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Reconstructing%20and%20Using%20Phylogenies

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Title: Reconstructing%20and%20Using%20Phylogenies


1
Reconstructing andUsing Phylogenies
16
2
Chapter 16 Reconstructing and Using Phylogenies
  • Key Concepts
  • 16.1 All of Life Is Connected through Its
    Evolutionary History
  • 16.2 Phylogeny Can Be Reconstructed from Traits
    of Organisms
  • 16.3 Phylogeny Makes Biology Comparative and
    Predictive
  • 16.4 Phylogeny Is the Basis of Biological
    Classification

3
Chapter 16 Opening Question
How are phylogenetic methods used to resurrect
protein sequences from extinct organisms?
4
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • All of life is related through a common ancestor
  • Phylogenythe evolutionary history of these
    relationships
  • Phylogenetic treea diagrammatic reconstruction
    of that history

5
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • A lineage is a series of ancestor and descendant
    populations, shown as a line drawn on a time axis

6
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • When a single lineage divides into two, it is
    depicted as a split or node

7
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Each descendant population gives rise to a new
    lineage, which continues to evolve

8
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • A phylogenetic tree may portray the evolutionary
    history of
  • All life forms
  • Major evolutionary groups
  • Small groups of closely related species
  • Individuals
  • Populations
  • Genes

9
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • The common ancestor of all the organisms in the
    tree forms the root of the tree.

10
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • The splits represent events where one lineage
    diverged into two, such as
  • A speciation event (for a tree of species)
  • A gene duplication event (for a tree of genes)
  • A transmission event (for a tree of viral
    lineages transmitted through a host population)

11
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Vertical distances between branches dont have
    any meaning, and the vertical order of lineages
    is arbitrary.

12
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Taxonany group of species that we designate with
    a name
  • Cladetaxon that consists of all the evolutionary
    descendants of a common ancestor
  • Identify a clade by picking any point on the tree
    and tracing all the descendant lineages.

13
Figure 16.1 Clades Represent All the Descendants
of a Common Ancestor
14
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Sister species Two species that are each others
    closest relatives
  • Sister clades Any two clades that are each
    others closest relatives

15
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Before the 1980s, phylogenetic trees were used
    mostly in evolutionary biology, and in
    systematicsthe study and classification of
    biodiversity.
  • Today trees are widely used in molecular biology,
    biomedicine, physiology, behavior, ecology, and
    virtually all other fields of biology.

16
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Evolutionary relationships among species form the
    basis for biological classification.
  • As new species are discovered, phylogenetic
    analyses are reviewed and revised.
  • The tree of lifes evolutionary framework allows
    us to make predictions about the behavior,
    ecology, physiology, genetics, and morphology of
    species.

17
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Homologous features
  • Shared by two or more species
  • Inherited from a common ancestor
  • They can be any heritable traits, including DNA
    sequences, protein structures, anatomical
    structures, and behavior patterns.

18
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Each character of an organism evolves from one
    condition (the ancestral trait) to another
    condition (the derived trait).
  • Shared derived traits provide evidence of the
    common ancestry of a group and are called
    synapomorphies.
  • The vertebral column is a synapomorphy of the
    vertebrates. The ancestral trait was an undivided
    supporting rod.

19
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • Similar traits can develop in unrelated groups
  • Convergent evolutionwhen superficially similar
    traits may evolve independently in different
    lineages

20
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • In an evolutionary reversal, a character may
    revert from a derived state back to an ancestral
    state.
  • These two types of traits are called homoplastic
    traits, or homoplasies.

21
Figure 16.2 The Bones Are Homologous, the Wings
Are Not
22
Concept 16.1 All of Life Is Connected through Its
Evolutionary History
  • A trait may be ancestral or derived, depending on
    the point of reference.
  • Example
  • Feathers are an ancestral trait for modern birds.
    But in a phylogeny of all living vertebrates,
    they are a derived trait found only in birds.

