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biol 335 > Phylogeny > Flashcards

Phylogeny Flashcards

1
Q

Is phylogeny equal to the tree of life

A

yes

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2
Q

Describe coalescence

A

This is going backwards on a phylogenetic tree where the tree narrows and eventually is a single line (so the merging of branches as you go backwards)

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3
Q

What is bifurcation

A

lines dividing into two lines on a phylogenetic tree

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4
Q

What is a character

A

this is a heritable trait posses by an organism. It must be observable.

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5
Q

What is a state

A

a state is an alternative condition of a character

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6
Q

character vs state

A

a character is a heritable trait that is observable, while a state is an alternative condition of a character

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7
Q

Describe what the character here is and what the state is: “hair present” vs. “hair absent”

A
  • hair = character
  • present vs. absent = state
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8
Q

Define polarity

A

this is the direction of change in a character (about determining the primitive vs. the derived state)

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9
Q

What are the 2 ways of determining polarity

A
  1. the outgroup criterion: based on the state in closely related groups
  2. the paleontological criterion: based on fossils
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10
Q

Do bursts of rapid change make character delimitation easier or harder

A

easier

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11
Q

What does plesiomorphic mean

A

this refers to the primitive/ancestral state

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12
Q

What does apomorphic mean

A

this refers to the derived character state

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13
Q

What are the 2 types of apomorphies

A

(apomorphic means derived character state)
1. autapomorphies = found in a SINGLE terminal taxon, evolved once
2. synapomorphies = found in two or more taxa, evolved once (these are inferred homologies and not homoplasies)

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14
Q

Are synapomorphies inferred homologies or homoplasies

A

homologies (their similarities are owed to inheritance from a common ancestor)

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15
Q

What are homoplasies

A

shared traits found among different taxa but inferred to have been independently derived and not to have occurred in their common ancestor
( so these are shared by two or more taxa and evolved more than once)
–> these are non-homologous similarities (similarity with multiple origins)

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16
Q

what are homologies

A

this is similarity owing to inheritance from a common ancestor
(so shared traits by two or more taxa which evolved only once)

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17
Q

What are the 3 different kinds of homoplasy

A
  • homoplasy (non-homologous similarity that evolved more than once)
  1. Parallelism
  2. Convergence
  3. Reversal
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18
Q

What is parallelism/parallel evolution

A
  • a type of homoplasy
  • independent evolution of same feature from SAME ancestral condition
19
Q

What is convergence/convergent evolution

A
  • a type of homoplasy
  • independent evolution of same feature from different ancestral condition
20
Q

What is reversal

A
  • a type of homoplasy
  • reversion to the ancestral condition
21
Q

Describe a monophyletic group

A

a group consisting of all the descendants of a single ancestor

–> this is a clade

22
Q

Describe a paraphyletic group

A

a group that includes most, but not all, of the descendants of a single ancestor

–> this is not a clade

23
Q

What is an example of a paraphyletic group

A

Reptiles

24
Q

Describe a polyphyletic group

A

a group of organisms whose last common ancestor is not a member of the group

25
Q

Clade vs Grade

A
  • clade = a monophyletic group that includes the common ancestor and all of its descendants
  • grade = usually a paraphyletic group - does not include all the descendants of a single ancestor
26
Q

What does LCA refer to

A

Last Common Ancestor

27
Q

Describe the study group

A

this is the group of interest whose phylogenetic history we are trying to resolve
–> study group = Ingroup : usually assumed to be monophyletic based on prior evidence

28
Q

Describe the outgroup

A

these are groups that are more or less closely related to the in group - these do not have to be monophyletic

29
Q

Describe sister groups

A

are any two groups that share a more recent common ancestry with each other than either does with any other group

–> only monophyletic groups (clades) or single species can be sister groups

30
Q

What is the crown group

A

this is the clade that includes ALL descendants of the LCA of all of the EXTANT (living) species

31
Q

What is the stem group

A

this is the set of extinct taxa that are not in the crown group but are more closely related to that crown group than they are to any other crown group

32
Q

Describe the most basal taxon

A

this is the taxon or clade that branched off earliest from the set of taxa included in the clade

–> this can be subjective since the clades can be rotated

33
Q

Compare a cladogram vs. additive tree vs. ultrametric tree

A
  1. cladogram = summary of relationships (this shows a simple tree with no other information but the terminal taxon names)
  2. additive tree = summary of relationships + amount of evolutionary change (this is a tree that also includes the branch lengths)
  3. ultrametric tree = summary of relationships + timing of events (this is a tree that also includes a time scale) (also called chronogram or time tree)
34
Q

soft polytomy vs hard polytomy

A

Soft polytomy = implies a lack of information to resolve the relationships at the node

Hard polytomy = implies true simultaneous speciation events

–> usually cladistics is a soft polytomy

35
Q

What are the 2 conventions of cladistics

A
  1. Evolution is strictly dichotomous
  2. when a lineage splits two new species are created ( which fits the concept of gradualism)
36
Q

Describe Gradualism and punctuated equilibrium (these are modes of speciation)

A
  • Gradualism is where species are always changing in small steps, which accumulate to yield new species and you get daughter species which may be different from each other and from their parent
  • punctuated equilibrium implies long periods of stasis interspersed by short episodes of rapid change - here only one of the daughter species is distinct from the parent species
37
Q

When is punctuated equilibrium thought to occur

A
  1. colonization of a new niche
  2. strong selection on the whole species
  3. small founding population
  4. genetic drift
38
Q

What are the questions raised by each mode of speciation

A

Gradualism = at what point does a gradually evolving lineage become a distinct species

Punctuated equilibrium = the parent species does not change when a daughter species evolves but cladistics assumes two new species were formed by the split

39
Q

Challenges in viewing trees

A
  • large trees
  • uncertainty
  • reconciled trees (where one tree is embedded inside another tree) and tangle grams (trees for different associated entities)
40
Q

Are gene trees the same as species trees

A

Not always - they can be exmaples of reconciled trees

41
Q

What are the 3 types of trees

A

cladogram, additive tree, ultrametric tree

42
Q

Describe a cladogram

A

shows a summary of relationships (this shows a simple tree with no other information but the terminal taxon names)

43
Q

Describe an additive tree

A

shows a summary of relationships + amount of evolutionary change (this is a tree that also includes the branch lengths)

44
Q

Describe an ultrametric tree

A

summary of relationships + timing of events (this is a tree that also includes a time scale) (also called chronogram or time tree)

biol 335 (21 decks)

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