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Ecology and diversity > Lecture 7- reconstructing and using phylogenies 1 > Flashcards

Lecture 7- reconstructing and using phylogenies 1 Flashcards

1
Q

What is phylogeny?

A

A description of the evolutionary history of relationships among organisms

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2
Q

What is a phylogentic tree?

A

A diagram that portrays a reconstruction of the history of the evolutionary relationships among organisms

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3
Q

What does a split or node on a phylogenetic tree represent?

A

The point at which lineages diverge

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4
Q

What is the name of the common ancestor of all the organisms in the tree?

A

The root

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5
Q

What is a taxon?

A

A group of species that are designated a name

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6
Q

What is a clade?

A

A taxon that consists of all of the evolutionary descendants of a common ancestor.

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7
Q

What are two species/clades that are each others closest relatives called?

A

Sister species/clades

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8
Q

What is systematics?

A

The study of biodiversity

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9
Q

Where are phylogentic trees used?

A

In all fields of biology

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10
Q

What do biologists use phylogenies to do?

A

Make comparisons and predictions about shared traits across genes populations and species.

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11
Q

How do comparisons among species require an evolutionary perspective?

A

Biologists determine traits that differ within a group of interest then try to determine when these traits evolved and how the trait was influenced by environmental conditions

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12
Q

What are features shared by two or more groups that were inherited from a common ancestor called?

A

Homogenous

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13
Q

Give an example of a homogenous trait.

A

The vertebral column is homologous among vertebrates.

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14
Q

What have phylogenetic analyses been used to discover?

A

Changes in the genome of HIV that confer resistance to particular drug treatments

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15
Q

What does the association of a particular genetic change in HIV with a particular treatment provide?

A

A hypothesis about resistance that can be tested experimentally.

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16
Q

What is a trait that differs from its ancestral form called?

A

A derived trait

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17
Q

What is a trait that was present in the ancestor of the group called?

A

An ancestral trait

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18
Q

What are derived traits that are shared among a group of organisms and are viewed as evidence of the common ancestry of the group called?

A

Synapomorphies

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19
Q

Why do similar traits evolve in unrelated groups of organisms?

A
  • Convergent evolution

- Evolutionary reversal

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20
Q

What is convergent evolution?

A

Independently evolved traits subjected to similar selection pressures may become superficially similar

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21
Q

Give an example of convergent evolution.

A

Bones of wing and bats are homologous (inherited from common ancestor)
Wings are not homologous- evolved independently from forelimbs of different non-flying ancestors.

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22
Q

What is evolutionary reversal?

A

A character reverts back from a derived state to an ancestral state.

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23
Q

Give an example of an evolutionary reversal.

A

Frogs lack teeth in lower jaw- ancestor had teeth

Teeth have been regained in lower jaw of genus Amphignathodon

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24
Q

What is the genus of the frogs that have regained teeth in their lower jaw?

A

Amphignathodon

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25
Q

What are traits that are similar for reasons other than inheritance from a common ancestor called? (for example, because of convergent evolution or evolutionary reversal.)

A

Homoplasies

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26
Q

What are traits ancestral or derived depending on?

A

The point of reference for that phylogeny.

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27
Q

What assumptions are made when constructing phylogenetic trees?

A

No convergent evolution

No derived traits have been lost

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28
Q

What is a species outside the group of interest when constructing a phylogenetic tree called?

A

The outgroup

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29
Q

What do comparisons with the outgroup show?

A

Which traits of the ingroup are derived and which are ancestral

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30
Q

What is used to construct a phylogenetic tree?

A

Information about synapomorphies

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31
Q

What is the parsimony principle?

A

The preferred explanation of the observed data is the simplest explanation

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32
Q

How is it determined which traits are homoplasies and which are synapomorphies?

A

Using the parsimony principle

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33
Q

The best hypothesis when constructing a phylogentic tree is the one that involves the fewest…

A

homoplasies

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34
Q

What is Occam’s razor?

A

The idea that the best explanation is the one that fits the data best and makes the fewest assumptions

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35
Q

Phylogenetic trees are continuously…

A

modified

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36
Q

How has tree construction been revolutionized?

A

Computer software for trait analysis and tree construction

Process more data

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37
Q

What traits can be used in phylogenetic analysis?

A

Genetically determined traits

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38
Q

Evolutionary relationships can be revealed through studies of what?

A 
Morphology
Development
Fossil record
Behavioral triats
Molecular traits (DNA and protein sequences)
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39
Q

What is morphology?

