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Biology 355 - Evolution > Topic 3 - Phylogeny and Classification > Flashcards

Topic 3 - Phylogeny and Classification Flashcards

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1
Q

What can be arranged into a tree of life?

A

Individual groups of organisms via extrapolations can be arranged into one.

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2
Q

What do closely adjacent branches indicate?

A
  • that they were more recently derived from a common ancestor
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3
Q

What do more distant branches indicate?

A
  • species derived from more ancient common ancestors
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4
Q

What 5 points can Phylogenentic Trees tell us?

A
  • how organisms are related
  • the inferred ages of organisms (and their lineages)
  • how traits evolved and their order
  • how species coevolved
  • evolutionary history of specific genes
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5
Q

What does phylogeny mean?

A
  • genealogical relationship of organisms which species share between a recent common ancestor
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6
Q

Give a specific example of what Phylogenetic Trees can tell us.

A
  • the relationship between photosynthesis ability versus cellular respiration
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7
Q

What was Darwins basis for evolutionary classification?

A
  • resemblance implying relationship (descent)
  • he used quantifiable information to expand his classification (an axis)
  • at the end of branches he implied a single ancestor may radiate multiple daughter species
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8
Q

What does Anagenesis refer to?

A
  • change within a single lineage

- the change occurring within a species before it splits to form most recent common ancestor into two new species

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9
Q

What does Cladogenesis refer to?

A
  • branching of a lineage into two or more descendant lineages
  • the change that occurred when an ancestor split into two different distinguishable species
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10
Q

What are examples of continuous line of descent (Ana or Clado?)

A
  • if there is a continuous line of descent from one ancestor it is still known as the same species (even if there is slight differences between ancestor and daughter species)
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11
Q

What do similarities among organisms indicate?

A
  • it would indicate their descent from a common ancestor

- ex. primates

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12
Q

What does Homology refer to?

A
  • it refers to similarity that is the result of common ancestry
  • ex. equivalent structures via skeletal elements
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13
Q

What does homologous from common descent mean?

A
  • similarities from the same structure being inherited down DIFFERENT LINEAGES
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14
Q

What shape does scientific classification occur in?

A
  • living organisms are classified in a hierarchy corresponding to divergences of lineages
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15
Q

What does a taxon refer to?

A
  • a group at any of these levels (species, family, order, class)
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16
Q

Define Synapomorphies

A

a shared derived character

- basis of phylogenetic trees

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17
Q

Define Apomorphies

A

a derived trait

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18
Q

How do we know what character state came first? Character Polarity.

A
  • we do not know what character state is ANCESTRAL or DERIVED
  • to perform phylogenetic analyses, it would require that we infer for all characters the direction of evolutionary change (polarity)
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19
Q

What is one way of inferring character polarity?

A
  • For any Characters
  • Out group analysis: character states in the out group taxa are taken as the starting point - by comparing taxa of interest with related taxa outside the group being studied
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20
Q

What is the other way of inferring polarity?

A
  • for morphological characters
  • evidence of a fossil record or developmental studies
  • character states occurring earlier in time or development are more likely to be ancestral
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21
Q

What is the basic assumption of Parsimony?

A
  • it is the assumption that the most likely phylogeny involves the fewest evolutionary steps (the fewest characters with multiple changes)
  • this assumption underlies all of sciene
22
Q

What does Maximum Parsimony refer to?

A
  • the simplest parsimony method
  • all character changes in a data set are assumed to be equally likely to occur (equally weighted)
  • only SHARED CHARACTER CHANGES are parsimony informative - provide evidence of species relationships
23
Q

What are the three key points of Maximum Parsimony

A
  • each character is equally valuable
  • look for derived characters
  • look for the shortest length of the tree
24
Q

What are the other two methods to perform phylogenetic analysis?

A
  • Maximum liklihood

- Bayesian inference

25
Q

What advantages do maximum liklihood and bayesian inference hold with phylogenetic analysis?

A
  • more complex models for character changes
  • they allow different weighting of these characters
  • these characters include: molecular data, different rates for kinds of base substitutions
26
Q

What do maximum liklihood and bayesian inference take into account? and what does it infer?

A
  • take branch length into account
  • branch lengths of phylogenetic trees represent changes/rates of evolutionary change - that takes into account the time it took to diverge into two lineages
27
Q

Define homoplasy.

A
  • a character state if independently evolved two or more times and therefore does not have a unique origin
28
Q

What is the simplified definition of homoplasy?

A
  • that resemblance of traits does not always indicate common ancestry; it could be a result of multiple independent changes of that trait
29
Q

What are the two methods in which derived character trait similarity is not a result of common descent - a result of homoplasy

A
  • Convergence

- Evolutionary reversal

30
Q

Define Convergence

A
  • aka parallel evolution

- is the INDEPENDENT origin of the SAME trait in SEPARATE lineages

31
Q

Define evolutionary reversal

A
  • evolution of a character trait back to its ancestral state
32
Q

Prior to the availability of DNA sequence data, how were phylogenetic relationships determined? How are they still useful?