23
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Ingroupthe group of organisms of primary
    interest
  • Outgroupspecies or group known to be closely
    related to, but phylogenetically outside, the
    group of interest

24
Table 16.1 Eight Vertebrates and the Presence or
Absence of Some Shared Derived Traits
25
Figure 16.3 Inferring a Phylogenetic Tree
26
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Parsimony principlethe preferred explanation of
    observed data is the simplest explanation
  • In phylogenies, this entails minimizing the
    number of evolutionary changes that need to be
    assumed over all characters in all groups.
  • The best hypothesis is one that requires the
    fewest homoplasies.

27
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Any trait that is genetically determined can be
    used in a phylogenetic analysis.
  • Morphologypresence, size, shape, or other
    attributes of body parts
  • Phylogenies of most extinct species depend almost
    exclusively on morphology.
  • Fossils provide evidence that helps distinguish
    ancestral from derived traits. The fossil record
    can also reveal when lineages diverged.

28
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Limitations of using morphology
  • Some taxa show few morphological differences
  • It is difficult to compare distantly related
    species
  • Some morphological variation is caused by
    environment

29
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Development
  • Similarities in developmental patterns may reveal
    evolutionary relationships.
  • Example
  • The larvae of sea squirts has a notochord,
    which is also present in all vertebrates.

30
Figure 16.4 The Chordate Connection (Part 1)
31
Figure 16.4 The Chordate Connection (Part 2)
32
Figure 16.4 The Chordate Connection (Part 3)
33
Figure 16.4 The Chordate Connection (Part 4)
34
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Behavior
  • Some traits are cultural or learned, and may not
    reflect evolutionary relationships (e.g. bird
    songs).
  • Other traits have a genetic basis and can be used
    in phylogenies (e.g. frog calls).

35
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Molecular data
  • DNA sequences have become the most widely used
    data for constructing phylogenetic trees.
  • Nuclear, chloroplast, and mitochondrial DNA
    sequences are used.
  • Information on gene products (such as amino acid
    sequences of proteins) are also used.

36
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Mathematical models are now used to describe DNA
    changes over time.
  • Models can account for multiple changes at a
    given sequence position, and different rates of
    change at different positions.
  • Maximum likelihood methods identify the tree that
    most likely produced the observed data. They
    incorporate more information about evolutionary
    change than do parsimony methods.

37
Concept 16.2 Phylogeny Can Be Reconstructed from
Traits of Organisms
  • Phylogenetic trees can be tested with computer
    simulations and by experiments on living
    organisms.
  • These studies have confirmed the accuracy of
    phylogenetic methods and have been used to refine
    those methods and extend them to new applications.

38
Figure 16.5 The Accuracy of Phylogenetic
Analysis (Part 1)
39
Figure 16.5 The Accuracy of Phylogenetic
Analysis (Part 2)
40
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Applications of phylogenetic trees
  • Phylogeny can clarify the origin and evolution of
    traits that help in understanding fundamental
    biological processes. This information is then
    widely applied in life sciences fields, including
    agriculture and medicine.

41
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Self-compatibility
  • Most flowering plants reproduce by mating with
    another individual (outcrossing)
  • Self-incompatible species have mechanisms to
    prevent self-fertilization.
  • Other plants are selfing, which requires that
    they be self-compatible.
  • The evolution of angiosperm fertilization
    mechanisms was examined in the genus Leptosiphon.

42
Figure 16.6 A Portion of the Leptosiphon
Phylogeny
43
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Zoonotic diseases
  • Caused by infectious organisms transmitted from
    an animal of a different species (e.g. rabies,
    AIDS)
  • Phylogenetic analyses help determine when, where,
    and how a disease first entered a human
    population.
  • One example is Human Immunodeficiency Virus
    (HIV).

44
Figure 16.7 Phylogenetic Tree of
Immunodeficiency Viruses
45
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Evolution of complex traits
  • Some adaptations relate to mating behavior and
    sexual selection.
  • One example is the tail of male swordfish.
    Phylogenetic analysis supported the sensory
    exploitation hypothesisfemale swordtails had a
    preexisting bias for males with long tails.

