Reconstructing and Using Phylogenies - PowerPoint PPT Presentation

Loading...

PPT – Reconstructing and Using Phylogenies PowerPoint presentation | free to download - id: 5a00f4-ZGNiM



Loading


The Adobe Flash plugin is needed to view this content

Get the plugin now

View by Category
About This Presentation
Title:

Reconstructing and Using Phylogenies

Description:

Reconstructing and Using Phylogenies 25 Reconstructing and Using Phylogenies 25.1 What Is Phylogeny? 25.2 How Are Phylogenetic Trees Constructed? 25.3 How Do ... – PowerPoint PPT presentation

Number of Views:161
Avg rating:3.0/5.0
Slides: 67
Provided by: imagesPcm5
Learn more at: http://images.pcmac.org
Category:

less

Write a Comment
User Comments (0)
Transcript and Presenter's Notes

Title: Reconstructing and Using Phylogenies


1
Reconstructing and Using Phylogenies
2
25 Reconstructing and Using Phylogenies
  • 25.1 What Is Phylogeny?
  • 25.2 How Are Phylogenetic Trees Constructed?
  • 25.3 How Do Biologists Use Phylogenetic Trees?
  • 25.4 How Does Phylogeny Relate to Classification?

3
25.1 What Is Phylogeny?
  • Phylogeny is a description of the evolutionary
    history of relationships among organisms.
  • This is portrayed in a diagram called a
    phylogenetic tree.
  • Each split or node represents the point at which
    lineages diverged. The common ancestor of all
    organisms in the tree is the root.

4
Figure 25.1 How to Read a Phylogenetic Tree (Part
1)
5
Figure 25.1 How to Read a Phylogenetic Tree (Part
2)
6
25.1 What Is Phylogeny?
  • The timing of divergences is shown by the
    position of nodes on a time or divergence axis.
  • Lineages can be rotated around nodes the
    vertical order of taxa is largely arbitrary.

7
25.1 What Is Phylogeny?
  • A taxon (plural taxa) is any group of species
    that we designate (e.g., vertebrates).
  • A taxon that consists of all the descendents of a
    common ancestor is called a clade.

8
25.1 What Is Phylogeny?
  • Two species that are each others closest
    relatives are sister species.
  • Two clades that are each others closest
    relatives are sister clades.
  • Phylogenetic trees were used mainly in
    systematics (study of biodiversity) but are now
    used in nearly all fields of biology.

9
25.1 What Is Phylogeny?
  • One of the greatest unifying concepts in biology
    is that all life is connected through
    evolutionary history.
  • The Tree of Life is the complete,
    4-billion-year history of life.
  • Knowledge of evolutionary relationships is
    essential for making comparisons in biology.

10
25.1 What Is Phylogeny?
  • Biologists determine traits that differ within a
    group of interest, then try to determine when
    these traits evolved.
  • Often, we wish to know how the trait was
    influenced by environmental conditions or
    selection pressures.

11
25.1 What Is Phylogeny?
  • Features shared by two or more species that were
    inherited from a common ancestor are homologous.
  • Example The vertebral column is homologous in
    all vertebrates.

12
25.1 What Is Phylogeny?
  • A trait that differs from the ancestral trait is
    called derived.
  • A trait that was present in the ancestor of a
    group is ancestral.

13
25.1 What Is Phylogeny?
  • Derived traits that are shared among a group and
    are viewed as evidence of the common ancestry of
    the group are known as synapomorphies.
  • The vertebral column is a synapomorphy of all
    vertebrates.

14
25.1 What Is Phylogeny?
  • Similar traits can develop in unrelated groups of
    organisms
  • Convergent evolutionindependently evolved traits
    subjected to similar selection pressures may
    become superficially similar.
  • Example the wings of bats and birds

15
Figure 25.2 The Bones Are Homologous the Wings
Are Not
16
25.1 What Is Phylogeny?
  • Evolutionary reversala character reverts from a
    derived state back to the ancestral state.
  • Example Most frogs do not have lower teeth, but
    the ancestor of frogs did. One frog genus has
    regained teeth in the lower jaw.

