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How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics

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Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437 in chapter 23: Reconstructing and ... – PowerPoint PPT presentation

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Title: How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics


1
Lecture V How to Determine Evolutionary
Relationships Concepts in Phylogeny and
Systematics Textbook Reading pp 425-433, 435-437
in chapter 23 Reconstructing and using
Phylogenies
2
Nature 413, 277 - 281 (2001) Skeletons of
terrestrial cetaceans and the relationship of
whales to artiodactyls. J. G. M. Thewissen, E.
M. Williams, L. J. Roe S. T. Hussain. See
webpage for link to pdf of this paper, and
summary/persptive of this paper
3
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4
Taxonomic classification is hierarchical and
nested
  • Taxonomy is the science of the classification
    (naming) of organisms
  • Linnean classification called binomial
    nomenclature, in reference to genus and specific
    epithet
  • Taxon is a generic term for any taxonomic unit
    (level)
  • Most inclusive taxon, not shown here, is Domain

5

Phylogeny history of descent of a group of
organisms from their common ancestor
Phylogenetic Tree or Cladogram. Depiction of a
phylogeny. Carries information only on branching
relationships no information about passage of
time or amount of phenotypic change. Each
branching point (node) reflects a divergence
(ie, speciation, cladogenesis) event that took
place in the species that is the most recent
common ancestor to the descendents of that
cladogenesis event Lineage Organisms in an
ancestor-descendent relationship
6
The nested polygons here show taxonomic
groupings, but with no regard for inclusion or
exclusion of ancestors common to the groupings
7
The nested polygons here do show taxonomic
groupings, but with regard for inclusion or
exclusion of ancestors common to the groupings
8
Determining monophyletic taxa is key to
classifying organisms according to their
evolutionary history
  • Monophyletic taxon is one in which a single
    ancestor gives rise to all species, and which
    includes all descendents of that single ancestor
  • Paraphyletic taxon excludes one or more species
    descended from the most recent common ancestor of
    the taxon
  • Polyphyletic taxon excludes the most recent
    common ancestor of all members of the taxon

A taxon that includes only A and B would be
paraphyletic
A taxon that includes B, C and D would be
polyphyletic
A taxon that includes D, E and F would be
monophyletic
9
  • SCHOOLS OF SYSTEMATICS
  • TRADITIONAL EVOLUTIONARY TAXONOMY Simpson and
    others
  • Establish taxa based on common ancestry (clades)
    and the extent of adaptive evolutionary change
  • evolutionary groups that represent adaptive zone
    constitute legitimate higher taxa -- a grade
  • adaptive zone characteristic reaction and
    mutual relationship between environment and
    organism, a way of life and not a place where
    life is led.
  • paraphyletic taxa may be acceptable
  • PHYLOGENETIC SYSTEMATICS (CLADISTICS) Hennig
  • Establish taxa based on clades monophyletic taxa
    only
  • Powerful methodological and analytic tool for
    determining relationships
  • The tools of cladistics now represent the
    prevailing approach to determining relationships
    the philosophy of strict monophyly wrt
    classification is still under debate -- bears on
    definition - concept- of species

George Gaylord Simpson (1902-1984). Mammalian
Paleontologist, regarded as one of the architects
of the modern synthesis. Formulated the
principles of evolutionary taxonomy
Willi Hennig (1913-1976). Hennig is best known
for developing phylogenetic systematics, a
coherent theory of the investigation and
presentation of the relations that exist among
species.
http//www.cladistics.org/about/hennig.html
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12
Systematists classify organisms and determine
evolutionary relationships based on analysis of
homologous characters (traits)
  • Systematic investigation is based on analysis of
    homologous characters (traits) characters may
    be morphological, molecular, behavioral,
    physiological..
  • Homologous character character that is shared by
    two or more taxa because those taxa inherited the
    character from a common ancestor
  • Expect shared character to be quite similar,
    perhaps, but not identical among taxa, as a
    result of descent with modification
  • Homology indicates common ancestry, which is
    information with which one can determine
    evolutionary history

Divergent Evolution of Homologous Characters
Homologous characters may evolve away from each
other in structure
13
  • Analagous character character occurring in two
    or more lineages because it evolved independently
    in each of those lineages,
  • Analagies may arise through convergent evolution
    lineages occupy similar ecological roles and
    similar selective forces
  • Misinterpretation of analagous characters for
    homologus ones may lead to erroneous conclusions
    regarding phylogenetic relationships and
    unintended taxanomic groupings

