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Biology 265 EVOLUTION

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Title: Biology 265 EVOLUTION


1
Biology 265EVOLUTION
  • Lecture 10

2
Overview
  • Biodiversity, systematics and classification
  • Two approaches to classification, phenetic and
    phylogenetic
  • Phenetics
  • Based on evolution (phylogeny)
  • cladistics
  • evolutionary

3
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

4
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

5
But back up a second!
  • How come we need systematics or classification?

6
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)

7
And because classification is useful
  • It provides an index to stored information.
  • It has heuristic value, allowing prediction.
  • It permits the making of generalizations.

8
Common approaches
  • Important to all methods of classification is the
    identification of
  • clusters to be classified
  • and characters to classify them with

9
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)

10
Tree of Life
11
Use evolution to classify?
  • Phenetics - NO
  • Phylogenetics - YES

12
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

13
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.

14
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

15
Use evolution to classify?
  • Phenetics - NO
  • Phylogenetics - YES

16
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)

17
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)

18
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

19
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

20
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

21
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.

22
Synapomorphy(sharing of an evolutionary novelty)
23
Simplesiomorphy(sharing a general character)
24
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

25
Monophyletic groups
Archaea outgroup
monophyletic groups (clades)
Bacteria
Bacteria
Bacteria
Eukaryote
Eukaryote
Eukaryote
Eukaryote
26
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

27
Archaea outgroup
Bacteria 1
Rooted by outgroup
Bacteria 2
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Root
Eukaryote 4
28
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)

29
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

30
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

31
Two schools use phylogenetic techniques to
classify
  • Cladistics (Hennig)
  • Evolutionary

32
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

33
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34
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35
Two schools of phylogenetics
  • Cladistics (Hennig)
  • Evolutionary

36
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

37
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)

38
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
39
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)

40
Holophyly cladistic monophyly
  • Synapomorphies - shared derived characters
  • a primitive character state (plesiomorphy)
  • a derived character state (apomorphy)

41
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)

42
Polyphyly
  • Homoplasy - convergence
  • a primitive character state (plesiomorphy)
  • a derived character state (apomorphy)

43
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44
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

45
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

46
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

47
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)
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