17
25.1 What Is Phylogeny?
  • Traits that are similar for reasons other than
    inheritance from a common ancestor are called
    homoplastic traits or homoplasies.
  • Traits may be ancestral or derived, depending on
    the point of reference in phylogeny. Bird
    feathers are ancestral in birds, but derived when
    considering all living vertebrates.

18
25.2 How Are Phylogenetic Trees Constructed?
  • Constructing a phylogenetic tree using eight
    vertebrate animals
  • Assume no convergent evolution and no derived
    traits have been lost.
  • Lampreys are the outgroupany species or group
    outside the group of interest. The group of
    interest is the ingroup.
  • Comparison with the outgroup shows which traits
    of the ingroup are derived and which are
    ancestral.

19
Table 25.1 (Part 1)
20
Table 25.1 (Part 2)
21
25.2 How Are Phylogenetic Trees Constructed?
  • Chimpanzees and mice share two derived traitsfur
    and mammary glands. Assume these traits evolved
    only once they are synapomorphies for this
    group.
  • Keratinous scales are a synapomorphy of the
    crocodile, pigeon, and lizard.
  • Information about the synapomorphies allows
    construction of the tree.

22
Figure 25.3 Inferring a Phylogenetic Tree
23
25.2 How Are Phylogenetic Trees Constructed?
  • Phylogenetic trees are typically constructed
    using hundreds or thousands of traits.
  • How are synapomorphies and homoplasies
    determined?

24
25.2 How Are Phylogenetic Trees Constructed?
  • The parsimony principle the simplest explanation
    of observed data is the preferred explanation.
  • Minimize the number of evolutionary changes that
    must be assumedthe fewest homoplasies.
  • Occams razor the best explanation fits the data
    with the fewest assumptions.

25
25.2 How Are Phylogenetic Trees Constructed?
  • Computer programs are now used to analyze traits
    and construct trees.
  • All kinds of traitsmorphological, fossil,
    developmental, molecular, behavioralare used by
    systematists to construct phylogenies.

26
25.2 How Are Phylogenetic Trees Constructed?
  • Morphology
  • Most species have been described on the basis of
    morphological data, such as features of the
    skeletal system in vertebrates, or floral
    structures in plants.
  • Limitations comparing distantly related species
    some morphological variation is caused by
    environment some species show few morphological
    differences.

27
25.2 How Are Phylogenetic Trees Constructed?
  • Development
  • Similarities in development patterns may reveal
    evolutionary relationships.
  • Example Sea squirts and vertebrates all have a
    notochord at some time in their development.

28
Figure 25.4 A Larva Reveals Evolutionary
Relationships
29
25.2 How Are Phylogenetic Trees Constructed?
  • Paleontology
  • Fossils provide information about the morphology
    of past organisms, and where and when they lived.
  • Important in determining derived and ancestral
    traits, and when lineages diverged.
  • Limitations fossil record is fragmentary and
    missing for some groups.

30
25.2 How Are Phylogenetic Trees Constructed?
  • Behavior
  • Behavior can be inherited or culturally
    transmitted.
  • Bird songs are often learned, and may not be a
    useful trait for phylogenies.
  • Frog calls are genetically determined and can be
    used in phylogenetic trees.

31
25.2 How Are Phylogenetic Trees Constructed?
  • Molecular data
  • DNA sequences have become the most widely used
    data for constructing phylogenetic trees.
  • Mitochondrial and chloroplast DNA is used as well
    as nuclear DNA.
  • Gene product information, such as amino acid
    sequences, are also used.

32
25.2 How Are Phylogenetic Trees Constructed?
  • Mathematical models are used to describe DNA
    changes over time.
  • Models can be used to compute maximum likelihood
    solutions, the probability of the observed data
    evolving on the specified tree.
  • Most often used for molecular data, models of
    evolutionary change are easier to develop.

