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EVOLUTION > Phylogenetics (7) > Flashcards

Phylogenetics (7) Flashcards

1
Q

Phylogeny?

A

= a diagram that shows lines of evolutionary descent from a common ancestor.

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2
Q

Cladogram?

A

= a branching diagram tracing evolutionary history.

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3
Q

Branch?

A

= unbroken lines of descent.

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4
Q

Terminal taxa?

A

= extant organisms.

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5
Q

Apomorphies?

A

= derived features.

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6
Q

What do branches do?/What do they show? (4)

A

• Show evolutionary histories.
• Show lineages.
• Summarize evolution across lineages.
• Show divergence from a common ancestor (speciation).

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7
Q

Natural groups?

A

= groups that share common ancestor, ie. monophyletic.

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8
Q

Monophyly?

A

= common ancestor + all its descendants.

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9
Q

Paraphyly?

A

= common ancestor + some of its descendants.

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10
Q

Polyphyly?

A

= no recent common ancestor/group that doesn’t contain a single common ancestor of the group.

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11
Q

Steps for Tree Reading? (3)

A

• Tree tip order = not important.
• No terminal node is ancestral to any other terminal node.
• No terminal node is more evolved than any other terminal node.

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12
Q

Tree styles? (2)

A

• Mammal phylogeny.
• Rectangular cladogram.

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13
Q

Transition?

A

= interchanges of purine for purine (A-T or G-C).

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14
Q

Transversion?

A

= interchanges of purine for pyramidine (A-G or T-C).

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15
Q

Which is slower between transversion & transition?

A

Transversion.

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16
Q

Molecular clock?

A

= probabilities of where you can estimate/calculate time.

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17
Q

How do we obtain a cladogram? (2)

A

• From Morphological data.
• From Fossils.

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18
Q

Why are polyploids important?

A

Important for biodiversity.

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19
Q

Eg of polyploidy & biodiversity?

A

Grey tree frogs.

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20
Q

How are polyploids formed?

A

Via autopolyploidy.

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21
Q

Autopolyploidy?

A

= polyploid within same species.

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22
Q

Phylogram?

A

= diagram that includes evolutionary change information.

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23
Q

Branch length in Phylogram?

A

= amount of change/ diversification rates.

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24
Q

Eg of Phylogram?

A

Dwarf chameleons.

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25
Q

Branch length of Phylogram occurs under what?

A

Mutation selections.

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26
Q

How do we obtain a cladogram from eg. Morphological data?

A

Use the categorical/binary (0,1,1,2…) scores.

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27
Q

Steps to draw a Phylogenetic tree? (5)

A

• Choose the taxa.
• Select the characters.
• Determine polarity (using fossil evidence).
• Group the features by synapomorphies.
• Work through all synapomorphies & group accordingly.

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28
Q

How do you choose the best tree?

A

Via the Principle of Maximum Parsimony.

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29
Q

Parsimony?

A

= the most likely phylogeny is the simplest one/the one with the least evolutionary events.

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30
Q

Principle of Maximum Parsimony?

A

= principle where we use simplest explanation with the least assumptions & the shortest tree is the preferred hypothesis of relationships.

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31
Q

Why use the Principle of Maximum Parsimony? (2)

A

• To avoid guessing & complication.
• Has the least number of steps.

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32
Q

Principle of Maximum Parsimony conclusion? / What does it conclude? (2)

A

• That it’s much easier to lose a trait than it is to gain it a second time.
• The simplest tree with the least no. of events is the best tree.

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33
Q

Bayesian?

A

= Stats & priors.

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34
Q

Homologous characters?

A

= features that are similar in structure/position due to common ancestry.

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35
Q

Analogous characters?

A

= features similar not due to common ancestry but due to function.

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36
Q

Homology?

A

= basis of analysis (that basis being the common ancestor).

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37
Q

Result of analogy?

A

Homoplasy.

