Biology 265 EVOLUTION

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Biology 265EVOLUTION

• Lecture 10

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Overview

• Biodiversity, systematics and classification
• Two approaches to classification, phenetic and
  phylogenetic
• Phenetics
• Based on evolution (phylogeny)
• cladistics
• evolutionary

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Systematics

• The scientific study of the kinds and diversity
  of organisms and of all relationships among them
• Systematics provides the essential framework
  without which we could not recognize or study
  biological diversity and evolution

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Systematics comprises of

• Classification - ordering of organisms into
  groups (taxa)
• Nomenclature - the naming of organisms
• Taxonomy - the theoretical study of
  classification
• All relationships among taxa

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But back up a second!

• How come we need systematics or classification?

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There is something to classify

• Biodiversity exists
• Biodiversity is not homogeneously distributed, it
  is clustered (10-35 million species)
• The clusters seem to be related in a hierarchical
  manner (unlike say the periodic table of elements)

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And because classification is useful

• It provides an index to stored information.
• It has heuristic value, allowing prediction.
• It permits the making of generalizations.

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Common approaches

• Important to all methods of classification is the
  identification of
• clusters to be classified
• and characters to classify them with

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Characters and Clusters

• Characters are heritable attributes of organisms
  about which a single statement can be made (e.g.
  this organism has wings)
• Clusters of biodiversity are groups of similar
  individuals that share common characters and are
  considered worthy of a name (e.g. species)

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Tree of Life
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Use evolution to classify?

• Phenetics - NO
• Phylogenetics - YES

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Phenetic Classification

• Phenetic classification (phenetics, numerical
  taxonomy) is based upon overall similarity
• Phenogram a branching diagram (tree) that links
  taxa by estimates of overall similarity (phenetic
  clustering)
• Theory free method - doesnt assume anything
  about how biodiversity came about or why it is
  how it is

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Constructing a phenogram

• Collect measurement data on various characters
  from the chosen groups known as operational
  taxonomic units (OTUs)
• All characters have equal weight
• Compute a measure of similarity for each pair of
  OTUs
• Use some kind of clustering algorithm to group
  OTUs.

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Example of a clustering algorithm

• Agglomerative clustering algorithm
• First, join the two most similar OTU's into a
  new, compound, OTU
• Second, recompute the similarity measure for the
  resulting cluster
• Repeat until all clusters have merged into one

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Use evolution to classify?

• Phenetics - NO
• Phylogenetics - YES

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Phylogenetic Classification

• Uses evolution to help classify biodiversity
• Assumes that species are related by common
  descent (tree of life)
• that new species are formed by old ones splitting
  (branching speciation)
• and subsequently species change over time
  (diverge)

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Which characters to use?

• In phenetics, all characters were used and had
  equal weight
• but in phylogenetic classification some
  characters are more revealing than others
• only homologous characters are important in
  reconstructing phylogeny (evolutionary history)

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Owens definition of homology

• Homologue the same organ under every variety of
  form and function (true or essential
  correspondence) e.g. whales fin and human limbs.
• Analogy superficial or misleading similarity
  e.g. whales and fishs fins.
• Richard Owen 1843

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Darwin and homology

• The natural system is based upon descent with
  modification .. the characters that naturalists
  consider as showing true affinity (i.e.
  homologies) are those which have been inherited
  from a common parent
• Charles Darwin, Origin of species
  1859

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A definition of homology

• Homology is the similarity that is the result of
  inheritance from a common ancestor
• Identification and analysis of homologies is
  central to phylogenetic (evolutionary and
  cladistic) classification

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Weighting homologous characters

• Synapomorphies (shared derived characters) have a
  high weighting, that is they are considered very
  important in revealing relatedness.
• Symplesiomorphies (shared ancestral characters)
  have a low weighting.

