Systematics and the phylogenetic revolution

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Chapter 23

• Systematics and the phylogenetic revolution

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Introduction

• All organisms
• Are composed of one or more cells
• Carry out metabolism
• Transfer energy with ATP
• Encode hereditary information in DNA
• Tremendous diversity of life
• Bacteria-----whales----sequoia trees
• Biologists group organisms based on shared
  characteristics

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Systematics

• Since fossil records are not complete, scientists
  rely on other types of evidence to establish the
  best hypothesis of evolutionary relationships
• Systematics the study of evolutionary
  relationships
• Phylogeny a hypothesis about patterns of
  relationship among species

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Systematics

• Darwin envisioned that all species were descended
  from a single common ancestor
• He depicted this history of life as a branching
  tree.
• Now called a cladogram

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Systematics

• Phylogenies depict evolutionary relatedness
• Key to interpreting a phylogeny look at how
  recently species share a common ancestor
• Similarity may not accurately predict
  evolutionary relationships
• Early systematists relied on the expectation that
  the greater the time since two species diverged
  from a common ancestor, more different would be

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Systematics

• Punctuated evolution- occurs rapidly

• Gradual evolution- occurs slowly (Gradualism)

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Systematics

• Oscillating selection Traits can evolve in one
  direction, then back the other way
• Evolution is not always divergent convergent
  evolution
• Use similar habitats
• Similar environmental pressures
• Evolutionary reversal process in which a
  species re-evolves the characteristics of an
  ancestral species

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Cladistics

• Derived characteristic similarity that is
  inherited from the most recent common ancestor of
  an entire group
• Ancestral similarity that arose prior to the
  common ancestor of the group
• In cladistics, only shared derived characters are
  considered informative about evolutionary
  relationships
• To use the cladistic method character variation
  must be identified as ancestral or derived

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Cladistics

• Characters can be any aspect of the phenotype
• Morphology - Physiology
• Behavior - DNA
• Characters should exist in recognizable character
  states
• Example Teeth in amniote vertebrates has two
  states, present in most mammals and reptiles and
  absence in birds and turtles

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Cladistics

• Examples of ancestral versus derived characters
• Presence of hair is a shared derived feature of
  mammals
• Presence of lungs in mammals is an ancestral
  feature also present in amphibians and reptiles

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Cladistics

• Determination of ancestral versus derived
• First step in a manual cladistic analysis is to
  polarize the characters (are they ancestral or
  derived)
• Example polarize teeth means to determine
  presence or absence in the most recent common
  ancestor

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Cladistics

• Outgroup comparison is used to assign character
  polarity
• A species or group of species not a member of the
  group under study is designated as the outgroup
• Outgroup species do not always exhibit the
  ancestral condition
• When the group under study exhibits multiple
  character states, and one of those states is
  exhibited by the outgroup, then that state is
  ancestral and other states are derived
• Most reliable if character state is exhibited by
  several different outgroups

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Cladistics

• Following the character state-outgroup method
• Presence of teeth in mammals and reptiles is
  ancestral
• Absence of teeth in birds and turtles is derived

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Cladistics

• ?Construction of a cladogram
• Polarize characteristics
• Clade species that share a common ancestor as
  indicated by the possession of shared derived
  characters
• Clades are evolutionary units and refer to a
  common ancestor and all descendants
• Synapomorphy a derived character shared by
  clade members

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Cladistics

• A simple cladogram is a nested set of clades
• Plesiomorphies ancestral states
• Symplesiomorphies shared ancestral states

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Cladistics
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Cladistics

• Homoplasy a shared character state that has not
  been inherited from a common ancestor
• Results from convergent evolution
• Results from evolutionary reversal
• If there are conflicts among characters, use the
  principle of parsimony which favors the
  hypothesis that requires the fewest assumptions

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Cladistics

• Parsimony and Homoplasy

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Cladistics

• A Cladogram DNA

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Cladistics
A Cladogram DNA
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Other Phylogenetic Methods

• Some characters evolve rapidly and principle of
  parsimony may be misleading
• Rate at which some parts of the DNA genome evolve
• Mutations in repetition sequences, not deleted by
  natural selection
• Statistical approaches
• Molecular clock rate of evolution of a molecule
  is constant through time

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Systematics and Classification

• Classification how we place species and higher
  groups into the taxonomic hierarchy
• Genus, family, class..
• Monophyletic group includes the most recent
  common ancestor of the group and all of its
  descendants (clade)
• Paraphyletic group includes the most recent
  common ancestor of the group, but not all its
  descendants

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Systematics and Classification

• Polyphyletic group does not include the most
  recent common ancestor of all members of the
  group
• Taxonomic hierarchies are based on shared traits,
  should reflect evolutionary relationships
• Why should you refer to birds as a type of
  dinosaur?

