Phylogeny

Question 1

application of phylogenetics

Answer 1

reconstruct evol history of organisms
understand evol of genes and proteins
framework to understand evol of traits
reconstruct evol of languages

Question 2

Was Darwin aware of Linnaeus’ classification

Answer 2

yes

Question 3

define phylogenetic tree

Answer 3

mathematical structure used to depict evol history of a group of organisms or genes
show historical relationship, not similarity

Question 4

define systematics

Answer 4

infers phylogenetic relationships of organisms and creating classifications based on their evol histories

Question 5

define bifurcation

Answer 5

resolved node- 1 ancestor gives rise to 2 descendents

Question 6

define polytomy

Answer 6

unresolved node, hard to decipher relatinship

1 ancestral branch giving rise to at least 3 taxa

Question 7

define resolution

Answer 7

when 1 ancestral lineage gives rise to 2 descendents

Question 8

t/F: can twist any branch and rearrange order of taxa

Answer 8

T

Question 9

define homology

Answer 9

ptypic and genetic similarities due to shared ancestry

Question 10

significance of cladograms

Answer 10

no meaning, just shows relationship

Question 11

signif of chronograms

Answer 11

show time

Question 12

signif of phylograms

Answer 12

show amount of change; genetic muts or bp changes

Question 13

T/F: the width of the horizonal axis is signif

Answer 13

F

Question 14

define rooted trees

Answer 14

implies dirction from last common ancestor to present

Question 15

define unrooted tree

Answer 15

don’t know where root is or direction of evol

Question 16

define homologous characters

Answer 16

present in a group of species due to shared ancestry

2 kinds

Question 17

what are the 2 types of homologous characters

Answer 17

shared derived

shared ancestral

Question 18

define analogous/homoplastic characters

Answer 18

present in certain species that have evolved through convergent evol

Question 19

define monophyletic

Answer 19

an ancestral species and all its descendants

Question 20

define paraphyletic

Answer 20

an ancestral species and some but not all of its descendents

Question 21

define polyphyletic

Answer 21

a group without a common ancestor

Question 22

what are 2 important assumptions about phylogen characters

Answer 22

they are homologous and are evolving independently from each other

Question 23

most phylogen analyses use…

Answer 23

moleculr data

Question 24

why do most phylogen analyses use molecular data

Answer 24

genetic basis of characters known
larger amount of phylogen info
any groups of organisms can be compared
     diff rates of evol in diff genes
      math modeling
character delimitation is straightforward (when u have same genes from diff organisms and align seq, each character in seq alignment is easy to identify)
DNA is ultimate level of info

Question 25

define parsimonious

Answer 25

fewest base changes

Question 26

what does parsimony use

Answer 26

only characters that are informative

Question 27

define informative

Answer 27

have same character in at least 2 diff seq

Question 28

challenges for phylogenetic inference

Answer 28

phylogencis are hypotheses about gene/organism relationship that are constantly updated w/ new data
genes can be transferred horizontally from 1 organism to an unrelated on leading to complications
genes undergoing selection can be repaidl evoloving and contain many convergently evolving sites
diff sires may be evolving at diff rates
rearrangements of geneitc mateiral can lead to false conclusions
ancient phylo relationships is hard