33
25.2 How Are Phylogenetic Trees Constructed?
  • Testing the accuracy of phylogenetic
    reconstructions experiments with living
    organisms and computer simulations.
  • Cultures of bacteriophage T7 were grown in the
    presence of a mutagen and allowed to evolve in
    the laboratory.

34
Figure 25.5 A Demonstration of the Accuracy of
Phylogenetic Analysis (Part 1)
35
Figure 25.5 A Demonstration of the Accuracy of
Phylogenetic Analysis (Part 2)
36
25.2 How Are Phylogenetic Trees Constructed?
  • At the end of the experiment, genomes of the
    endpoints were sequenced and investigators built
    phylogenetic trees that accurately reflected the
    known evolutionary history of the cultures.

37
25.2 How Are Phylogenetic Trees Constructed?
  • Phylogenetic methods can be used to reconstruct
    traits or nucleotide sequences for ancestral
    species.
  • Example Reconstruction of opsin (pigment
    involved in vision) in the ancestral archosaur
    (last common ancestor of birds, crocodiles, and
    dinosaurs).

38
25.2 How Are Phylogenetic Trees Constructed?
  • Analysis of opsin from living vertebrates was
    used to estimate the amino acid sequence of opsin
    in the archosaur.
  • A protein of this sequence was constructed in the
    laboratory and then wavelengths of light it
    absorbs were measured.
  • Activity in the red range indicated that the
    animal may have been nocturnal.

39
25.2 How Are Phylogenetic Trees Constructed?
  • Molecular clock hypothesis Rates of molecular
    change are constant enough to predict timing of
    evolutionary divergence.
  • Among closely related species, a given gene
    usually evolves at a reasonably constant rate,
    and can be used to determine time elapsed since a
    divergence.

40
25.2 How Are Phylogenetic Trees Constructed?
  • Molecular clocks must be calibrated using
    independent data, such as the fossil record, and
    known divergences or biogeographic dates (e.g.,
    from continental drift).
  • Example 500 species of cichlid fishes of Lake
    Victoria.

41
25.2 How Are Phylogenetic Trees Constructed?
  • Mitochondrial DNA sequences were used to
    construct a phylogenetic tree of the cichlids.
  • It has been suggested that the ancestors came
    from the older Lake Kivu, and they colonized Lake
    Victoria on two occasions.
  • Molecular clock analysis suggested that some
    endemic cichlid lineages split at least 100,000
    years ago.

42
25.2 How Are Phylogenetic Trees Constructed?
  • The analyses suggest that Lake Victoria did not
    dry up completely between 15,600 and 14,700 years
    ago, and many species survived in rivers and in
    the remnants of the lake during the dry period.

43
Figure 25.6 Origins of the Cichlid Fishes of Lake
Victoria (Part 1)
44
Figure 25.6 Origins of the Cichlid Fishes of Lake
Victoria (Part 2)
45
25.3 How Do Biologists Use Phylogenetic Trees?
  • Most flowering plants reproduce by outcrossing or
    mating with another individual.
  • Other plants are selfing, which requires that
    they be self-compatible.
  • Phylogenetic analysis can show how often
    self-compatibility has evolved.

46
25.3 How Do Biologists Use Phylogenetic Trees?
  • The genus Linanthus has a variety of breeding
    systems.
  • Outcrossing species have long petals and are
    self-incompatible. Self-compatible species have
    short petals.
  • A phylogeny was constructed using ribosomal DNA.
  • Self-incompatibility is the ancestral state.

47
Figure 25.7 Phylogeny of a Section of the Plant
Genus Linanthus (Part 1)
48
Figure 25.7 Phylogeny of a Section of the Plant
Genus Linanthus (Part 2)
49
25.3 How Do Biologists Use Phylogenetic Trees?
  • Phylogenetic analysis can be important in
    understanding zoonotic diseases (infectious
    organisms are transmitted to humans from another
    animal host).
  • Example HIV was acquired from chimpanzees and
    sooty mangabeys.