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Synapomorphy(sharing of an evolutionary novelty)
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Simplesiomorphy(sharing a general character)
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Phylogenetic systematics

• Sees homology as evidence of common ancestry
• Uses tree diagrams to portray relationships based
  upon recency of common ancestry
• Monophyletic groups (clades) - contain species
  which are more closely related to each other than
  to any outside of the group

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Monophyletic groups
Archaea outgroup
monophyletic groups (clades)
Bacteria
Bacteria
Bacteria
Eukaryote
Eukaryote
Eukaryote
Eukaryote
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Outgroup Comparison

• A taxon from outside the group being studied is
  selected
• to determine which characters are ancestral or
  derived
• The outgroup is used to root the tree

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Archaea outgroup
Bacteria 1
Rooted by outgroup
Bacteria 2
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Root
Eukaryote 4
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Phylogenetic analysis requires careful thought

• Phylogenetic analysis is frequently treated as a
  black box into which data are fed (often gathered
  at considerable cost) and out of which The Tree
  springs
• Hillis, Moritz Mable (1996)

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Phylogenetic analysis is an attempt to infer the
past

• Inferring a phylogeny is an attempt to produce a
  best estimate of an evolutionary history based
  upon incomplete information
• We do not have direct information about the past
  - only access to contemporary species and
  molecules

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Some premises underlying phylogenetic inferences

• Phylogenetic inferences assume the inheritance of
  ancestral characters, and the existence of an
  evolutionary history defined by changes in these
  characters
• A tree-like model of evolution

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Two schools use phylogenetic techniques to
classify

• Cladistics (Hennig)
• Evolutionary

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Cladistics

• Based upon branching patterns where parental
  species split into two daughter species
• Focuses on bifurcations (splits) of the tree, not
  the amount of divergence

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Two schools of phylogenetics

• Cladistics (Hennig)
• Evolutionary

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Constructing an evolutionary classification

• Determine which species are most closely related
  (i.e. which had the most recent common ancestor)
• Search for gaps that separate higher taxa
  (genera, families etc)
• Takes into account branching pattern and amount
  of divergence

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Two types of phylogenetic tree

• Cladogram a tree diagram which depicts a
  hypothesized evolutionary history all the taxa
  are at the tips (cladistic)
• Phylogram a tree which indicates by branch
  length the degree of change believed to have
  occurred along each lineage (evolutionary)

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Cladograms and phylograms
Bacteria 1
Bacteria 2
Cladograms show branching order - branch lengths
are meaningless
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
Phylograms show branch order and branch lengths
Bacteria 1
Bacteria 2
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
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Three types of group

• Monophyletic
• for cladists holophyly ancestor and all its
  descendents
• Paraphyletic
• ancestor and some of its descendents
• Polyphyletic
• no common ancestor in group (not allowed in
  phylogenetic classification)

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Holophyly cladistic monophyly

• Synapomorphies - shared derived characters
• a primitive character state (plesiomorphy)
• a derived character state (apomorphy)

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Paraphyly(OK in evolutionary classification)

• Symplesiomorphies(persistence of shared
  primitive states)
• reptiles including crocodiles but not birds
• a primitive character state (plesiomorphy)
• a derived character state (apomorphy)

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Polyphyly

• Homoplasy - convergence
• a primitive character state (plesiomorphy)
• a derived character state (apomorphy)

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Problems with phenetics

• Seeks to be objective but is in fact completely
  subjective
• Depends entirely on which characters you use and
  on which algorithms
• No reason to prefer one algorithm over another
• No theory to refer to in order to test which
  alternative phenograms are closer to the truth -
  because there is no truth

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Classification is evidence for Darwinian evolution

• Why is biodiversity hierarchical?
• Even phenetic methods build a hierarchy
• That seems to be the way nature is organized
• and gradual divergence, modification by descent,
  Darwinian evolution expects such a pattern

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Truth

• All classifications based on evolution, first
  seek to find a truth
• The truth is the real relationships among taxa
  (i.e. the tree of life)
• Evolutionists believe that a branching hierarchy
  (a phylogeny) exists because species evolved
• They believe that this should be the basis for
  classification

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Reconstructing Phylogeny

• Trees are inferred approximations of phylogenetic
  history
• Different techniques can give different estimates
  of the real phylogeny, but all are aiming for the
  same truth (what actually happened) and so they
  can be judged by how well they perform
  (objective)
• How one uses the phylogeny to classify taxa is
  really where cladists and evolutionary
  taxonomists differ (subjective)