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38
Q

Homoplasy type?

A

• Convergence.

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39
Q

Result of homology?

A

Congruence.

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40
Q

Eg of homology?

A

Protea &

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41
Q

Egs of analogy? (2)

A

• Vertebrate eye & Octopus eye.
• Pitcher plants.

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42
Q

How do we identify homology?

A

• Common ancestor via same structure/position.

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43
Q

Egs of convergence? (3)

A

• Human & Octopus eye.
• Bird & Bat wings.
• Capitula in sunflowers/daisies & Protea.

44
Q

Significance of rooting phylogenetic trees? (2)

A

• Provides evolutionary direction.
• Defines the point on a tree of a hypothetical ancestor.

45
Q

Methods of Phylogenetic tree rooting? (3)

A

• No rooting.
• Mid-point rooting.
• Outgroup rooting.

46
Q

Which rooting “system” is commonly used?

A

Outgroup rooting.

47
Q

Outgroup rooting attributes? (3)

A

• Seeks to maintain monophyly.
• Selects a taxonomy related to the study group but not part of the study group.
• Gives conclusions about relatedness.

48
Q

Types of data that we can use to infer a phylogeny? (2)

A

• Morphological data.
• Molecular data.

49
Q

Polytomy?

A

= internal node of a cladogram that has more than 2 sister taxa/immediate descendants.

50
Q

Aim in Phylogenetics?

A

To get informative characters to get relationships.

51
Q

What can Phylogenetic trees tell us? (4)

A

• Enable us to visualize evolution.
• Show us patterns of speciation.
• Enable us to classify diversity in a natural way.
• Enable us to make predictions about fossils.

52
Q

Apomorphy?

A

= derived features.

53
Q

Pleisiomorphy?

A

= ancestral features/traits.

54
Q

Autapomorphy?

A

= features unique to a specific group.

55
Q

Synapomorphy?

A

= shared derived features.

56
Q

What do synapomorphies do?

A

Provide information on relationships.

57
Q

Outgroup?

A

= a taxon that has no shared characters with other taxa.

58
Q

Eg of patterns of speciation?

A

Spiny leg blades of Orb-weaving spiders on Hawaiian islands.

59
Q

Eg of evolutionary relationships?

A

Mammals.

60
Q

How do we classify organisms in a natural way?

A

Via natural groups, which should be monophyletic.

61
Q

What are the 3 natural groups that organisms are classified under?

A

• Monophyly.
• Paraphyly.
• Polyphyly.

62
Q

Eg of enables us to make predictions about fossils?

A

Whale’s ankles.

63
Q

Root of Phylogenetic trees?

A

= oldest common ancestor.

64
Q

How do you determine which organisms are more closely related than other organisms?

A

They share a more recent common ancestor.

65
Q

Sister taxa?

A

= groups that are more closely related to each other than either is to another group.

66
Q

Homoplasy types? (3)

A

• Parallel homoplasy.
• Convergent homoplasy.
• Reversion homoplasy.

67
Q

Parallel homoplasy?

A

= ancestral condition of a variable trait (plesiomorphy) is present in common ancestor but derived state (apomorphy) has evolved independently.

68
Q

Convergent homoplasy?

A

= trait is absent in common ancestor (analogous traits).

69
Q

Reversion homoplasy?

A

= transition within a lineage that goes back to the ancestral state.

70
Q

Phylogenetic tree?

A

= branching diagram representing the pattern of relatedness of organisms.

71
Q

Other definition of Phylogeny?

A

= a hypothesis about how organisms are related & how groups diversified.

72
Q

What does a phylogeny show us?

A

Shows us the relationship between different species or genes.

73
Q

What do Phylogenetic trees show us?

A

The patterns of descent of organisms from their ancestors.

74
Q

What do we mean by “if we use different parts of the genome, we can determine the different evolutionary processes”?

A
75
Q

Main components of a phylogeny? (4)

A

• Branches.
• Nodes.
• Tips.
• Root.

