Phylogenetics

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Phylogenetics

• Reconstructing Evolutionary Relationships

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Taxonomy and systematics

• Taxonomy
• Field of biology concerned with the theory,
  practice, and rules of classifying living and
  extinct organisms and viruses
• Systematics/Phylogeny
• Study of biological diversity and the
  evolutionary relationships among organisms, both
  extinct and modern
• Taxonomic groups are now based on hypotheses
  regarding evolutionary relationships derived from
  systematics

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Taxonomy

• Hierarchical system involving successive levels
• Each group called a taxon
• Domain
• Highest level
• All of life belongs to one of 3 domains
• Bacteria, Archaea, and Eukarya

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Taxonomy
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Binomial Nomenclature
The domestic dog
Scientific names are always italicized or
underlined
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Systematics

• Phylogeny evolutionary history of a species or
  group of species
• Gather morphological or molecular data
• Use mathematical strategies to analyze data
• Construct evolutionary trees
• Molecular data has caused many revisions, but it
  has also confirmed many old relationships

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Phylogenetic tree

• Diagram that describes phylogeny
• A hypothesis of evolutionary relationships among
  various species
• Based on available information
• New species can be formed by
• Anagenesis single species evolves into a
  different species
• Cladogenesis a species diverges into 2 or more
  species

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• Monophyletic group or clade
• Group of species, taxon, consisting of the most
  recent common ancestor and all of its ancestors
• Smaller and more recent clades are subsets of
  larger clades
• For larger taxa, common ancestor existed a long
  time ago (kingdom)
• For smaller taxa, common ancestor more recent
  (family or genus)

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Interpreting Phylogenetic Trees
Identify the monophyletic groups
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Homology

• Similarities among various species that occur
  because they are derived from a common ancestor
• Bat wing, human arm and cat front leg
• Genes can also be homologous

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Morphological analysis

• First systematic studies focused on morphological
  features of extinct and modern species
• Convergent evolution (traits arise independently
  due to adaptations to similar environments) can
  cause problems
• Example Phylogeny of the modern horse Equus.
  /'e.kwus/

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Cladistics

• Cladistics is a method that applies the
  scientific method to the construction of
  evolutionary relationships.
• Computer programs use algorithms to apply
  assumptions to a data set
• Data set can be DNA or RNA sequences
• Amino acid sequences of proteins
• Morphological characters

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Cladistic approach

• Compares traits shared or not shared
• Shared trait shared primitive character or
  symplesiomorphy
• Shared primitive characters suggest a distant
  common ancestor
• Not shared shared derived character or
  synapomorphy
• Trait that is shared by a group of organisms, but
  NOT by a distant common ancestor
• Shared derived characters indicate a more recent
  common ancestor

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• Branch point 2 species differ in shared derived
  characters
• Ingroup monophyletic group we are interested in
• Outgroup species or group of species that is
  most closely related to an ingroup
• All traits shared by the outgroup and the ingroup
  must have arisen in a common ancestor that
  predates the divergence of the 2 groups

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What shared derived character is common to the
salmon, lizard, and rabbit, but not the lamprey?
See animation!
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Outgroup Analysis

• Determines which characters in a given group of
  taxa are primitive or which are derived
• An outgroup is usually a taxon that represents
  the primitive condition
• The lancelet is the outgroup because it is a
  chordate without vertebrae. Also because of
  evidence based on the fossil record, and
  development
• All other taxa are grouped according to shared
  derived characters

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• Cladogram can also be constructed with gene
  sequences
• 7 species called A- G
• A mutation that changes the DNA sequence is
  analogous to a modification of a characteristic

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Constructing a cladogram

• Choose species
• Choose characters
• Each character has different character states
• Determine order of character states
• primitive or derived?
• Use the fossil record
• Many simple parts came before fewer, more
  specialized parts
• Vestigial organs
• Mutation rate of DNA nucleotides
• Group species (or higher taxa) based on shared
  derived characteristics

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Cladistics Assumptions

• Many simple parts came before fewer, more
  specialized parts
• Mutation rate of DNA nucleotides