A
  • estimations were based on observable phenotypic traits (morphological and anatomical traits)
  • they are still useful when comparing modern and fossil organisms
33
Q

What are the two general methods used in phylogenetic analysis

A
  • explicitly phylogenetic methods (parsimony)

- distance methods

34
Q

Differentiate between explicit phylogenetic methods and and distance based methods

A
  • is based on shared derived characters (synapomorphies) which identify nested groups in connections to branches of evolutionary trees
  • compared to the over resemblance or similarity (no regard for ancestral/derived traits) - used in the traditional classification methods
35
Q

Same question. Why is it possible to get such different results with parsimony and distance methods for phylogenetic analysis?

A
  • parsimony uses synapomorphies (shared derived characters) to identify groupings and out-groups to differentiate ancestral vs derived character states
  • distance based methods or set on overall similarity (particularly when POLARITY cannot be determined)
36
Q

Why are molecular clocks useful for the formation of phylogenetic trees?

A
  • since DNA sequences tend to diverge at a relative constant rate (in contrast to morphological traits)
37
Q

What are molecular clocks useful for? and how are they calibrated?

A
  • to create a timeline for the phylogeny of a group (an estimation for the divergence of branches in a tree)
  • using dated fossils (by interpolating the ages of other branches known to those estimating)
  • the basis of an APPROXIMATE TIMELINE
38
Q

What is the one challenge with molecular clocks? and how are they confirmed?

A
  • the rate of DNA divergence is not constant - when it varies over time over different branches of a phylogenetic tree
  • using a relative rate test
39
Q

What are a few challenges faced with gene and species trees? and why is this important?

A
  • that genes do not always have the same phylogenies as the species that contain them
  • genes evolve within species, and a given species may have multiple copies of the SAME gene (important)
  • OR different genes from the same species may have different phylogenetic histories (resulting in different trees)
40
Q

What can we do when gene trees disagree? How are we supposed to find the species tree?

A
  • the correct species tree will be supported by the largest number of gene trees
  • if there are equal numbers of gene trees supporting different species trees, we need more data
41
Q

What are the 5 reasons phylogeny reconstruction is a challenge? - see notes for supporting questions

A
  1. Scoring characters may not be straightforward
  2. Evolutionary change is not always parsimonious
  3. Evolutionary events from long ago are hard to detect
  4. Rates of evolutionary change varies.
  5. Evolution does not always involve divergence
42
Q

What is another way evolution can occur without involving divergence?

A
  • could be a result of hybridization
43
Q

What are two examples of reticulate evolution?

- what is an implicit assumption of phylogenetic analysis?

A
  • horizontal gene transfer and hybridization

- that branches diverge but DO NOT rejoin

44
Q

Define HGT, what is it mediated by and where does it occur more often than not?

A
  • horizontal gene transfer is the transfer of DNA between UNRELATED lineages (often mediated by viral DNA)
  • HGT is rare in Eukarya, but common in bacteria and archaea (through endosymbiosis)
45
Q

Define hybridization and where it would be most commonly observed.

A
  • expected to occur in CLOSELY-RELATED species
  • it is the interbreeding between parents of different species (it occurs in many groups and gives rise to hybrid species)
46
Q

How do you detect hybrids in phylogenetic trees?

A
  • catch! phylogenetic methods don’t detect hybridization well… why? because they assume the tree is diverging
  • if they are present we need the COMBINATION OF TRAITS from the hypothesized parents (POLYPHYLETIC orogins)
47
Q

What is one example of hybridization?

A
  • ancient cotton, combination of African and North American species
48
Q

Define Monophyletic

A
  • includes all the descendants of a single ancestor (the most common ancestor for a species trait is shared by all the descendants)
49
Q

Define Paraphyletic

A
  • SOME but NOT ALL of the descendants of a single ancestor
  • all species examined come from a common ancestor, however only some retain the ancestral trait more than others (ex. a late change of trait)
50
Q

Define Polyphyletic

A
  • descendants of two or more ancestors both of which have descendants that are not included in the taxon
  • a group with multiple ancestors
51
Q

Name the 5 examples discussed in Lecture.

A
  1. Plasmodium parasite used to figure out the origins of a clade of gorillas through other parasites
  2. The evolution of hemaphrodite plants
  3. Heliconius butterflies and their mimicry rings in two morphologically evolved in tandem
  4. the coevolution of ecologically lineages (by examining predator-prey groups)
  5. The origin of disjunct distribution of fawn-lillies across similar latitudes in the northern hemisphere
52
Q

Since plants are typically hermaphorditic, how many times have the following traits evolved in flowering plants? what are these traits?

A
  • separate sexes (dioecy)
  • sex chromosomes
  • observing phenotyptic evolution

Biology 355 - Evolution (7 decks)

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