Phylogeny Flashcards

midterm 1

1
Q

How many percent are undiscovered species

A

86%

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2
Q

Phylogenies

A
  • diagrams that represent ancestor-descendant relationships among organisms (evolutionary process)
  • make prediction about evolution
  • testable hypothesis
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3
Q

3 styles of phylogenetic tree

A

horizontal (box test), vertical(triangle test), circular

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4
Q

speciation (definition and represented as ___ on tree)

A

an ancestral lineage splits into two descendants

represented by node

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5
Q

taxa / taxon

A

-taxa = plural
-the tips
taxon can be anything from lineaen hierarchy (KPCOFGS)

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6
Q

what does a node represent?

A

node represents the MRCA and the speciation event

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7
Q

root node vs. internal node

A

root node is the MCRA of all the taxa in the phylogeny

internal node is all the other node except root node

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8
Q

sister taxa

A

share a node

by definition arise at the same time

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9
Q

How is time represented in phylogeny

A

preceding nodes represent earlier speciation events

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10
Q

branches

A

represent evolution overtime

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11
Q

root branch

A

root branch lead to root node

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12
Q

give examples of how phylogenetic trees are oversimplified

A

1) populations within species are not shown. There populations are from the speciation event.
2) some taxa not included (extinct)`

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13
Q

monophyly

A

MRCA and ALL descendants

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14
Q

clade

A

monophyly

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15
Q

mathematical relationship to find how many monophyletic groups in a tree

A

count the nodes

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16
Q

the two (artificial) nonmonophyletic group

A

1) paraphyletic : includes MRCA but excludes at least one descendant
2) polyphyletic : no MRCA : has a most common ancestor but not most recent (usually the root)

17
Q

the science of systematics : relationship between phylogeny and taxonomy

A

systematics combines taxonomy and phylogenetics to produce classifications that reflect the evolutionary history of organisms
(KPCOFGS) species is italicized

18
Q

polytomy

A

uncertain in branching

19
Q

two kinds of polytomy

A

soft : polytomy can be resolved with more data

hard : speciation happened so fast that there is no way of fixing it

20
Q

3 different types of phylogeny tree and difference in the information they give

A

cladogram : only order of branching is shown ; branch lengths have no meaning
phylogram : branch lengths are proportional to amount of character change
chronogram : branch lengths are proportional to absolute time

21
Q

character vs. character state

A

character : a heritable feature (character trait)
character state: the form that a character takes
character: wings …. character state : present/absent

22
Q

4 factors that causes speciation

A

mutation, drift, recombination, selection

23
Q

synamorphy

A

a monophyletic group that shares a derived state

24
Q

ancestral state vs. derived state

A

same character from ancestor group vs. different character from ancestor group

25
homoplasy vs. homologous
homoplasy : similarity not due to common ancestry caused by independent evolution homology : similarity due to common ancestor
26
Trees are hypothesis. They are inferred from (3 factors)?
morphology, genetics, behavior
27
how are tree hypothesis tested?
by adding more data, taxa or using different analytical data
28
what's a data matrix and what are the basic elements of it
a data matrix summarizes data for taxa understudy. | consists of character, character state, and code
29
unrooted tree
phylogenetic tree where the location of the root node is unknown
30
how many possible unrooted tree for four taxa
3
31
are there more ways to draw rooted or unrooted
rooted. increases exponentially
32
why use unrooted trees?
too many rooted trees possibility. we it for mathematical expediency
33
parsimony
the tree with the least amount of changes is the best tree
34
limitations of unrooted tree
-do not completely specify relationships but exclude some possibilities
35
outgroup vs. ingroup
``` outgroup = earliest species... connected to root branch in-group = everything else ```
36
limitations of parsimony
-all cost change are weighted the same though some happen more easily than others
37
Transitions vs. Transversion
Transition : change of purine to purine (A,G) and change of pyrimidine to pyrimidine (C,T) Transversion : change of purine to pyrimidine and vice versa Transition is more likely to happen due to molecular shape
38
wobble base
- third position may change without changing amino acid | - genetic code is redundant because an amino acid can be encoded by multiple codons
39
how do model-based (statistical) approaches to phylogengenetic inference differ from parsimony
model based use probability rather than just number of changes