76
Q

Thing to note for the main components of a phylogeny?

A

Know these & how they fit into different parts of the time.

77
Q

Bifurcating tree?

A

= a tree that diverges/branches.

78
Q

Where do terminal taxa originate from?

A

They came from a common ancestor, ie., their common ancestor are species events.

79
Q

What do the branch length tells us? (2)

A

• How many changes occurred in the evolutionary history.
• How long the time frame of the evolutionary history of events is.

80
Q

Node attribute?

A

Can rotate.

81
Q

Other points to note under the 1st Reading trees tip? (2)

A

• Adjacent taxa aren’t necessarily more closely related to each other than taxa placed further away.

• Phylogenies are all identical but the ordering isn’t the same.

82
Q

Eg of 2nd tree reading tip?

A

You & your cousins vs your aunts & grandparents.

83
Q

Egs of 3rd tree reading tip? (2)

A

• Dogs & wolves.
• Chimpanzees & humans.

84
Q

Differences between phylogeny, phylogenetic tree, cladogram & phylogram?

A

● Phylogeny = same as phylogenetic tree.

● Phylogenetic tree = same as phylogeny.

● Phylogram = shows changes/relatedness with inclusion of time.

● Cladogram = shows relatedness with exclusion of time.

85
Q

Types of Phylogenetic trees? (2)

A

• Phylogram.
• Cladogram.

86
Q

Important thing to note about branches?

A

They are non-temporal UNLESS branched with time.

87
Q

How did homologous characters evolve?

A

Due to a common ancestor.

88
Q

What is a basis for analysis of traits/trait changes?

A

Homology.

89
Q

How are Orb-weaving spiders an eg of Patterns of speciation?

A

They are known to show the largest radiation on Hawaiian islands.

90
Q

Phylogeny principles? (2)

A

• Must be based on homology/homologous characters.
• Trees must be rooted to give evolutionary direction.

91
Q

Parsimony basis?

A

Okhan’s Razor.

92
Q

Parsimony’s goal?

A

To reduce homoplasy when constructing a tree.

93
Q

Difference between homoplasy & synapomorphy regarding definition?

A

● Homoplasy = shared characters due to separate mutations.

● Synapomorphy = shared characters due to common ancestor.

94
Q

Homoplasy?

A

= share characters due to separate mutations.

95
Q

Difference between homoplasy & synapomorphy relatedness?

A

● Homoplasy = same character but not related (analogy).

● Synapomorphy = same character but related (homology).

96
Q

Incorrect assumption of homoplasy?

A

Misleading about relationships.

97
Q

Eg of Homoplasy due to convergence?

A

Wings arising twice.

98
Q

What do branch length tell us? (2)

A

• Time (if tree is dated).
• Trait changes.

99
Q

Mid-point rootingmethod attributes? (3)

A

• Doesn’t use outgroup as a root.
• Character changes are more clock-like.
• Focuses on how characters are changing through time.

100
Q

What do we mean by “Character changes are more clock-like”?

A

We mean that character changes happen at about the same speed/are relatively the same.

101
Q

What does a dated phylogeny tell us?

A

Tells us when groups originated & went extinct.

102
Q

How can a phylogeny be dated? (2)

A

• Fossils.
• Rate of mutation in DNA sequence data.

103
Q

Egs of how a phylogeny can be dated using fossils? (2)

A

• Oldest angiosperm fossil.
• Oldest Asteraceae (daisy family) pollen.

104
Q

Explain how the rate of mutation in DNA sequence data can be used to date a phylogeny?

A

Through one assuming a constant rate within a group (molecular clock) or adjusting for rate differences in groups.

105
Q

Based on phylogeny, are Brown bears & Polar bears distinct species?

A

No.

106
Q

3 types of genome/gene?

A

• Chloroplastic gene.
• Mitochondrial gene.
• Nuclear gene.

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