46
Figure 16.8 The Origin of a Sexually Selected
Trait
47
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Reconstructing ancestral traits
  • Morphology, behavior, or nucleotide and amino
    acid sequences of ancestral species
  • Example
  • Opsin proteins (pigments involved in vision) were
    reconstructed in the ancestral archosaur, and it
    was inferred that it was probably active at night.

48
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • Molecular clocks
  • The molecular clock hypothesis states that rates
    of molecular change are constant enough to
    predict the timing of lineage splits.
  • A molecular clock uses the average rate at which
    a given gene or protein accumulates changes to
    gauge the time of divergence .
  • They must be calibrated using independent
    datathe fossil record, known times of
    divergence, or biogeographic dates.

49
Figure 16.9 A Molecular Clock of the Protein
Hemoglobin
50
Concept 16.3 Phylogeny Makes Biology Comparative
and Predictive
  • A molecular clock was used to estimate the time
    when HIV-1 first entered human populations from
    chimpanzees.
  • The clock was calibrated using the samples from
    the 1980s and 1990s, then tested using the
    samples from the 1950s.
  • The common ancestor of this group of HIV-1
    viruses can also be determined, with an estimated
    date of origin of about 1930.

51
Figure 16.10 Dating the Origin of HIV-1 in Human
Populations (Part 1)
52
Figure 16.10 Dating the Origin of HIV-1 in Human
Populations (Part 2)
53
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • The biological classification system was started
    by Swedish biologist Carolus Linnaeus in the
    1700s.
  • Binomial nomenclature gives every species a
    unique name consisting of two parts the genus to
    which it belongs, and the species name.
  • Example
  • Homo sapiens Linnaeus (Linnaeus is the person who
    first proposed the name)

54
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • Species and genera are further grouped into a
    hierarchical system of higher categories such as
    familythe taxon above genus.
  • Examples
  • The family Hominidae contains humans, plus our
    recent fossil relatives, plus our closest living
    relatives, the chimpanzees and gorillas.
  • Rosaceae is the family that includes the genus
    Rosa (roses) and its relatives.

55
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • Families are grouped into orders
  • Orders into classes
  • Classes into phyla (singular phylum)
  • Phyla into kingdoms
  • The ranking of taxa within the Linnaean
    classification is subjective.

56
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • Linnaeus recognized the hierarchy of life, but he
    developed his system before evolutionary thought
    had become widespread.
  • Today, biological classifications express the
    evolutionary relationships of organisms.

57
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • But detailed phylogenetic information is not
    always available.
  • Taxa are monophyleticthey contain an ancestor
    and all descendants of that ancestor, and no
    other organisms (clade).

58
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • Polyphyletica group that does not include its
    common ancestor
  • Paraphyletica group that does not include all
    the descendants of a common ancestor

59
Figure 16.11 Monophyletic, Polyphyletic, and
Paraphyletic Groups
60
Concept 16.4 Phylogeny Is the Basis of Biological
Classification
  • Codes of biological nomenclature
  • Biologists around the world follow rules for the
    use of scientific names, to facilitate
    communication and dialogue.
  • There may be many common names for one organism,
    or the same common name may refer to several
    species. But there is only one correct scientific
    name.

61
Figure 16.12 Same Common Name, Not the Same
Species
62
Answer to Opening Question
  • Biologists can reconstruct DNA and protein
    sequences of a clades ancestors if there is
    enough information about the genomes of their
    descendants.
  • Real proteins that correspond to proteins in
    long-extinct species can be reconstructed.
  • Mathematical models that incorporate rates of
    replacement among different amino acid residues,
    substitution rates among nucleotides, and changes
    in the rate of molecular evolution among
    different lineages, are used.

63
Figure 16.13 Evolution of Fluorescent Proteins
of Corals
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