Reconstructing and Using Phylogenies

1
Reconstructing and Using Phylogenies
2
25 Reconstructing and Using Phylogenies

• 25.1 What Is Phylogeny?
• 25.2 How Are Phylogenetic Trees Constructed?
• 25.3 How Do Biologists Use Phylogenetic Trees?
• 25.4 How Does Phylogeny Relate to Classification?

3
25.1 What Is Phylogeny?

• Phylogeny is a description of the evolutionary
  history of relationships among organisms.
• This is portrayed in a diagram called a
  phylogenetic tree.
• Each split or node represents the point at which
  lineages diverged. The common ancestor of all
  organisms in the tree is the root.

4
Figure 25.1 How to Read a Phylogenetic Tree (Part
1)
5
Figure 25.1 How to Read a Phylogenetic Tree (Part
2)
6
25.1 What Is Phylogeny?

• The timing of divergences is shown by the
  position of nodes on a time or divergence axis.
• Lineages can be rotated around nodes the
  vertical order of taxa is largely arbitrary.

7
25.1 What Is Phylogeny?

• A taxon (plural taxa) is any group of species
  that we designate (e.g., vertebrates).
• A taxon that consists of all the descendents of a
  common ancestor is called a clade.

8
25.1 What Is Phylogeny?

• Two species that are each others closest
  relatives are sister species.
• Two clades that are each others closest
  relatives are sister clades.
• Phylogenetic trees were used mainly in
  systematics (study of biodiversity) but are now
  used in nearly all fields of biology.

9
25.1 What Is Phylogeny?

• One of the greatest unifying concepts in biology
  is that all life is connected through
  evolutionary history.
• The Tree of Life is the complete,
  4-billion-year history of life.
• Knowledge of evolutionary relationships is
  essential for making comparisons in biology.

10
25.1 What Is Phylogeny?

• Biologists determine traits that differ within a
  group of interest, then try to determine when
  these traits evolved.
• Often, we wish to know how the trait was
  influenced by environmental conditions or
  selection pressures.

11
25.1 What Is Phylogeny?

• Features shared by two or more species that were
  inherited from a common ancestor are homologous.
• Example The vertebral column is homologous in
  all vertebrates.

12
25.1 What Is Phylogeny?

• A trait that differs from the ancestral trait is
  called derived.
• A trait that was present in the ancestor of a
  group is ancestral.

13
25.1 What Is Phylogeny?

• Derived traits that are shared among a group and
  are viewed as evidence of the common ancestry of
  the group are known as synapomorphies.
• The vertebral column is a synapomorphy of all
  vertebrates.

14
25.1 What Is Phylogeny?

• Similar traits can develop in unrelated groups of
  organisms
• Convergent evolutionindependently evolved traits
  subjected to similar selection pressures may
  become superficially similar.
• Example the wings of bats and birds

15
Figure 25.2 The Bones Are Homologous the Wings
Are Not
16
25.1 What Is Phylogeny?

• Evolutionary reversala character reverts from a
  derived state back to the ancestral state.
• Example Most frogs do not have lower teeth, but
  the ancestor of frogs did. One frog genus has
  regained teeth in the lower jaw.

17
25.1 What Is Phylogeny?

• Traits that are similar for reasons other than
  inheritance from a common ancestor are called
  homoplastic traits or homoplasies.
• Traits may be ancestral or derived, depending on
  the point of reference in phylogeny. Bird
  feathers are ancestral in birds, but derived when
  considering all living vertebrates.

18
25.2 How Are Phylogenetic Trees Constructed?

• Constructing a phylogenetic tree using eight
  vertebrate animals
• Assume no convergent evolution and no derived
  traits have been lost.
• Lampreys are the outgroupany species or group
  outside the group of interest. The group of
  interest is the ingroup.
• Comparison with the outgroup shows which traits
  of the ingroup are derived and which are
  ancestral.

