Table of Contents

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Phylogenetics - Reconstructing the Tree of Life
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http//www.harvardmagazine.com
http//www.amren.com
http//www.pupress.princeton.edu
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Aristotle

• Through classification, one might discover the
  essence and purpose of species.

http//www.geophysics.geol.uoa.gr
Nelson Platnick (1981) Systematics and
Biogeography
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Nelson Platnick (1981) Systematics and
Biogeography
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Linnaeus

• Swedish botanist (1700s)
• Listed all known species
• Developed scheme of classification to discover
  the plan of the Creator

http//bibbild.abo.fi/Linneana
http//www2.nrm.se/fbo/hist
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Nelson Platnick (1981) Systematics and
Biogeography
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Nelson Platnick (1981) Systematics and
Biogeography
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Linnaeus Main Contributions
1) Hierarchical classification scheme
Kingdom Phylum Class Order Family Genus
Species
2) Binomial nomenclature
Before Linnaeus
Apis pubescens, thorace subgriseo, abdomine
fusco, pedipus posticus glabris utrinque margine
ciliatus
After Linnaeus
Apis mellifera
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Darwin

• Species evolved from common ancestors
• Community of descent is the hidden bond
  naturalists have been unconsciously seeking,
  and not some unknown plan of creation.

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Nelson Platnick (1981) Systematics and
Biogeography
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An Evolutionary Perspective Reveals that
Hierarchical Classification is Rather Arbitrary
http//www.zoologi.su.se/research/wahlberg
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But an Accurate Tree is Necessary for Grouping
Organisms
http//www.zoologi.su.se/research/wahlberg
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http//www.life.uiuc.edu/plantbio/260
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http//www.life.uiuc.edu/plantbio/260
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But an Accurate Tree is Necessary for Grouping
Organisms
http//www.zoologi.su.se/research/wahlberg
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How Do We Infer An Accurate Tree?
http//www.zoologi.su.se/research/wahlberg
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Evolutionary Taxonomy

• Based on an overall impression of similarities
  and differences, borne out of years of study of
  a group of organisms.

http//www.archeodroit.net/anthro
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http//www.stanford.edu/petelat1
http//www.birdsasart.com
http//www.birdsasart.com
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http//www.birdphotography.com
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Numerical Taxonomy

• Based on a numerical comparison of similarities
  and differences of a group of organisms.
• Gave a new sense of rigor (eventually used
  computers!).
• The source of data characters and character
  states.

http//www.southalabama.edu
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Source A Field Guide to the Beetles
Source The Birders Handbook
http//www.mun.ca/biology/scarr
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Caminalcules
http//www.uprm.edu/biology/cursos/biologiageneral
/
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Character State Matrix
Species A B C D E Char. 1 1 1 1 1 1 Char.
2 2 2 2 2 2 Char. 3 3 3 3 3 3 Char.
4 4 4 4 4 4 Char. 5 5 5 5 5 5 Char.
6 6 6 6 6 6 Char. 7 7 7 7 7 7 Char.
8 8 8 8 8 8
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Similarity Matrix
Species A B C D B 5 C 5 6 D 1 4 4 E 0 3 3 7
Species A B C B 5 C 5 6 D/E 0.5 3.5 3.5
Species A B/C B/C 5 D/E 0.5 3.5
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Why Might Similarities and Differences Be
Unreliable for Inferring Phylogenies?
http//www.madcowsracing.org
http//www.brookebondsale.com
Homology vs. homoplasy (e.g. convergence,
reversal)
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http//www.ucl.ac.uk/taxome/jim/Mim2
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Why Might Similarities and Differences Be
Unreliable for Inferring Phylogenies?
http//www.iucn-isg.org
http//www.nasa.gov/centers/kennedy
http//yokido.cocolog-nifty.com

• Unequal rates of evolution

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The Terminology of Cladistics
Synapomorphy a shared, derived character
state Autapomorphy a unique, derived character
state Symplesiomorphy a shared, ancestral
character state
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Ancestral vs. derived character states
For lizards, dolphins, and horses, the
ancestral character state is 4 limbs. A derived
character state is the presence of mammary glands.
Phylogeny based on mammary glands.
Phylogeny based on number of limbs.
L H D
L H D
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How do we determine if a trait (character state)
is ancestral or derived?

• fossil record
• outgroup analysis

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How Do We Build A Phylogeny?

• Parsimony - the best tree requires the fewest
  evolutionary changes to explain the
  distribution of shared derived character states
  (synapomorphies) in the organisms.

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A B C D
B A C D
C B A D
A B C D
D C A B
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A B C D
B A C D
C B A D
A B C D
D C A B
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Difficulties in Phylogenetics

• Scoring characters can be challenging
• Homoplasy may be common
• Evolutionary change may erase signs of
  evolutionary history

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Difficulties in Phylogenetics

• Scoring characters can be challenging
• Homoplasy may be common
• Evolutionary change may erase signs of
  evolutionary history
• Rapid radiation from a common ancestor

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Difficulties in Phylogenetics

• Scoring characters can be challenging
• Homoplasy may be common
• Evolutionary change may erase signs of
  evolutionary history.
• Rapid radiation from a common ancestor
• Gene trees may imply the wrong phylogeny

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Difficulties in Phylogenetics

• Scoring characters can be challenging
• Homoplasy may be common
• Evolutionary change may erase signs of
  evolutionary history
• Rapid radiation from a common ancestor
• Gene trees may imply the wrong phylogeny
• Hybridization and horizontal gene transfer

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In spite of such difficulties, independent trees
are often similar