50
Figure 25.8 Phylogenetic Tree of Immunodeficiency
Viruses
51
25.3 How Do Biologists Use Phylogenetic Trees?
  • Reproductive success of male swordtails is
    associated with long swords (sexual selection).
    Evolution of the sword may result from a
    preexisting bias of female sensory
    systemssensory exploitation hypothesis.
  • Phylogenetics identified platyfishes as the
    closest relatives.

52
25.3 How Do Biologists Use Phylogenetic Trees?
  • Artificial swords were attached to platyfish
    males.
  • Female platyfish preferred males with the
    artificial swords, supporting the idea that
    females had a preexisting bias even before the
    swords evolved.

53
Figure 25.9 The Origin of a Sexually Selected
Trait in the Fish Genus Xiphophorus
54
25.3 How Do Biologists Use Phylogenetic Trees?
  • Rate of evolution of influenza virus is high.
  • Phylogenetic analysis indicates there is a strong
    selection by the human immune system for most
    strains.
  • Only strains with the greatest number of
    substitutions on hemagglutinin (surface protein
    recognized by the immune system) are likely to
    leave descendents.

55
Figure 25.10 Model of Hemagglutinin, a Surface
Protein of Influenza
56
25.3 How Do Biologists Use Phylogenetic Trees?
  • Phylogenetic analysis helps biologists predict
    which of the currently circulating strains are
    most likely to survive and leave descendents.
  • This information is then used to formulate
    influenza vaccines.

57
25.4 How Does Phylogeny Relate to Classification?
  • The biological classification system was started
    by Swedish biologist Carolus Linnaeus in the
    1700s.
  • Binomial nomenclature gives every species a
    unique, unambiguous name.

58
Figure 25.11 Many Different Plants Are Called
Bluebells
59
25.4 How Does Phylogeny Relate to Classification?
  • Every species has two names the genus (group of
    closely related species) to which it belongs, and
    the species name.
  • The name of the taxonomist who first described
    the species is often included.
  • Example Homo sapiens Linnaeus

60
25.4 How Does Phylogeny Relate to Classification?
  • A taxon is any group of organisms that is treated
    as a unit, such as a genus, or all insects.
  • Species and genera are further grouped into a
    hierarchical classification system.
  • Genera are grouped into families (e.g., the
    family Rosaceae includes the genus Rosa and its
    close relatives).

61
25.4 How Does Phylogeny Relate to Classification?
  • Families are grouped into orders
  • Orders into classes
  • Classes into phyla
  • Phyla into kingdoms
  • Application of these levels is somewhat
    subjective.

62
25.4 How Does Phylogeny Relate to Classification?
  • Biological classifications are used to express
    the evolutionary relationships of organisms.
  • Taxa are expected to be monophyletic a taxon
    contains an ancestor and all descendents of that
    ancestor, and no other organisms. Also known as a
    clade.

63
25.4 How Does Phylogeny Relate to Classification?
  • But detailed phylogenetic information is not
    always available.
  • A group that does not include its common ancestor
    is polyphyletic.
  • A group that does not include all descendents of
    a common ancestor is paraphyletic.

64
25.4 How Does Phylogeny Relate to Classification?
  • A true clade or monophyletic group can be removed
    from the tree by making a single cut.
  • Taxonomists agree that polyphyletic and
    paraphyletic groups are not appropriate taxonomic
    units. These groups are gradually being
    eliminated and taxonomic classifications revised.

65
Figure 25.12 Monophyletic, Polyphyletic, and
Paraphyletic Groups
66
25.4 How Does Phylogeny Relate to Classification?
  • Explicit rules govern the use of scientific
    names.
  • Ensures that there is only one correct scientific
    name for any taxon.
  • Different taxonomic rules have been developed for
    zoology, botany, and microbiology, but
    taxonomists are now working towards common sets
    of rules.
About PowerShow.com