Phylogeny and Systematics

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Phylogeny and Systematics

• Chapter 10

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Taxonomy

• Taxonomy produces a formal system for naming and
  classifying species to illustrate their
  evolutionary relationship.

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Taxonomy Systematics

• Taxonomy
• Formal system for naming and classifying species.
• Systematics
• Broader science of classifying organisms based on
  similarity, biogeography, etc.
• Systematic zoologists have three goals
• To discover all species of animals.
• To reconstruct their evolutionary relationships.
• To classify animals according to their
  evolutionary relationships.

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Taxonomy

• Introduction of evolutionary theory into animal
  taxonomy changed taxonomists role from one of
  classification to systematization.
• Classification denotes the construction of
  classes.
• Grouping of organisms that possess a common
  feature called an essence used to define the
  class.

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Taxonomy

• Systematization places groups of species into
  units of common evolutionary descent.
• Character variation is used to diagnose systems
  of common descent.
• No requirement that an essential character be
  maintained throughout the system for its
  recognition as a taxon.

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Taxonomy

• In classification
• Taxonomist asks whether a species being
  classified contains the defining feature of a
  particular taxonomic class.
• In systematization
• Taxonomist asks whether the characteristics of a
  species confirm or reject the hypothesis that it
  descends from the most recent common ancestor of
  a particular taxon.

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Linnaeus and Classification

• Carolus Linnaeus designed our hierarchical
  classification scheme.
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

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Linnaeus and Classification

• All animals are placed in Kingdom Animalia.
• Names of animal groups at each rank in the
  hierarchy are called taxa (taxon).
• Each rank can be subdivided into additional
  levels of taxa.
• Superclass, suborder, etc.

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Linnaeus and Classification
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Linnaeus and Classification

• Binomial nomenclature is the system Linnaeus used
  for naming species.
• Genus and species
• Names are latinized and italicized, only the
  genus is capatilized.
• Sitta carolinensis

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Linnaeus and Classification

• A trinomial name includes a subspecies epithet.
• Ensatina escholtzii escholtzii
• E. e. klauberi

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Species

• Defining a species can be difficult.
• Criteria
• Common descent
• The smallest distinct groupings of organisms
  sharing a pattern of descent.
• Morphological molecular techniques
• Members of a species must form a reproductive
  community that excludes other species.

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Species

• The geographic range of a species is its
  distribution in space.
• Evolutionary duration of a species is its
  distribution in time.
• A worldwide species is cosmopolitan.
• One with a very localized range is called endemic.

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Typological Species Concept

• The typological or morphological species concept
  relies on type specimens that represent the ideal
  form for the species. When trying to name a
  specimen, the type specimens were compared.

• Scientists still name species by designating a
  type specimen.

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The Biological Species Concept

• The biological species concept emerged during the
  evolutionary synthesis.
• A species is a reproductive community of
  populations (reproductively isolated from others)
  that occupies a specific niche in nature. Mayr
  1982
• Sibling species fit this category, but can only
  be differentiated with molecular techniques.
• Lacks a temporal dimension.
• Degree of reproductive isolation necessary?
• Species that reproduce asexually?

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Evolutionary Species Concept

• The evolutionary species concept states that a
  single lineage of ancestor-descendant populations
  that maintains its identity from other such
  lineages and that has its own evolutionary
  tendencies and historical fate.
• Definition accommodates both sexual and asexual
  forms as well as fossils.

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Phylogenetic Species Concept

• The phylogenetic species concept is defined as an
  irreducible (basal) grouping of organisms
  diagnosably distinct from other such groupings
  and within which there is a parental pattern of
  ancestry and descent.
• Both asexual and sexual groups are covered.

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Phylogenetic Species Concept

• Main difference in practice between the
  evolutionary and phylogenetic species concepts
• The latter emphasizes recognizing as separate
  species the smallest groupings of organisms that
  have undergone independent evolutionary change.
• Discerns the greatest number of species but may
  be impractical.
• Disregards details of evolutionary process.

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Investigating the Tree of Life

• A major goal of systematics is to infer the
  evolutionary tree or phylogeny the evolutionary
  history of a species or group of related species.

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Phylogeny

• Phylogenies are inferred by identifying
  organismal features, characters, that vary among
  species.
• Morphological
• Chromosomal
• Molecular
• Behavioral or ecological

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Phylogeny

• Shared characters that result from common
  ancestry are homologous.
• Independent evolution of similar characters that
  are NOT homologous is called homoplasy.