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Systematics and Classification

• Monophyletic Group

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Systematics and Classification

• Paraphyletic Group

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Systematics and Classification

• Polyphyletic Group

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Systematics and Classification

• Old plant classification system

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Systematics and Classification

• New plant classification system

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Systematics and Classification

• Phylogenetic species concept (PSC)
• Focuses on shared derived characters
• Biological species concept (BSC)
• Defines species as groups of interbreeding
  population that are reproductively isolated
• Phylogenetic species concept species should be
  applied to groups of populations that have been
  evolving independently of other groups

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Systematics and Classification

• BSC cannot be applied to allopatric populations
• PSC can be applied to allopatric populations
• PSC can be applied to both sexual and asexual
  species
• BSC can be applied only to sexual species
• PSC still controversial

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Systematics and Classification

• Paraphyly and phylogenetic species concept

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Comparative Biology

• Phylogenetics is the basis of all comparative
  biology
• Homologous structures are derived from the same
  ancestral source (e.g. dolphin flipper and horse
  leg)
• Homoplastic structures are not (e.g. wings of
  birds and dragonflies)
• -Parental care
• Dinosaurs, birds, crocodiles
• Homologous behavior

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Comparative Biology

• Parental care in dinosaurs and crocodiles

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Comparative Biology

• Homoplastic convergence saber teeth
• Occurred in different groups of extinct
  carnivores
• Similar body proportions (cat)
• Similar predatory lifestyle
• Most likely evolved independently at least 3 times

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Comparative Biology

• Distribution of saber-toothed mammals

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Comparative Biology

• Homoplastic convergence plant conducting tubes
• Sieve tubes facilitate long-distance transport of
  food that is essential for the survival of tall
  plants
• Brown algae also have sieve elements
• Closest ancestor a single-celled organism

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Comparative Biology

• Convergent evolution of conducting tubes

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Comparative Biology

• Most complex characters evolve through a sequence
  of evolutionary changes
• Modern-day birds
• wings, feathers, light bones, breastbone
• Initial stages of a character evolved as an
  adaptation to some environmental selective
  pressure
• First featherlike structure evolved in theropod
  phylogeny
• Insulation or perhaps decoration

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Comparative Biology
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Comparative Biology

• Phylogenetic methods can be used to distinguish
  between competing hypotheses
• Larval dispersal in marine snails
• Some snails produce microscopic larvae that drift
  in the ocean currents
• Some species have larvae that settle to the ocean
  bottom and do not disperse
• Fossils show increase in nondispersing snails

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Comparative Biology

• Increase through time in proportion of species
  whose larvae do not disperse

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Comparative Biology

• Two processes could produce an increase in
  nondispersing larvae
• Evolutionary change from dispersing to
  nondispersing occurs more often than change in
  the opposite direction
• Species that are nondispersing speciate more
  frequently, or become extinct less frequently
  than dispersing species
• The two processes would result in different
  phylogenetic patterns

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Comparative Biology
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Comparative Biology

• Analysis indicates
• Evolutionary increase in nondispersing larvae
  through time may be a result of both a bias in
  the evolutionary direction and an increase in
  rate of diversification
• Lack of evolutionary reversal

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Comparative Biology

• Loss of larval stage in marine invertebrates
• Nonreversible evolutionary change
• Marine limpets show direct development has
  evolved many times
• 3 cases where evolution reversed and larval stage
  re-evolved

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Comparative Biology
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Comparative Biology

• Phylogenetics helps explain species
  diversification
• Use phylogenetic analysis to suggest and test
  hypotheses
• Species richness in beetles
• Coleoptera 60 of all animals are insects and
  80 of all insects are beetles
• Phytophaga clade with most herbivorous beetles
• Family Nemonychidae specialized on conifers
  since Jurassic

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Comparative Biology

• Evolutionary diversification of the Phytophaga

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Comparative Biology

• Phylogenetic explanations for beetle
  diversification
• Not the evolution of herbivory
• Specialization on angiosperms a prerequisite for
  diversification
• Risen 5 times independently within herbivorous
  beetles
• Angiosperm specializing clade is more
  species-rich than the clade most closely related

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Disease Evolution

• HIV evolved from a simian (monkey) viral
  counterpart SIV
• First recognized in 1980s
• Current estimate gt39 million people infected gt
  3 million die each year
• SIV found in 36 species of primates
• Does not usually cause illness in monkeys
• Around for more than a million years as SIV

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Disease Evolution
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Disease Evolution

• Phylogenetic analysis of HIV and SIV
• First HIV descended from SIV
• All strains of HIV are nested within clades of
  SIV
• Second a number of different strains of HIV
  exits
• Independent transfers from different primate
  species
• Each human strain is more closely related to a
  strain of SIV than to other HIV strains

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Disease Evolution

• Third humans have acquired HIV from different
  host species