflyTc - BeetleJc - ButterflyAk - Onycho- phoran

Amino acid sequences compared for the homeotic gene Ubx

insects

arthropods

Decides six legs or more

Parsimony

Under the principle of parsimony, tree A would bepreferred over B and C as it is one step shorter.

Ockham's razor.: when trying to choose between multiple competing theories the simplest theory is probably the best.

How to construct a cladogram:

• Choose a study group• Choose an appropriate outgroup• Compile data matrix• Polarize characters• Use shared derived characters to associate

study group taxa and construct the cladogram

The outgroup is the group used to polarize characterstates in the study group. It should be the group most closely related (on the basis of other lines ofevidence) to the study group that is not actually part of the study group.

lancelet

How to construct a cladogram:

• Choose a study group• Choose an appropriate outgroup• Compile data matrix• Polarize characters• Use shared derived characters to associate

study group taxa and construct the cladogram

The primitive character is the one shared by the outgroup and some, but not all, of the study group.

How to construct a cladogram:

• Choose a study group• Choose an appropriate outgroup• Compile data matrix• Polarize characters• Use shared derived characters to associate

study group taxa and construct the cladogram

Kinds of Characters

• Apomorphy - a derived character state

• Synapomorphy - a shared derived character state

• Autapomorphy - a derived character state unique to one study group member

• Symplesiomorphy – a shared primitive character state

Cladistic Analysis and Classification: Kinds of Groups

A monophyletic group includes a common ancestor andall of its descendents

Example: Reptilia (defined to include birds)

A paraphyletic group includes a common ancestor and some but not all of its descendents

Example: Reptilia (defined to exclude birds)

A polyphyletic group is a group whose members do not share a recent common ancestor

Example: homeotherms (warm-blooded animals)

In a phylogenetic classification, only monophyletic groups are named.

If a paraphyletic group bears a name, it will be an informal one (e.g., ‘gymnosperms’)

For Phylogenetic Classification, taxa (taxonomic groups) should be natural groups,

that is groups reflecting phylogeny.

The nested relationship of cladesclades is reflected in the nested relationship of taxataxa in the resultant classification. All are monophyletic groups.

Fungi

EUKARYA

Trypanosomes

Green algaeLand plants

Red algae

ForamsCiliates

Dinoflagellates

Diatoms

Animals

AmoebasCellular slime molds

Leishmania

Euglena

Green nonsulfur bacteria

Thermophiles

Halophiles

Methanobacterium

Sulfolobus

ARCHAEA

COMMONANCESTOR

OF ALLLIFE

BACTERIA

(Plastids, includingchloroplasts)

Greensulfur bacteria

(Mitochondrion)

Cyanobacteria

ChlamydiaSpirochetes

both are prokaryotic

eukaryotes