A

Presence, size, shape and other attributes of body parts

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40
Q

How do sytematists analyze morphological structures in finer detail?

A

New technological tools: electron microscope, CT scans

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41
Q

Why is there a wealth of recorded morphological data?

A

Living organisms have been studied for centuries- very comprehensive

42
Q

Give an example of the features of morphology that are important for phylogenetic analysis being specific to a particular group of organisms.

A

Presence, development, shape and size of skeletal system is important in vertebrate phylogeny, whereas floral structures are important in studying relationships of flowering plants.

43
Q

What are limitations of the morphological approach to phylogenetic analysis?

A
  • Taxa with little morphological diversity
  • Few morphological traits can be compared between distantly related species
  • Morphological variation that is environmental
44
Q

Why are observations of similarities in developmental patterns used to reveal evolutionary relationships?

A

Similarities in early developmental stages may be lost during later development

45
Q

Give an example of similarities in early developmental stages may be lost during later development that are used to infer evolutionary relationships.

A

Larvae of marine creatures called sea squirts have a notochord that dissapears as they develop
All vertebrate animals have a notochord at some point in development
Shared structure infers closer relationship

46
Q

What do fossils reveal about organisms?

A

Where and when organisms lived

What they looked like

47
Q

What do fossils help distinguish between?

A

Ancestral and derived traits

48
Q

What else do fossil records reveal?

A

When lineages diverged and began independent evolutionary histories

49
Q

What do fossil records reveal about groups that have few species that have survived to the present?

A

Information on extinct species is critical to understanding large divergences between surviving species

50
Q

What are the limitations of fossil records?

A

Few or no fossils for some groups

Fossil record is fragmentary

51
Q

What type of behavior does not reflect evolutionary relationships?

A

Culturally transmitted behavior

52
Q

Give an example of a behavior that is genetically determined.

A

Frog calls

53
Q

What genome is used extensively in phylogenetic studies of plants?

A

cpDNA

The chloroplast genome

54
Q

How does cpDNA change over time and why is this useful?

A

Slowly

To study ancient phylogenetic relationships

55
Q

What type of DNA changes rapidly in animals?

A

mtDNA

Mitochondrial DNA

56
Q

What is comparisons between mtDNA used for?

A

Studying evolutionary relationships between closely related species

57
Q

What do mathematical models to describe how DNA changes over time account for?

A

Multiple changes at given position in a DNA sequence

Different rates of change at different positions in a codon and among different nucleotides

58
Q

What type of changes in DNA are more likely?

A

Transitions (changes between 2 purines or 2 pyrimidines) are more likely than transversions

59
Q

What are transversions?

A

Changes between a purine and a pyrimidine

60
Q

What can mathematical models be used to compute?

A

Maximum likelihood solutions for phylogenetic estimations

61
Q

How is a likelihood score for a tree determined?

A

The probability of the observed data evolving from a specific tree

62
Q

What are maximum likelihood methods used for mostly and why?

A

Molecular data

Explicit mathematical models of evolutionary change are easier to develop

63
Q

What are the advantages to the maximum likelihood analyses?

A

They incorporate more information about evolutionary change than parsimony methods
Easier to treat in a statistical framework

64
Q

What are the disadvantages to the maximum likelihood analyses?

A

Computationally intensive and require explicit models of evolutionary change

65
Q

Why is it a disadvantage that maximum likelihood analyses require explicit models of evolutionary change?

A

Explicit models may not be available for some kinds of character change

66
Q

Describe how the hypothesis that evolutionary history can be correctly reconstructed from the DNA sequences of living organisms using phylogenetic analysis can be tested.

A
  • Single viral bacteriophage culture T7 was selected (this was the common ancestor)
  • Lineages were able to evolve in the presence of mutagen
67
Q

What does mutagen do?

A

Increase the rate of mutation

68
Q

What happened when the bacteriophage cultures were evolving?

A

Every 400 generations each ingroup lineage were split into two

69
Q

What was the final step in the experiment to determine the accuracy of phylogenetic methods?

A

Isolate and sequence viruses from the end points of each lineage (8 in group, one outgroup)
Phylogenetic analysis

70
Q

What were the results of the experiment to determine the accuracy of phlogenetic methods?

A

The evolutionary history of the lineages and the ancestral sequences of the viruses were reconstructed successfully

71
Q

Why was mutagen added to the experiment that determined the accuracy of phylogenetic analysis?

