Ozzie Vilhelmsson

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Ozzie Vilhelmsson Zoology Building, Room
213 Tel. [phone] Email
o.vilhelmsson_at_abdn.ac.uk
Estimating and using phylogenies
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Taxonomy and Phylogeny

• What fossils tell us
• What living organisms tell us
• Cladistics
• Constructing phylogenies
• Classification Evolutionary Relationships
• Molecular Analyses - the way ahead!

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Fossils

• Incompleteness of fossil record
• Fossilization an unlikely event
• Only found in sedimentary rocks
• Habitat bias
• Age known
• Intermediates observed
• Can access extinct lines

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PHYLOGENETIC TREES

• Pedigree of a lineage
• Evidence of dates of separation

(trees)
Time
Time
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Tree construction
Gather data

• Morphology
• Development
• Metabolic
• Biochemical
• Genetic
• Anything, really

Similarity matrix (numerical taxonomy)
Tree
Simple, right?
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But, ....
Turtle/birds/crocodile picture
... Different data can yield different trees!
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CLADISTICS

• Aims to distinguish reliable from unreliable
  characters
• Homologies vs. Homoplasies
• Derived vs. ancestral homologies

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CLADISTICS

• Method of determining evolutionary
  histories - displayed as trees
• Clade entire portion of phylogeny from a
  common ancestor
  Monophyletic group
• Cladogram unrooted evolutionary tree (no
  ancestors but points where lineages diverged)

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HOMOLOGIES

• A trait shared between species and inherited from
  their common ancestor homologous
• Ancestral (general) homologies shared by all
  species in lineage - eg. vertebrae in vertebrates
• Derived (special) homologies shared by few
  species in lineage - eg. indeterminate incisors
  in vertebrates

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Why the fuss?
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To reiterate

• Derived homologous traits order TIME of
  separation
• Ancestral homologous traits no use for this -all
  members of lineage have them

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Identifying non-useful traits

• Divergence traits unrecognizable
• eg. plant leaves

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(fig. 23.4 in textbook)
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Identifying non-useful traits

• Divergence traits unrecognizable
• eg. plant leaves
• Homoplasy trait evolves more than once
• different structures resemble each other by
  convergent evolution eg. bat/bird/insect wings
• Both cases analogous traits

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Hennigs Method

• Same trait in 2 species provisionally
  homologous ie. innocent, until proven guilty
• Ancestral homology found in group and outside
  in species outgroup
• Outgroup branched off from below base of
  lineage

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What about wings?
Homoplaseous? Ancestral? Derived?
Fig. 23.2 in textbook
Homoplasy/homology depends on reference/outgroup
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Rooting the tree
Having figured out which traits are important, we
can draw a cladogram. But, where does it root?
(Possible roots picture)
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Distance

• Simple principle How similar are the species?
  (similarity matrix/measurement)
• Works well for simple molecular methods, such as
  DNADNA hybridization data
• Molecular clock assumption

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(Panda example)
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PARSIMONY

• Simple distance rooting assumes
• trait evolution irreversible, ie. ancestral to
  derived
• trait can change only once per lineage
  UNREALISTIC
• But, cladogram requiring fewest reversals/changes
  most likely to be correct
• PARSIMONY simplest is correct!

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PARSIMONY
(counting changes picture)
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Maximum likelihood

• Requires a lot of data, massive computing power
• Need model of evolutionary change to calculate
  probabilities
• Probably the most widely used method today
  (sequence homologies, etc.)

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Drawing a cladogram

• 8 vertebrates
• traits /-
• hagfish outgroup
• derived traits acquired since hagfish
• cladistics minimizes branching - ie. assumes
  minimal homoplasy

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Drawing a cladogram
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A phylogenetic tree
Hagfish Perch Salamander Lizard Crocodile Pig
eon Mouse Chimpanzee
Jaws
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Properties of cladogams

• Temporal order of splits
• Horizontal axis NOT correlated with similarity
• 8 vertibrates cladogram perfect because traits
  arose not lost - BUT SNAKES???

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Classification Evolutionary Relationships

• Linnaeus - predated evolution as central concept
  of biology
• but what features natural? important?
• Modern taxonomists - classification reflects
  evolutionary relationships
• BUT should classification reflect time or rate of
  evolution??

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Defining clades

• Monophyletic - share common ancestor
• Polyphyletic - NO common ancestor
• Paraphyletic - some, but not all, from common
  ancestor

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(mon/para/polyphyletic picture similar to 23.12
in textbook)
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The problem of paraphyly

• Birds and crocodiles - more recent ancestor than
  crocs. and snakes/lizards
• Crocs. evolved more slowly than birds since
  lineages separated
• Birds as separate class recognizes their rapid
  evolution major unique derived traits

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Systematicists

• Still many polyphylectic groups
• Detect convergent evol. change classification
• BUT favour retaining paraphyletic groups to
  underscore rapid evolution
• STABILITY of taxonomic system

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Future of Systematics

• Molecular genetics powerful computers
• Fossil history - dating and derived vs ancestral
  traits
• Molecular more traits than ever before
• Combining two lines of evidence produces accurate
  dated phylogenies