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Phylogenetics

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Bat wing, human arm and cat front leg. Genes can also be homologous. 13. Morphological analysis ... Alopex (Arctic fox) Pseudoalopex (South American foxes) ... – PowerPoint PPT presentation

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Title: Phylogenetics


1
Phylogenetics
  • Reconstructing Evolutionary Relationships

2
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

3
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
6
Binomial Nomenclature
The domestic dog
Scientific names are always italicized or
underlined
7
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

8
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)

11
Interpreting Phylogenetic Trees
Identify the monophyletic groups
12
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

13
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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15
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

16
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

17
  • 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

18
What shared derived character is common to the
salmon, lizard, and rabbit, but not the lamprey?
See animation!
19
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

20
  • 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

23
Cladistics Assumptions
  • Many simple parts came before fewer, more
    specialized parts
  • Mutation rate of DNA nucleotides

24
  • 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

25
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)

26
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

27
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

28
  • Ideal goal of taxonomy to place organisms in
    monophyletic groups

29
Monophyletic
  • All descendants of most recent common ancestor

30
Paraphyletic
  • A common ancestor and some (not all) of its
    descendants

31
Polyphyletic
  • Organisms evolved from different recent ancestors

32
  • The classification of reptiles and birds
  • Are birds monophyletic with reptiles?

33
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?

34
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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37
Canis lupus familiaris
Canis sp.
38
Lycaon sp. African hunting dog
Urocyon cinereoargenteus North American grey fox
Vulpes vulpes Red foxes
Alopex lagopus Arctic fox
Possible Outgroups Other Canids
39
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?

40
Results?
41
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?

42
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)

43
Canis lupus
Are the morphologies of different dog breeds a
result of having come from different wolf
lineages ? or different geographic regions?
44
  • 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
45
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

46
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)

47
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