Phylogeny

Question 1

How many percent are undiscovered species

Answer 1

86%

Question 2

Phylogenies

Answer 2

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

Question 3

3 styles of phylogenetic tree

Answer 3

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

Question 4

speciation (definition and represented as ___ on tree)

Answer 4

an ancestral lineage splits into two descendants

represented by node

Question 5

taxa / taxon

Answer 5

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

Question 6

what does a node represent?

Answer 6

node represents the MRCA and the speciation event

Question 7

root node vs. internal node

Answer 7

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

internal node is all the other node except root node

Question 8

sister taxa

Answer 8

share a node

by definition arise at the same time

Question 9

How is time represented in phylogeny

Answer 9

preceding nodes represent earlier speciation events

Question 10

branches

Answer 10

represent evolution overtime

Question 11

root branch

Answer 11

root branch lead to root node

Question 12

give examples of how phylogenetic trees are oversimplified

Answer 12

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

Question 13

monophyly

Answer 13

MRCA and ALL descendants

Question 14

clade

Answer 14

monophyly

Question 15

mathematical relationship to find how many monophyletic groups in a tree

Answer 15

count the nodes

Question 16

the two (artificial) nonmonophyletic group

Answer 16

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)

Question 17

the science of systematics : relationship between phylogeny and taxonomy

Answer 17

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

Question 18

polytomy

Answer 18

uncertain in branching

Question 19

two kinds of polytomy

Answer 19

soft : polytomy can be resolved with more data

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

Question 20

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

Answer 20

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

Question 21

character vs. character state

Answer 21

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

Question 22

4 factors that causes speciation

Answer 22

mutation, drift, recombination, selection

Question 23

synamorphy

Answer 23

a monophyletic group that shares a derived state

Question 24

ancestral state vs. derived state

Answer 24

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

Question 25

homoplasy vs. homologous

Answer 25

homoplasy : similarity not due to common ancestry caused by independent evolution homology : similarity due to common ancestor

Question 26

Trees are hypothesis. They are inferred from (3 factors)?

Answer 26

morphology, genetics, behavior

Question 27

how are tree hypothesis tested?

Answer 27

by adding more data, taxa or using different analytical data

Question 28

what's a data matrix and what are the basic elements of it

Answer 28

a data matrix summarizes data for taxa understudy. | consists of character, character state, and code

Question 29

unrooted tree

Answer 29

phylogenetic tree where the location of the root node is unknown

Question 30

how many possible unrooted tree for four taxa

Answer 30

3

Question 31

are there more ways to draw rooted or unrooted

Answer 31

rooted. increases exponentially

Question 32

why use unrooted trees?

Answer 32

too many rooted trees possibility. we it for mathematical expediency

Question 33

parsimony

Answer 33

the tree with the least amount of changes is the best tree

Question 34

limitations of unrooted tree

Answer 34

-do not completely specify relationships but exclude some possibilities

Question 35

outgroup vs. ingroup

Answer 35

``` outgroup = earliest species... connected to root branch in-group = everything else ```

Question 36

limitations of parsimony

Answer 36

-all cost change are weighted the same though some happen more easily than others

Question 37

Transitions vs. Transversion

Answer 37

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

Question 38

wobble base

Answer 38

- third position may change without changing amino acid | - genetic code is redundant because an amino acid can be encoded by multiple codons

Question 39

how do model-based (statistical) approaches to phylogengenetic inference differ from parsimony

Answer 39

model based use probability rather than just number of changes