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Sorting Homology from Analogy

• A potential misconception in constructing a
  phylogeny is similarity due to convergent
  evolution, called analogy, rather than shared
  ancestry.

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Sorting Homology from Analogy

• Convergent evolution occurs when similar
  environmental pressures and natural selection
  produce similar (analogous) adaptations in
  organisms from different evolutionary lineages.

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Sorting Homology from Analogy

• Analogous structures or molecular sequences that
  evolved independently are also called
  homoplasies.

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Shared Primitive and Shared Derived
Characteristics

• A shared primitive (ancestral) character
• Is a homologous structure that predates the
  branching of a particular clade from other
  members of that clade.
• Is shared beyond the taxon we are trying to
  define.
• Example mammals all have a backbone, but so do
  other vertebrates.

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Shared Primitive and Shared Derived
Characteristics

• A shared derived character is an evolutionary
  novelty unique to a particular clade.
• All mammals have hair, and no other animals have
  hair.

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Phylogeny

• The form of the character that was present in the
  common ancestor of the entire group is called
  ancestral.
• Variant forms of the character arose later and
  are called derived character states.
• Determining polarity of a character involves
  determining which state is ancestral.

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Phylogeny

• Polarity is determined by using outgroup
  comparison.
• An outgroup is closely related, but not part of
  the group being examined (the ingroup).
• If a character is found in both the study group
  and the outgroup, it is considered ancestral for
  the study group.
• Character groups found in the study groups but
  not the outgroups are derived.

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Phylogeny

• Clades are organisms or species that share
  derived character states and form a subset within
  a larger group.
• A synapomorphy is a derived character shared by
  the members of the clade.
• A clade corresponds to a unit of evolutionary
  common descent.
• A nested hierarchy is formed by the derived
  states of all characters in a study group.

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Phylogeny

• Ancestral character states for a taxon are called
  plesiomorphic.
• Sharing these ancestral characters is called
  symplesiomorphy.
• Symplesiomorphies, unlike synapomorphies, do not
  provide information on nesting of clades groups
  with derived characters get left out.

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Phylogeny

• The nested hierarchy of clades can be represented
  as a cladogram that is based on shared
  synapomorphies.

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Phylogeny

• A phylogenetic tree is another way of
  representing evolutionary relationships.
• Branches represent real lineages that occurred in
  the evolutionary past.
• Includes information about ancestors, duration of
  evolutionary lineages, amounts of evolutionary
  change that has occurred.

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Sources of Phylogenetic Information

• Characters used to construct cladograms can be
  found using
• Comparative morphology examine shapes and sizes
  of organismal structures, including developmental
  origins.
• Comparative biochemistry examine sequences of
  amino acids and nucleotides to identify variable
  characters.
• Comparative cytology uses variation in numbers,
  shapes, and sizes of chromosomes and their parts.

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Taxonomy

• A theory of taxonomy allows us to rank taxonomic
  groups.
• Two popular theories
• Evolutionary taxonomy
• Phylogenetic systematics
• Both based on evolutionary principles, sometimes
  results conflict.

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Cladistics

• A valid clade is monophyletic.
• Signifying that it consists of the ancestor
  species and all its descendants.

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Cladistics

• A paraphyletic clade is a grouping that consists
  of an ancestral species and some, but not all, of
  the descendants.

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Cladistics

• A polyphyletic grouping includes numerous types
  of organisms that lack a common ancestor.

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Traditional Evolutionary Taxonomy

• Evolutionary taxonomy utilizes common descent and
  the amount of adaptive evolutionary change to
  rank higher taxa.
• Sometimes this type of classification includes
  paraphyletic groupings.

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Phylogenetic Systematics

• Phylogenetic systematics, or cladistics,
  emphasizes common descent and is based on
  cladograms.
• All taxa must be monophyletic.
• Cladistic taxonomists have moved chimpanzees,
  gorillas, and orangutans into the family
  Hominidae with humans.
• Humans and chimps form a sister group, as do the
  human/chimp group and gorillas.

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Theories of Taxonomy

• Both evolutionary and cladistic taxonomy
• Accept monophyletic groups.
• Reject polyphyletic groups.
• Differ on accepting paraphyletic groups.
• Traditional evolutionary taxonomy does.
• Phylogenetic systematics does not.
• Difference has important evolutionary
  implications.