19
Table 25.1 (Part 1)
20
Table 25.1 (Part 2)
21
25.2 How Are Phylogenetic Trees Constructed?

• Chimpanzees and mice share two derived traitsfur
  and mammary glands. Assume these traits evolved
  only once they are synapomorphies for this
  group.
• Keratinous scales are a synapomorphy of the
  crocodile, pigeon, and lizard.
• Information about the synapomorphies allows
  construction of the tree.

22
Figure 25.3 Inferring a Phylogenetic Tree
23
25.2 How Are Phylogenetic Trees Constructed?

• Phylogenetic trees are typically constructed
  using hundreds or thousands of traits.
• How are synapomorphies and homoplasies
  determined?

24
25.2 How Are Phylogenetic Trees Constructed?

• The parsimony principle the simplest explanation
  of observed data is the preferred explanation.
• Minimize the number of evolutionary changes that
  must be assumedthe fewest homoplasies.
• Occams razor the best explanation fits the data
  with the fewest assumptions.

25
25.2 How Are Phylogenetic Trees Constructed?

• Computer programs are now used to analyze traits
  and construct trees.
• All kinds of traitsmorphological, fossil,
  developmental, molecular, behavioralare used by
  systematists to construct phylogenies.

26
25.2 How Are Phylogenetic Trees Constructed?

• Morphology
• Most species have been described on the basis of
  morphological data, such as features of the
  skeletal system in vertebrates, or floral
  structures in plants.
• Limitations comparing distantly related species
  some morphological variation is caused by
  environment some species show few morphological
  differences.

27
25.2 How Are Phylogenetic Trees Constructed?

• Development
• Similarities in development patterns may reveal
  evolutionary relationships.
• Example Sea squirts and vertebrates all have a
  notochord at some time in their development.

28
Figure 25.4 A Larva Reveals Evolutionary
Relationships
29
25.2 How Are Phylogenetic Trees Constructed?

• Paleontology
• Fossils provide information about the morphology
  of past organisms, and where and when they lived.
• Important in determining derived and ancestral
  traits, and when lineages diverged.
• Limitations fossil record is fragmentary and
  missing for some groups.

30
25.2 How Are Phylogenetic Trees Constructed?

• Behavior
• Behavior can be inherited or culturally
  transmitted.
• Bird songs are often learned, and may not be a
  useful trait for phylogenies.
• Frog calls are genetically determined and can be
  used in phylogenetic trees.

31
25.2 How Are Phylogenetic Trees Constructed?

• Molecular data
• DNA sequences have become the most widely used
  data for constructing phylogenetic trees.
• Mitochondrial and chloroplast DNA is used as well
  as nuclear DNA.
• Gene product information, such as amino acid
  sequences, are also used.

32
25.2 How Are Phylogenetic Trees Constructed?

• Mathematical models are used to describe DNA
  changes over time.
• Models can be used to compute maximum likelihood
  solutions, the probability of the observed data
  evolving on the specified tree.
• Most often used for molecular data, models of
  evolutionary change are easier to develop.

33
25.2 How Are Phylogenetic Trees Constructed?

• Testing the accuracy of phylogenetic
  reconstructions experiments with living
  organisms and computer simulations.
• Cultures of bacteriophage T7 were grown in the
  presence of a mutagen and allowed to evolve in
  the laboratory.

34
Figure 25.5 A Demonstration of the Accuracy of
Phylogenetic Analysis (Part 1)
35
Figure 25.5 A Demonstration of the Accuracy of
Phylogenetic Analysis (Part 2)
36
25.2 How Are Phylogenetic Trees Constructed?

• At the end of the experiment, genomes of the
  endpoints were sequenced and investigators built
  phylogenetic trees that accurately reflected the
  known evolutionary history of the cultures.

37
25.2 How Are Phylogenetic Trees Constructed?

• Phylogenetic methods can be used to reconstruct
  traits or nucleotide sequences for ancestral
  species.
• Example Reconstruction of opsin (pigment
  involved in vision) in the ancestral archosaur
  (last common ancestor of birds, crocodiles, and
  dinosaurs).