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• Build a cladogram based on
• All species are placed on tips in the
  phylogenetic tree, not at branch points
• Each cladogram branch point should have a list of
  one or more shared derived characters that are
  common to all species above the branch point
  unless the character is later modified
• All shared derived characters appear together
  only once in a cladogram unless they arose
  independently during evolution more than once
• Choose the most likely cladogram among possible
  options

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Strategies for a likely cladogram

• Challenge in a cladistic approach is to determine
  the correct order of events
• May not always be obvious which traits are
  ancestral and came earlier, and which are derived
  and came later in evolution
• Different approaches can be used to deduce the
  correct order
• Assume that the best hypothesis is the one that
  requires the fewest number of evolutionary
  changes (principle of parsimony)

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Example

• 4 taxa (A-D)
• A is the outgroup
• Has all the primitive states
• 3 potential trees
• Tree 3 requires fewest number of mutations so is
  the most parsimonous

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Classification and Cladistics

• The branching pattern among organisms fall into 3
  catagories
• Monophyletic
• Paraphyletic
• Polyphyletic
• A taxon (genus, family, order etc.) is usually
  defined as a monophyletic group

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• Ideal goal of taxonomy to place organisms in
  monophyletic groups

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Monophyletic

• All descendants of most recent common ancestor

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Paraphyletic

• A common ancestor and some (not all) of its
  descendants

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Polyphyletic

• Organisms evolved from different recent ancestors

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• The classification of reptiles and birds
• Are birds monophyletic with reptiles?

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Cladistics in Action

• With whom do domestic dogs share a common
  ancestor? How is the domestic dog related to
  other canids?
• Possibilities
• wolves
• jackal species
• hybrid canid
• contemporary relative of ancient wolves that has
  since gone extinct
• Was there a single common ancestor to the
  domestic dog or did dog evolution happen many
  times in different parts of the world?

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Canidae The Dog Family

• 14 genera, 34 species
• Vulpes (foxes)
• Alopex (Arctic fox)
• Pseudoalopex (South American foxes)
• Canis
• domestic dogs
• wolves
• coyotes
• jackals

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Canis lupus familiaris
Canis sp.
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Lycaon sp. African hunting dog
Urocyon cinereoargenteus North American grey fox
Vulpes vulpes Red foxes
Alopex lagopus Arctic fox
Possible Outgroups Other Canids
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Cladistics in Action

• How is the domestic dog related to other canids?
• Sequenced 12 exons and 4 introns from different
  genes
• Sequenced the exons and introns from 30 different
  animals
• Results?

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Results?
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Results

• Who is most closely related to the domestic dog?
• Is the genus Canis a monophyltic group?
• Should Jackals be classified with dogs?
• Should the African wild dog be classified in a
  separate genus from Canis?

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The Evolution of Dogs

• Are the morphologies of different dog breeds a
  result of having come from
• different wolf lineages
• or different geographic regions?
• Data set
• 654 domestic dogs from Europe, Asia, Africa,
  Arctic American dogs, including 100 Chinese dogs
• 38 wolves from Asia and Europe
• Sequenced mitochondrial DNA (mtDNA)

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Canis lupus
Are the morphologies of different dog breeds a
result of having come from different wolf
lineages ? or different geographic regions?
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• Clade A wolves are from China and Mongolia
• Domestic dogs from all geographic areas
• Clade B wolves are from Afghanistan and Eastern
  Europe
• Domestic dogs from all regions except America

P. Savolainen et al., Science 298, 1610 -1613
(2002)
Fig. 2.
Published by AAAS
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The Evolution of Dogs

• When and where did the modern dog evolve from the
  wolf?
• Fossil evidence
• 14,000 yrs ago?
• Central Europe
• 10,000/3,500 yrs ago?
• Italy
• 12,000 yrs ago?
• Israel

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From which region did dogs originate? (refer to
Table 1)

• Geographic areas with the highest genetic
  diversity represent the center of origin for the
  species
• Populations containing unique alleles have been
  around a long time (enough to accumulate unique
  mutations)

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