Reconstructing and Using Phylogenies

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Reconstructing andUsing Phylogenies
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Reconstructing and Using Phylogenies

• Key Concepts
• Phylogeny Is the Basis of Biological
  Classification
• All of Life Is Connected through Its
  Evolutionary History
• Phylogeny Can Be Reconstructed from Traits of
  Organisms
• Phylogeny Makes Biology Comparative and Predictive

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Phylogeny Is the Basis of Biological
Classification

• Phylogenythe evolutionary history of
  evolutionary relationships
• Phylogenetic treea diagrammatic reconstruction
  of that history

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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)

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Phylogeny Is the Basis of Biological
Classification

• Species and genera are further grouped into a
  hierarchical system of higher categories such as
  familythe taxon (classification group) 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.

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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.

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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.

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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.
• Polyphyletica group that does not include its
  common ancestor
• Paraphyletica group that does not include all
  the descendants of a common ancestor

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Figure 16.11 Monophyletic, Polyphyletic, and
Paraphyletic Groups
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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.

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Figure 16.12 Same Common Name, Not the Same
Species
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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

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All of Life Is Connected through Its Evolutionary
History

• When a single lineage divides into two branches,
  it is depicted as a split or node

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All of Life Is Connected through Its Evolutionary
History

• Each descendant population gives rise to a new
  lineage, which continues to evolve

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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

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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.

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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)

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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.

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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.

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Figure 16.1 Clades Represent All the Descendants
of a Common Ancestor
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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
• Refer back to Figure 16.1 and identify the sister
  species and clades

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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.

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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.

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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.

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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.

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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.
• 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.

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Figure 16.2 The Bones Are Homologous, the Wings
Are Not
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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.

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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

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Table 16.1 Eight Vertebrates and the Presence or
Absence of Some Shared Derived Traits
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Figure 16.3 Inferring a Phylogenetic Tree
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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.

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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.

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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

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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.

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Figure 16.4 The Chordate Connection
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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).

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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.

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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.

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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.

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Figure 16.5 The Accuracy of Phylogenetic
Analysis (Part 1)
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Figure 16.5 The Accuracy of Phylogenetic
Analysis (Part 2)
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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.

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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.

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Figure 16.6 A Portion of the Leptosiphon
Phylogeny
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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).

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Figure 16.7 Phylogenetic Tree of
Immunodeficiency Viruses
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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.

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Figure 16.8 The Origin of a Sexually Selected
Trait
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logeny 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.

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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.

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Figure 16.9 A Molecular Clock of the Protein
Hemoglobin
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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.

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Figure 16.10 Dating the Origin of HIV-1 in Human
Populations (Part 1)
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Figure 16.10 Dating the Origin of HIV-1 in Human
Populations (Part 2)
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Figure 16.13 Evolution of Fluorescent Proteins
of Corals
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Chapter 16 Opening Question
How are phylogenetic methods used to resurrect
protein sequences from extinct organisms?
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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.