LECTURE 1: Phylogeny and Systematics

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LECTURE 1 Phylogeny and Systematics
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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

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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

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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

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HOW DO THESE ORGANISMS DISPLAY EXAMPLES OF
CONVERGENT EVOLUTION?
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How would you compare the fins in these 2
organisms?
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What are Homoplasies?

• Analogous structures or molecular sequences that
  evolved independently
• Example the four-chambered heart of birds
  mammals is analogous

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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

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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

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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
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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
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LE 25-13
Drosophila
Bird
Rat
Mouse
Lancelet
Fish
Human
Amphibian
Cenozoic
65.5
Mesozoic
251
Paleozoic
542
Neoproterozoic
Millions of years ago
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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

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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

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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

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LE 25-10a
Grouping 1
A valid clade is monophyletic, signifying that it
consists of the ancestor species and all its
descendants
Monophyletic
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LE 25-10b
Grouping 2
A paraphyletic grouping consists of an ancestral
species and some, but not all, of the descendants
Paraphyletic
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LE 25-10c
Grouping 3
A polyphyletic grouping consists of various
species that lack a common ancestor
Polyphyletic
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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

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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)
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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

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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

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

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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

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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

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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

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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

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LE 25-17a
Ancestral gene
Speciation
Orthologous genes
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LE 25-17b
Ancestral gene
Gene duplication
Paralogous genes
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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

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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