38
25.2 How Are Phylogenetic Trees Constructed?

• Analysis of opsin from living vertebrates was
  used to estimate the amino acid sequence of opsin
  in the archosaur.
• A protein of this sequence was constructed in the
  laboratory and then wavelengths of light it
  absorbs were measured.
• Activity in the red range indicated that the
  animal may have been nocturnal.

39
25.2 How Are Phylogenetic Trees Constructed?

• Molecular clock hypothesis Rates of molecular
  change are constant enough to predict timing of
  evolutionary divergence.
• Among closely related species, a given gene
  usually evolves at a reasonably constant rate,
  and can be used to determine time elapsed since a
  divergence.

40
25.2 How Are Phylogenetic Trees Constructed?

• Molecular clocks must be calibrated using
  independent data, such as the fossil record, and
  known divergences or biogeographic dates (e.g.,
  from continental drift).
• Example 500 species of cichlid fishes of Lake
  Victoria.

41
25.2 How Are Phylogenetic Trees Constructed?

• Mitochondrial DNA sequences were used to
  construct a phylogenetic tree of the cichlids.
• It has been suggested that the ancestors came
  from the older Lake Kivu, and they colonized Lake
  Victoria on two occasions.
• Molecular clock analysis suggested that some
  endemic cichlid lineages split at least 100,000
  years ago.

42
25.2 How Are Phylogenetic Trees Constructed?

• The analyses suggest that Lake Victoria did not
  dry up completely between 15,600 and 14,700 years
  ago, and many species survived in rivers and in
  the remnants of the lake during the dry period.

43
Figure 25.6 Origins of the Cichlid Fishes of Lake
Victoria (Part 1)
44
Figure 25.6 Origins of the Cichlid Fishes of Lake
Victoria (Part 2)
45
25.3 How Do Biologists Use Phylogenetic Trees?

• Most flowering plants reproduce by outcrossing or
  mating with another individual.
• Other plants are selfing, which requires that
  they be self-compatible.
• Phylogenetic analysis can show how often
  self-compatibility has evolved.

46
25.3 How Do Biologists Use Phylogenetic Trees?

• The genus Linanthus has a variety of breeding
  systems.
• Outcrossing species have long petals and are
  self-incompatible. Self-compatible species have
  short petals.
• A phylogeny was constructed using ribosomal DNA.
• Self-incompatibility is the ancestral state.

47
Figure 25.7 Phylogeny of a Section of the Plant
Genus Linanthus (Part 1)
48
Figure 25.7 Phylogeny of a Section of the Plant
Genus Linanthus (Part 2)
49
25.3 How Do Biologists Use Phylogenetic Trees?

• Phylogenetic analysis can be important in
  understanding zoonotic diseases (infectious
  organisms are transmitted to humans from another
  animal host).
• Example HIV was acquired from chimpanzees and
  sooty mangabeys.

50
Figure 25.8 Phylogenetic Tree of Immunodeficiency
Viruses
51
25.3 How Do Biologists Use Phylogenetic Trees?

• Reproductive success of male swordtails is
  associated with long swords (sexual selection).
  Evolution of the sword may result from a
  preexisting bias of female sensory
  systemssensory exploitation hypothesis.
• Phylogenetics identified platyfishes as the
  closest relatives.

52
25.3 How Do Biologists Use Phylogenetic Trees?

• Artificial swords were attached to platyfish
  males.
• Female platyfish preferred males with the
  artificial swords, supporting the idea that
  females had a preexisting bias even before the
  swords evolved.

53
Figure 25.9 The Origin of a Sexually Selected
Trait in the Fish Genus Xiphophorus
54
25.3 How Do Biologists Use Phylogenetic Trees?

• Rate of evolution of influenza virus is high.
• Phylogenetic analysis indicates there is a strong
  selection by the human immune system for most
  strains.
• Only strains with the greatest number of
  substitutions on hemagglutinin (surface protein
  recognized by the immune system) are likely to
  leave descendents.

