BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

A. Phylogeny1. Defined

2. Phylogeny vs. tokogeny

3. Clade and monophyletic group

4. Sister group

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

A. Phylogeny1. Defined

2. Phylogeny vs. tokogeny

3. Clade and monophyletic group

4. Sister group

Willi Hennig (German; 1913-1976)

Grundzüge einer Theorie der Phylogenetischen Systematik (Hennig, 1950).

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

B. Cladogram1. Defined

2. Styles

2. Branches and nodes; internal vs. external branches

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

e.g., useful characters for tetrapod phylogenetics

Skeletal Limbs (legs): zero, fourFur: no, yesTail: yes, noBipedality: no, yes

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

e.g., useful characters for tetrapod phylogenetics

Skeletal Limbs (legs): zero, fourFur: no, yesTail: yes, noBipedality: no, yes

Outgroup: fish (also some invertebrate)

Ingroup: (amphibians, reptiles, monkeys, non-human apes, humans)

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

Bats

Birds

Insects

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

Modern cetaceans: vesitigial pelvis &, occassionally hind “limbs”

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

C. Characters and homology1. Cladogram as a framework for studying the origin of variation among species.

2. Characters and character states

3. Apomorphies vs. plesiomorphies

Autapomorphy vs. synapomorphy

Synapomorphy vs. symplesiomorphy

Hashmarks

4. Homology, analogy, and homoplasy

Basilosaurus had 2 tiny legs, probably used

as claspers when mating.

basilosaurids and dorudontids (ca. 40-30 Ma)

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

II. Cladistics

A. The taxon-by-character matrix

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

II. Cladistics

B. Synapomorphies as evidence of recency of common ancestry1. Ingroup vs. outgroup2. Parsimony and Ockham’s Razor3. Parsimony the optimality criterion as a means of dealing with incongruence

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

II. Cladistics

C. Minmizing “steps” is the practical application of parsimony

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

Snail

Hagfish

Perch

Salamander

Lizard

Mouse

Chimp

Human

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

Notochord; hollow dorsal nerve chord

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

Notochord; hollow dorsal nerve chord

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

Notochord; hollow dorsal nerve chord

vertebrae; jaws

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

Lungs, 4-legs

Notochord; hollow dorsal nerve chord

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

Claws or nails

Lungs, 4-legs

Notochord; hollow dorsal nerve chord

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

Claws or nails

Fur; mammary glands

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

Claws or nails

Fur; mammary glands

Loss of tail

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

Claws or nails

Fur; mammary glands

Loss of tail

Notochord; hollow dorsal nerve chord

Lungs, 4-legs10 “steps”

BIOL 471 – Methods in Systematics: Topic -- PhylogeneticsHow to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

Notochord; hollow dorsal nerve chord

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

Lungs, 4-legs

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mammary glands

Fur; mammary glands

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mammary glands

Fur; mammary glands

tail

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

vertebrae; jaws

vertebrae; jaws

Notochord; hollow dorsal nerve chord

Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mammary glands

Fur; mammary glands

tail

17 “steps”

How to evaluate an alternative cladogram?

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

II. Cladistics

C. Minmizing “steps” is the practical application of parsimony

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

III. Sources of variation for characters

A. Morphological and anatomical variation

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

III. Sources of variation for characters

B. Genetic (e.g., DNA sequence) variation1. Source of genetic data

2. Alignment of DNA sequences.

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

III. Sources of variation for characters

B. Genetic (e.g., DNA sequence) variation1. Source of genetic data

2. Alignment of DNA sequences.

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

III. Sources of variation for characters

B. Genetic (e.g., DNA sequence) variation1. Source of genetic data.

2. Alignment of DNA sequences.

BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

I. Phylogenetic terms and concepts

A. Phylogeny1. Defined

2. Phylogeny vs. tokogeny

3. Clade and monophyletic group

4. Sister group