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Theories of Taxonomy

• Current State of Animal Taxonomy
• Modern animal taxonomy was established using
  evolutionary systematics and recent cladistic
  revisions.
• PhyloCode
• New taxonomic system
• Being developed as an alternative to Linnean
  taxonomy.
• Replaces Linnean ranks with codes that denote the
  nested hierarchy of monophyletic groups conveyed
  by cladograms.
• The terms primitive, advanced, specialized
  and generalized are used for specific
  characteristics and not for groups as a whole.

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Maximum Parsimony and Maximum Likelihood

• Systematists can never be sure of finding the
  single best tree in a large data set.
• Narrow the possibilities by applying the
  principles of maximum parsimony and maximum
  likelihood.

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Parsimony

• Among phylogenetic hypotheses the most
  parsimonious tree is the one that requires the
  fewest evolutionary events to have occurred in
  the form of shared derived characters.
• Occams Razor

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Parsimony

• The principle of maximum likelihood states that,
  given certain rules about how DNA changes over
  time, a tree can be found that reflects the most
  likely sequence of evolutionary events.

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Phylogenetic Trees as Hypotheses

• The best hypotheses for phylogenetic trees are
  those that fit the most data morphological,
  molecular, and fossil.

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Molecular Systematics

• Much of an organisms evolutionary history is
  documented in its genome.
• Comparing nucleic acids or other molecules to
  infer relatedness is a valuable tool for tracing
  organisms evolutionary history.

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Major Divisions of Life

• Aristotles two kingdom system included plants
  and animals.
• One-celled organisms became a problem
• Haeckel (1866) proposed Protista for
  single-celled organisms.
• R.H. Whittaker (1969) proposed a five-kingdom
  system to distinguish prokaryotes and fungi.

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Major Divisions of Life

• Woese, Kandler and Wheelis (1990) proposed three
  monophyletic domains above kingdom levelEucarya,
  Bacteria and Archaeabased on ribosomal RNA
  sequences.

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Major Divisions of Life

• More revisions are necessary to clarify taxonomic
  kingdoms based on monophyly.
• Protozoa
• Neither animals nor a valid monophyletic taxon.
• Protista
• Not a monophyletic kingdom.
• Most likely composed of seven or more kingdoms.

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Major Subdivisions of the Animal Kingdom

• Traditional groupings based on embryological and
  anatomical characters
• Branch A (Mesozoa) phylum Mesozoa,
  the mesozoa
• Branch B (Parazoa) phylum Porifera,
  the sponges and phylum Placozoa
• Branch C (Eumetazoa) all other phyla

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Major Subdivisions of the Animal Kingdom

• Branch C (Eumetazoa) all other phyla
• Grade I (Radiata) phyla Cnidaria, Ctenophora
• Grade II (Bilateria) all other phyla
• Division A (Protostomia) Protostome
  characteristics
• Acoelomates phyla Platyhelminthes,
  Gnathostomulida, Nemertea
• Pseudocoelomates phyla Rotifera, Gastrotricha,
  Kinorhyncha, Nematoda, Nematomorpha,
  Acanthocephala, Entoprocta, Priapulida,
  Loricifera
• Eucoelomates phyla Mollusca, Annelida,
  Arthropoda, Echiurida, Sipunculida, Tardigrada,
  Onychophora.

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Major Subdivisions of the Animal Kingdom

• Division B (Deuterostomia) Deuterostome
  characteristics
• phyla Phoronida, Ectoprocta, Chaetognatha,
  Brachiopoda, Echinodermata, Hemichordata, Chordata

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Major Subdivisions of the Animal Kingdom

• Recent molecular phylogenetic studies have
  challenged traditional classification of
  Bilateria.
• Grade II Bilateria
• Division A (Protostomia)
• Lophotrochozoa phyla platyhelminthes, Nemertea,
  Rotifera, Gastrotricha, Acanthocephala, Mollusca,
  Annelida, Echiurida, Sipunculida, Phoronida,
  Ectoprocta, Entoprocta, Gnathostomulida,
  Chaetognatha, Brachiopoda
• Ecdysozoa phyla Kinorhyncha, Nematoda,
  Nematomorpha, Priapulida, Arthropoda, Tardigrada,
  Onychophora, Loricifera
• Division B (Deuterostomia)
• phyla Chordata, Hemichordata, Echinodermata

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