Phylogenetics

Question 2

Phylogeny

Answer 2

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

Question 3

Phylogenetic Tree

Answer 3

graphical summary of relatedness that describes the pattern among lineages

Question 4

Taxon

Answer 4

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

Question 5

Clade

Answer 5

a group of taxa derived from a common ancestor

Question 6

Nodes on a phylogenetic trees are

Answer 6

branching points

Question 7

What are tips/terminal nodes

Answer 7

the end points of branches where nothing else branches

Question 8

Time moves from ____ to ___ on a phylogenetic tree

Answer 8

left to right

Question 9

Polytomy

Answer 9

unresolved branching on a phylogenetic tree

Question 10

Out-group

Answer 10

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

Question 11

2 factors that make phenotypic similarity approach bad

Answer 11

convergence and reversals

Question 12

Convergence is

Answer 12

unrelated groups evolve similar phenotypes independently

Question 13

Reversals is

Answer 13

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

Question 14

Homologous trait

Answer 14

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

Question 15

Convergence and reversals together are called

Answer 15

homoplasys

Question 16

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

Answer 16

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

Question 17

What is phenotypic noise

Answer 17

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

Question 18

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

Answer 18

1 , homoplasy

Question 19

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

Answer 19

convergence, and reversals

Question 20

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

Answer 20

False- every error prone due to homoplasy

Question 21

Cladistic analysis is

Answer 21

a more accurate way to draw P-trees

Question 22

3 major factors needed to construct a phylogeny

Answer 22

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

Question 23

2 major characters needed to construct a phylogeny

Answer 23

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

Question 24

Synapomorphies

Answer 24

shared derived characters (ex: hooves)

Question 25

Cladistic Method

Answer 25

Identifies groups based on synapomorphies

Question 26

The difference between synapomorphy and homologous trait

Answer 26

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

Question 27

To start a P-tree we need an

Answer 27

out-group

Question 28

In a P-tree the traits need to be polarized, whats does that mean?

Answer 28

arranged in chronological order.

Question 29

Phylogenies are _____

Answer 29

hypotheses- the best fit with available data

Question 30

In making a tree using molecular data, the base sequence used to determine all placement is…

Answer 30

the reference point

Question 31

The reference point is..

Answer 31

the sequence of the out-group; the sequenced used to base all change

Question 32

Major problems of producing homoplasy in molecular data are:

Answer 32

reversalsconvergencemultiple hitssaturation(only 4 bases to work with)

Question 33

Another type of phylogenetic tree is a

Answer 33

genetic distance tree

Question 34

Each vertical line in a genetic distance tree is…..

Answer 34

a common ancestor

Question 35

Each horizontal line in a genetic distance tree is…

Answer 35

an evolving lineage

Question 36

The length of each ___ line is proportional to its ______ from a common ancestor. It determines the number of ______ differences

Answer 36

length, genetic divergence, base pair differences

Question 37

Using a genetic distance tree on HIV we can see that _____ increases over time and pays out as predicted by the _____ hypothesis

Answer 37

clonal diversity; escape hypothesis

Question 38

Phylogenomics

Answer 38

Constructing P-trees based on whole genome sequences. (large sequences)