Phylogenetics Flashcards

2
Q

Phylogeny

A

the evolutionary history of a group of organisms (a summary of relatedness among groups)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Phylogenetic Tree

A

graphical summary of relatedness that describes the pattern among lineages

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Taxon

A

A group of genetically related organisms (populations, species, families, etc)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Clade

A

a group of taxa derived from a common ancestor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Nodes on a phylogenetic trees are

A

branching points

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are tips/terminal nodes

A

the end points of branches where nothing else branches

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Time moves from ____ to ___ on a phylogenetic tree

A

left to right

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Polytomy

A

unresolved branching on a phylogenetic tree

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Out-group

A

the taxon that is indisputably most distantly related to all other members

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

2 factors that make phenotypic similarity approach bad

A

convergence and reversals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Convergence is

A

unrelated groups evolve similar phenotypes independently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Reversals is

A

related taxa no long share a homologous trait found in a common ancestor (one of both taxa lose the trait)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Homologous trait

A

one that evolved originally in the same ancestor and were then passed on to all descendant taxa (ex: feathers on birds)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Convergence and reversals together are called

A

homoplasys

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

In terms of homoplasy convergence is a _____ and reversal is a _______

A

convergaence is a phenotypic similarityreversal is a dissimilarity (all among closely related taxa)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is phenotypic noise

A

something that increases/decreases phenotypic similarity among taxa (ex: homoplasy)

18
Q

On a graph of similarity to evolutionary relatedness the ideal slope is ____ and scattered plots are due to _____

A

1 , homoplasy

19
Q

Plots above the ideal phone are ____ and plots below are ____

A

convergence, and reversals

20
Q

T/F: it is accurate to make P-trees based on p-similarity alone

A

False- every error prone due to homoplasy

21
Q

Cladistic analysis is

A

a more accurate way to draw P-trees

22
Q

3 major factors needed to construct a phylogeny

A

1) homologous traits2) minimize homoplasy3) many independently evolving characters (to counter homoplasy “noise” )

23
Q

2 major characters needed to construct a phylogeny

A

1) molecular data (DNA, RNA)2) Gross phenotypic data (bones, teeth, behavior)

24
Q

Synapomorphies

A

shared derived characters (ex: hooves)

25
Q

Cladistic Method

A

Identifies groups based on synapomorphies

26
The difference between synapomorphy and homologous trait
Homologous trait deals with any characteristic similarity between organisms from a common ancestor; synapomophy is sorta the same except the trait as changed so the ancestor doesnt have the same ones as the descendants
27
To start a P-tree we need an
out-group
28
In a P-tree the traits need to be polarized, whats does that mean?
arranged in chronological order.
29
Phylogenies are \_\_\_\_\_
hypotheses- the best fit with available data
30
In making a tree using molecular data, the base sequence used to determine all placement is...
the reference point
31
The reference point is..
the sequence of the out-group; the sequenced used to base all change
32
Major problems of producing homoplasy in molecular data are:
reversalsconvergencemultiple hitssaturation(only 4 bases to work with)
33
Another type of phylogenetic tree is a
genetic distance tree
34
Each vertical line in a genetic distance tree is.....
a common ancestor
35
Each horizontal line in a genetic distance tree is...
an evolving lineage
36
The length of each ___ line is proportional to its ______ from a common ancestor. It determines the number of ______ differences
length, genetic divergence, base pair differences
37
Using a genetic distance tree on HIV we can see that _____ increases over time and pays out as predicted by the _____ hypothesis
clonal diversity; escape hypothesis
38
Phylogenomics
Constructing P-trees based on whole genome sequences. (large sequences)