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LECTURE 1: Phylogeny and Systematics

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Title: LECTURE 1: Phylogeny and Systematics


1
LECTURE 1 Phylogeny and Systematics
2
What is Phylogeny?
  • the evolutionary history of a species
  • Evolutionary biology is about both process and
    history
  • A major goal of evolutionary biology is to
    reconstruct the history of life on earth
  • To reconstruct phylogeny, scientists use
    SYSTEMATICS
  • The study of biodiversity in an evolutionary
    context

3
How are Phylogenies Constructed?
  • The Fossil Record
  • Morphological similarities
  • Homologous Structures (remember those?)
  • Molecular similarities
  • DNA
  • Organisms with very similar morphologies or
    similar DNA sequences are likely to be more
    closely related than organisms with vastly
    different structures or sequences

4
How can Scientists determine whether structure
are Homologous or Analagous?
  • HOMOLOGY is similarity due to SHARED ANCESTRY
  • ANALOGY is similarity due to CONVERGENT EVOLUTION
  • CONVERGENT EVOLUTION two organisms develop
    similarities as they adapted to similar
    environmental challenges not because they
    evolved from a common ancestor
  • EXAMPLE both birds and bats have adaptations
    that allow them to fly
  • However, a close examination of a bats wing
    shows a greater similarity to a cats forelimb
    than to a birds wing
  • Fossil evidence also documents that bat and bird
    wings arose independently from walking forelimbs
    of different ancestors
  • Thus a bats wing is homologous to other
    mammalian forelimbs but is analogous in function
    to a birds wing

5
HOW DO THESE ORGANISMS DISPLAY EXAMPLES OF
CONVERGENT EVOLUTION?
6
How would you compare the fins in these 2
organisms?
7
What are Homoplasies?
  • Analogous structures or molecular sequences that
    evolved independently
  • Example the four-chambered heart of birds
    mammals is analogous

8
What are Molecular Homologies?
  • Systematists compare long stretches of DNA and
    even entire genomes to assess relationships
    between species
  • If genes in two organisms have closely similar
    nucleotide sequences, it is highly likely that
    the genes are homologous
  • In closely related species, sequences may differ
    at only one or a few base sites
  • Distantly related species may have many
    differences or sequences of different length

9
How is Phylogeny linked with Classification?
  • Systematists explore phylogeny by examining
    various characteristics in living and fossil
    organisms
  • They construct branching diagrams called
    PHYLOGENETIC TREES to depict their hypotheses
    about evolutionary relationships
  • The branching of the tree reflects the
    hierarchical classification of groups nested
    within more inclusive groups

10
LE 25-9
Panthera pardus (leopard)
Mephitis mephitis (striped skunk)
Lutra lutra (European otter)
Canis familiaris (domestic dog)
Canis lupus (wolf)
Species
Genus
Panthera
Mephitis
Lutra
Canis
Family
Felidae
Mustelidae
Canidae
Carnivora
Order
11
LE 25-UN497
Leopard
Domestic cat
Each branch point represents the divergence of
two species
Common ancestor
Leopard
Domestic cat
Wolf
Deeper branch points represent progressively
greater amounts of divergence
Common ancestor
12
LE 25-13
Drosophila
Bird
Rat
Mouse
Lancelet
Fish
Human
Amphibian
Cenozoic
65.5
Mesozoic
251
Paleozoic
542
Neoproterozoic
Millions of years ago
13
What is Cladistics?
  • classifying organisms based on RESEMBLANCES among
    clades
  • Determining which similarities between species
    are relevant to grouping the species in a clade
    is a challenge
  • It is especially important to distinguish
    similarities that are based on shared ancestry or
    homology from those that are based on convergent
    evolution or analogy
  • CLADISTICS enables us to identify the sequence of
    the evolution of derived characteristics

14
What is a Cladogram?
  • depicts patterns of shared derived
    characteristics among taxa
  • Synapomorphies
  • the chronological sequence of branching during
    the evolutionary history of a set of organisms
  • This chronology DOES NOT indicate the TIME of
    origin of the species that we are comparing, only
    the groups to which they belong
  • A cladogram is NOT a phylogenetic tree
  • To convert it to a phylogenetic tree, we need
    more information from sources such as the fossil
    record, which can indicate when and in which
    groups the characters first appeared

15
What is a Clade?
  • a group of species that includes an ancestral
    species and all its descendants
  • THREE TYPES OF CLADES
  • MONOPHYLETIC
  • single ancestor that gives rise to all species in
    that taxon and to no species in any other taxon
    legitimate cladogram
  • PARAPHYLETIC
  • members of a taxa are derived from 2 or more
    ancestral forms not common to all members does
    not meet cladistic criterion
  • POLYPHYLETIC
  • lacks the common ancestor that would unite the
    species does not meet cladistic criterion