55
Figure 25.10 Model of Hemagglutinin, a Surface
Protein of Influenza
56
25.3 How Do Biologists Use Phylogenetic Trees?

• Phylogenetic analysis helps biologists predict
  which of the currently circulating strains are
  most likely to survive and leave descendents.
• This information is then used to formulate
  influenza vaccines.

57
25.4 How Does Phylogeny Relate to Classification?

• The biological classification system was started
  by Swedish biologist Carolus Linnaeus in the
  1700s.
• Binomial nomenclature gives every species a
  unique, unambiguous name.

58
Figure 25.11 Many Different Plants Are Called
Bluebells
59
25.4 How Does Phylogeny Relate to Classification?

• Every species has two names the genus (group of
  closely related species) to which it belongs, and
  the species name.
• The name of the taxonomist who first described
  the species is often included.
• Example Homo sapiens Linnaeus

60
25.4 How Does Phylogeny Relate to Classification?

• A taxon is any group of organisms that is treated
  as a unit, such as a genus, or all insects.
• Species and genera are further grouped into a
  hierarchical classification system.
• Genera are grouped into families (e.g., the
  family Rosaceae includes the genus Rosa and its
  close relatives).

61
25.4 How Does Phylogeny Relate to Classification?

• Families are grouped into orders
• Orders into classes
• Classes into phyla
• Phyla into kingdoms
• Application of these levels is somewhat
  subjective.

62
25.4 How Does Phylogeny Relate to Classification?

• Biological classifications are used to express
  the evolutionary relationships of organisms.
• Taxa are expected to be monophyletic a taxon
  contains an ancestor and all descendents of that
  ancestor, and no other organisms. Also known as a
  clade.

63
25.4 How Does Phylogeny Relate to Classification?

• But detailed phylogenetic information is not
  always available.
• A group that does not include its common ancestor
  is polyphyletic.
• A group that does not include all descendents of
  a common ancestor is paraphyletic.

64
25.4 How Does Phylogeny Relate to Classification?

• A true clade or monophyletic group can be removed
  from the tree by making a single cut.
• Taxonomists agree that polyphyletic and
  paraphyletic groups are not appropriate taxonomic
  units. These groups are gradually being
  eliminated and taxonomic classifications revised.

65
Figure 25.12 Monophyletic, Polyphyletic, and
Paraphyletic Groups
66
25.4 How Does Phylogeny Relate to Classification?

• Explicit rules govern the use of scientific
  names.
• Ensures that there is only one correct scientific
  name for any taxon.
• Different taxonomic rules have been developed for
  zoology, botany, and microbiology, but
  taxonomists are now working towards common sets
  of rules.

67
Photo 25.1 Virginia bluebells (lungwort,
Mertensia virginica), Riverbend Park.
68
Photo 25.2 Bluebell (Campanula sp.), Killdeer
Mountain, ND.
69
Photo 25.3 Four-limbed vertebrates California
red-legged frog (Rana aurora draytoni). Amphibia.
70
Photo 25.4 Four-limbed vertebrates sagebrush
lizard (Sceloporus graciosus). Reptilia.
71
Photo 25.5 Four-limbed vertebrates American
alligator (Alligator mississipiensis).
Archosauria.
72
Photo 25.6 Rodent teeth black-tailed prairie
dog (Cynomys ludoviciansus). Order Rodentia.
73
Photo 25.7 Spines on the barrel cactus
(Ferrocactus acanthodes) are modified stem/leaf
units.
74
Photo 25.8 Brightly colored bracts on lobster
claws (Heliconia tostrata).
75
Photo 25.9 Modified insect-trapping leaves of
Sarracenia rubra.
76
Photo 25.10 Large floating leaves of the water
lily Victoria amazonica.
77
Photo 25.11 Pieris protodice, a butterfly with
the ancestral trait of six functional legs.
78
Photo 25.12 The monarch butterfly (Danaus
plexippus), with the derived trait of four
functional legs.
79
Photo 25.13 The great blue heron (Ardea
herodias) San Francisco, CA.