A

Increase mutation rate so degree of homoplasy would be typical of organisms analyzed in average phylogenetic analyses.

72
Q

In the experiment to determine accuracy of phylogenetic methods, what percent of amino acids changes and nucleotide positions were reconstructed accurately?

A

100% amino acid changes in viral proteins

Over 98% nucleotide positions

73
Q

The experiment described did not take into account…

A

All possible conditions, for example:

  • sensitivity to phylogenetic analysis to convergent environments
  • highly variable rates of evolutionary change
74
Q

How else has the effectiveness of phylogenetic analysis been shown?

A
  • Other experimental studies that account for other possible conditions
  • Computer simulations based on evolutionary models
75
Q

Other than inferring evolutionary relationships among lineages, phylogenetic trees can be used to…

A

Reconstruct:

morphology, behavior, nucleotide and amino acid sequence

76
Q

What was phylogenetic analysis used to reconstruct?

A

An opsin protein in the ancestral archosaur

77
Q

What is an archosaur?

A

The last common ancestor of birds, dinosaurs and crocodiles

78
Q

What are opsins?

A

Pigment proteins involved in vision

79
Q

How do opsins differ?

A

Different opsins have different amino acid sequences

Different opsins are excited by different wavelengths

80
Q

What does knowledge about opsin sequences reveal?

A

Clues about the animals visual capabilities and some probable behaviors

81
Q

How was the opsin sequence on archosaurs determined?

A

Phylogenetic analysis of opsin from living vertebrates to estimate amino acid sequence of opsin in archosaurs

82
Q

Once the amino acid sequence of archosaurs was determined what happened?

A

The protein was reconstructed in a lab

Testing showed shift towards the red end of the spectrum (compared with modern opsins)

83
Q

What does a shift towards the red end of the spectrum in opsin sensitivity infer?

A

Nocturnal vision

84
Q

In 1965, what did Emile Zuckerkandl and Linus Pauling hypothesize?

A

The molecular clock hypothesis

85
Q

What is the molecular clock hypothesis?

A

Rates of molecular change are constant enough that they can be used to predict evolutionary divergence times

86
Q

What can effect the molecular clock hypothesis?

A
  • Different genes evolve at different rates

- Different evolutionary rates depending on generation times, environments, efficiencies in DNA repair etc.

87
Q

Despite different rates of evolution, why can the molecular clock theory still be used?

A

Among closely related species a given gene evolves at a reasonably constant rate

88
Q

What is the rate of evolution being used as a metric to gauge time of divergence for a split in phylogeny called?

A

Molecular clocks

89
Q

How are molecular clocks calibrated?

A

Independent data such as fossil record, known time of divergence, biogeographic dates

90
Q

What are biogeographic dates?

A

Such as dates of separation of continents

91
Q

Studies of what animals provide an example of molecular clocks?

A

Cichlid fish in Lake Victoria, eastern Africa

92
Q

How many species cichlid of fish in one group did the evolutionary radiation in Lake Victoria produce?

A

More than 500 species

93
Q

When was it originally assumed the evolutionary radiation of cichlid fish in Lake Victoria occur?

A

750,000 years ago (presumed age of lake basin)

94
Q

What does recently discovered geological data suggest about Lake Victoria?

A

It dried up between 15600 years ago and 14700 years ago

95
Q

What effect did the fact that Lake Victoria dried up have on the theory of the evolutionary radiation of cichlid fish?

A

The fish could not have evolved in such a short time so other hypothesis were made

96
Q

How were theories about the cichlid fish tested?

A

Phylogenetic analysis based on molecular data of 300 species

97
Q

What type of molecular data was used to construct phylogenetic trees of cichlid fish in Lake Victoria and other lakes in the region?

A

Mitochondrial DNA sequences

98
Q

What did phylogenetic analysis of cichlids in and around Lake Victoria suggest about the origins of the cichlids in the lake?

A

Ancestors of Lake Vicotria cichlids come from geologically older Lake Kivu

99
Q

How many species of cichlid live in Lake Kivu?

A

15

100
Q

How did cichlids from Lake Kivu colonize Lake Victoria?

A

Colonized on 2 different occasions

101
Q

What else did phylogenetic analysis of cichlids reveal about Lake Victoria?

A

Some cichlid lineages found only in Lake Victoria split 100,000 years ago- thus Lake Victoria did not completely dry 15000 years ago

Ecology and diversity (17 decks)

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