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BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
I.
Phylogenetic terms and concepts
A.
Phylogeny
1. 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.
Phylogeny
1. 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.
Cladogram
1. 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 homology
1. 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 homology
1. Cladogram as a framework for studying the origin of variation among species.
2. Characters and character states
e.g., useful characters for tetrapod phylogenetics
3. Apomorphies vs. plesiomorphies
Autapomorphy vs. synapomorphy
Synapomorphy vs. symplesiomorphy
Hashmarks
4. Homology, analogy, and homoplasy
Skeletal Limbs (legs): zero, four
Fur: no, yes
Tail: yes, no
Bipedality: no, yes
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
I.
Phylogenetic terms and concepts
C.
Characters and homology
1. Cladogram as a framework for studying the origin of variation among species.
2. Characters and character states
e.g., useful characters for tetrapod phylogenetics
3. Apomorphies vs. plesiomorphies
Autapomorphy vs. synapomorphy
Synapomorphy vs. symplesiomorphy
Hashmarks
Skeletal Limbs (legs): zero, four
Fur: no, yes
Tail: yes, no
Bipedality: no, yes
4. Homology, analogy, and homoplasy
Outgroup: fish (also some invertebrate)
Ingroup: (amphibians, reptiles, monkeys, nonhuman apes, humans)
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
I.
Phylogenetic terms and concepts
C.
Characters and homology
1. 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
Birds
Bats
Insects
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
I.
Phylogenetic terms and concepts
C.
Characters and homology
1. 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.
basilosaurids and dorudontids (ca. 40-30 Ma)
Characters and homology
1. 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.
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 ancestry
1. Ingroup vs. outgroup
2. Parsimony and Ockham’s Razor
3. 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
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
Lungs, 4-legs
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
Claws or nails
Lungs, 4-legs
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
Fur; mammary glands
Claws or nails
Lungs, 4-legs
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
Loss of tail
Fur; mammary glands
Claws or nails
Lungs, 4-legs
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
Loss of tail
Fur; mammary glands
Claws or nails
10
“steps”
Lungs, 4-legs
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
Lungs, 4-legs
Lungs, 4-legs
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
Claws or nails
Claws or nails
Lungs, 4-legs
Lungs, 4-legs
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
Fur; mamm
Fur; mammary glands
Claws or nails
Claws or nails
Lungs, 4-legs
Lungs, 4-legs
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
Fur; mamm
Fur; mammary glands
Claws or nails
Claws or nails
Lungs, 4-legs
Lungs, 4-legs
vertebrae; jaws
tail
vertebrae; jaws
Notochord; hollow dorsal nerve chord
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
How to evaluate an alternative cladogram?
17
“steps”
Fur; mamm
Fur; mammary glands
Claws or nails
Claws or nails
Lungs, 4-legs
Lungs, 4-legs
vertebrae; jaws
tail
vertebrae; jaws
Notochord; hollow dorsal nerve chord
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) variation
1. 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) variation
1. 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) variation
1. Source of genetic data.
2. Alignment of DNA sequences.
BIOL 471 – Methods in Systematics: Topic -- Phylogenetics
I.
Phylogenetic terms and concepts
A.
Phylogeny
1. Defined
2. Phylogeny vs. tokogeny
3. Clade and monophyletic group
4. Sister group

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