Giant Anteater (at a termite mound), native to
Latin America from Southern Mexico to Northern
Argentina
Aardvark, native to central, southern and eastern
Africa
Pangolin, native to Africa and southern and
southeastern Asia
Convergent Evolution of Analogous Characters.
Three distantly related mammals have structural
similarities (analogous characters, homoplasious
characters) due to convergent evolution. Each
taxon independently evolved morphological traits
for feeding on ants and termites.
14
The supporting structures of bird and bat wings
are homologous structures derived from a common
ancestor The supporting structures of insect
wings are analogous to the structures of bird and
bat wings evolved independently.
15
Shoot develops from axillary bud
Thorn develops from axillary bud
Thorn of downy hawthorn is a modified stem
Spine of Japanese barberry is a modified leaf
Analagous traits, or homoplasies, in two
distantly related plant taxa
16
  • Phylogenetic Systematics Dr.
    Willi Hennig (1913-1976)
  • The history of diversification is recorded
    through descent with modification
  • Modification exists in the form of evolutionary
    transformation of characters from one state to
    another state.
  • Plesiomorphy Ancestral character state
  • Apomorphy Derived character state
  • Synapomorphy Derived character state that is
    exclusively shared by a subset of taxa under
    investigation.
  • A synapomorphy is evidence that taxa bearing it
    are descended from the same common ancestor --
    the ancestor in which the derived character
    arose.
  • Cladistic or Phylogenetic Analysis
    Procedural Outline
  • SELECT ORGANISMS
  • Identify the ingroup
  • Select an appropriate outgroup
  • BUILD TRANSFORMATION MATIX
  • Select characters for analysis
  • Assign character states
  • Determine polarity of character states
  • ANALYZE AND INTERPRET DATA
  • Subject data to optimization algorithm
  • (usually parsimony criteria) to produce an
    optimal tree, perhaps a concensus tree
  • Seek congruence
  • Product Phylogenetic Hypothesis

17
  • Phylogenetic Systematics Dr.
    Willi Hennig (1913-1976)
  • The history of diversification is recorded
    through descent with modification
  • Modification exists in the form of evolutionary
    transformation of characters from one state to
    another state.
  • Plesiomorphy Ancestral character state
  • Apomorphy Derived character state
  • Synapomorphy Derived character state that is
    exclusively shared by a subset of taxa under
    investigation.
  • A synapomorphy is evidence that taxa bearing it
    are descended from the same common ancestor --
    the ancestor in which the derived character
    arose.
  • Cladistic or Phylogenetic Analysis
    Procedural Outline
  • SELECT ORGANISMS
  • Identify the ingroup
  • Select an appropriate outgroup
  • BUILD TRANSFORMATION MATIX
  • Select characters for analysis
  • Assign character states
  • Determine polarity of character states
  • ANALYZE AND INTERPRET DATA
  • Subject data to optimization algorithm
  • (usually parsimony criteria) to produce an
    optimal tree, perhaps a concensus tree
  • Seek congruence
  • Product Phylogenetic Hypothesis

18
Reconstruct the phylogeny of three closely
related bird species
Species A Species
B Species C
  • Determine characters to use for analysis
  • bill shape (derived character state hooked
    ancestral not hooked)
  • head feathers (derived crest ancestral no
    crest)
  • toe condition (derived webbed ancestral no
    webbing)

19
  • Species A Species B
    Species C
  • Hooked Bill Hooked Bill No
    Hooked Bill
  • Crested Head No Crested Head
    Crested Head
  • Webbed Toes Webbed Toes
    No Webbed Toes
  • Character states variously arise in lineages.
  • Character states variously accumulate in
    lineages, in descendents of the ancestor in which
    the character states arose

20
A B
C
?
21
Outgroup Closely related species that we know
diverged from ancestral lineage before our three
species of interest diverged
Ingroup
22
Outgroup Species A
Species B Species C
Transformation
Series
Closely related species that diverged from
ancestral lineage before our three species of
interest diverged (outgroup)
Bill Shape Head Plumage Toe
Condition Outgroup H- C-
W- Species A H
C W Species B
H C-
W Species C H-
C W-
?
(ingroup)
Hhooked billCcrestWwebbed toes species has
trait -species lacks trait Assume character
state seen in outgroup is ancestral character
state.
23
Choosing Among Competing Hypotheses The
Parsimony Principle
  • The Parsimony Principle holds that, all other
    things being equal, the hypothesis requiring the
    fewest number of evolutionary transformations has
    the highest likelihood of being the correct
    hypothesis

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25
Evolutionary relationships may be determined
through analysis of molecular characters DNA,
RNA and proteins
  • Molecular biology provides powerful tools for
    systematics
  • Nucleotide sequences and therefore amino acid
    sequences, are inherited both undergo descent
    with modification following divergence of one
    lineage into two
  • Extent of sequence differences between taxa is an
    indicator, an estimator, of time since divergence
    from a common ancestor
  • DNA , RNA and proteins are used to classify
    organisms and determine evolutionary
    relationships

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27
Normal RBCs and normal hemoglobin
Sickled RBCs and sickle-cell hemoglobin
Phenotypic consequence of a point mutation - a
substitution
28
Molecules evolve at different rates, some, at
constant rates
Raven and Johnson 1999)
29
  • Hemoglobin Evolution
  • Gene duplication ?Multigene Families
  • Evolution of molecular function

Tetrameric Human hemoglobin
30
  • Gene family
  • -two or more genes in a genome, identical or
    highly similar in nucleotide sequence
  • -descended from the same ancestral gene
  • Origin of gene families
  • -Repeated gene duplication from errors during DNA
    replication and recombination

31
  • Globin gene families are well-studied across taxa
    for sequence, structure and function
  • Hemoglobin multigene families in humans
  • Alpha globin family (on chr. 16)
  • Beta globin family (on chr. 13)
  • Hemoglobin families probably descended from a
    myoglobin-like ancestral gene

32
Evolutionary Time
33
  • Evolution of the Globin Gene
  • Genes encoding proteins have undergone continual
    evolution, accumulating increasing numbers of
    changes over time
  • Length of lines corresponds to number of
    nucleotide substitutions in the gene
  • Raven and Johnson 1999

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