16
LE 25-10a
Grouping 1
A valid clade is monophyletic, signifying that it
consists of the ancestor species and all its
descendants
Monophyletic
17
LE 25-10b
Grouping 2
A paraphyletic grouping consists of an ancestral
species and some, but not all, of the descendants
Paraphyletic
18
LE 25-10c
Grouping 3
A polyphyletic grouping consists of various
species that lack a common ancestor
Polyphyletic
19
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20
How are Cladograms Constructed?
  • In cladistic analysis, clades are defined by
    their evolutionary features (novelties)
  • A CHARACTER
  • any feature that a particular taxon possesses
  • A SHARED DERIVED CHARACTER (SYNAPOMORPHIES)
  • an evolutionary novelty unique to a particular
    clade
  • A SHARED PRIMITIVE CHARACTER
  • found not only in the clade being analyzed, but
    also in older clades
  • Systematists must also sort through homologous
    features, or characters, to separate shared
    derived characters from shared primitive
    characters

21
SHARED DERIVED CHARACTERISTICS
  • Need to differentiate between shared primitive
    characters and shared derived characters

ANALOGIES
All similar characters
PRIMITIVE (ANCESTRAL)
HOMOLOGIES
DERIVED (UNIQUE TO A CLADE)
22
SHARED PRIMITIVE SHARED DERIVED CHARACTERISTICS
  • EXAMPLE the presence of hair is a good character
    to distinguish the clade of mammals from other
    tetrapods.
  • It is a shared derived character that uniquely
    identifies mammals
  • However, the presence of a backbone can qualify
    as a shared derived character, but at a deeper
    branch point that distinguishes all vertebrates
    from other mammals.
  • Among vertebrates, the backbone is a shared
    primitive character because it evolved in the
    ancestor common to all vertebrates
  • SHARED DERIVED CHARACTERS ARE USEFUL IN
    ESTABLISHING A PHYLOGENY, BUT SHARED PRIMITIVE
    CHARACTERS ARE NOT

23
How are Cladograms built Using Outgroups?
  • OUTGROUP COMPARISON
  • used to differentiate shared primitive
    characters from shared derived ones
  • OUTGROUP
  • a species or group of species that is closely
    related to the INGROUP (the various species being
    studied)
  • ASSUMPTION homologies shared by the outgroup
    and ingroup must be a primitive character that
    predate the divergence of both groups from a
    common ancestor

24
PERFORMING OUTGROUP COMPARISON
What is the shared primitive characteristic?
DOES NOT MEAN THAT TURTLES EVOLVED MORE RECENTLY
THAN SALAMANDER
25
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26
BUILDING A CLADOGRAM
27
THE CHARACTER TABLE
28
THE RESULT
29
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30
AND SOMETIMES THE SIMPLEST EXPLANATION IS NOT THE
BEST
Parsimony does not always work, nature does not
always take the simplest course
31
  • Much of an organisms evolutionary history is
    documented in its genome

32
What are Gene Duplications and Gene Families?
  • GENE DUPLICATION
  • increases the number of genes in the genome,
    providing more opportunities for evolutionary
    changes
  • GENE FAMILIES
  • groups of related genes within an organisms
    genome
  • Like homologous genes in different species,
    duplicated genes have a common genetic ancestor
  • There are two types of homologous genes
    ORTHOLOGOUS genes and PARALOGOUS genes

33
TWO REMARKABLE FACTS ABOUT GENE FAMILIES
  • All living things share many biochemical and
    development pathways
  • The number of genes seems not to have increased
    at the same rate as phenotypic complexity
  • Humans have only five times as many genes as
    yeast, a simple unicellular eukaryote, although
    we have a large, complex brain and a body that
    contains more than 200 different types of tissues
  • Many human genes are more versatile than yeast
    and can carry out a wide variety of tasks in
    various body tissues

34
What are Orthologous Genes?
  • genes found in a single copy in the genome
  • They can diverge only after speciation occurs
  • i.e. The ß hemoglobin genes in humans and mice
    are orthologous
  • Orthologous genes are widespread and can extend
    over enormous evolutionary distances
  • Approximately 99 of the genes of humans and mice
    are demonstrably orthologous, and 50 of human
    genes are orthologous with those of yeast

35
What are Paralogous Genes?
  • result from gene duplication, so they are found
    in more than one copy in the genome
  • They can diverge within the clade that carries
    them, often adding new functions
  • i.e. Olfactory receptor genes have undergone many
    gene duplications in vertebrates
  • Humans and mice each have huge families of more
    than 1,000 of these paralogous genes

36
LE 25-17a
Ancestral gene
Speciation
Orthologous genes
37
LE 25-17b
Ancestral gene
Gene duplication
Paralogous genes
38
What are Molecular Clocks?
  • The MOLECULAR CLOCK is a yardstick for measuring
    absolute time of evolutionary change
  • They are based on the observation that some
    regions of the genome evolve at constant rates
  • For these regions, the number of nucleotide
    substitutions in orthologous genes is
    proportional to the time that has elapsed since
    the two species last shared a common ancestor
  • In the case of paralogous genes, the number of
    substitutions is proportional to the time since
    the genes became duplicated
  • Proteins and mitochondrial genomes have constant
    rate of change over time

39
APPLYING A MOLECULAR CLOCK THE ORIGIN OF HIV
  • Phylogenetic analysis shows that HIV is descended
    from viruses that infect chimpanzees and other
    primates
  • Comparison of HIV samples throughout the epidemic
    shows that the virus evolved in a very clocklike
    way
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