Lecture 2

Question 1

What is Phylogeny?

Answer 1

the evolutionary history of a group of related species

Question 2

What is a phylogeny?

Answer 2

is an evolutionary tree which shows the evolutionary relationship between species

Question 3

what is an internal node?

Answer 3

a branch point representing the divergence of two hypothetically common ancestors

Question 4

What are the three phylogenetic groups?

Answer 4

Monophyletic
Paraphyletic
Polyphyletic

Question 5

What is the only valid phylogenetic group?

Answer 5

Monophyletic

Question 6

What are monophyletic groups?

Answer 6

includes all descendants of a most recent common ancestor

Question 7

What are paraphyletic groups?

Answer 7

include only some descendants of a common ancestor, it does not include all descendants of a common ancestor

Question 8

What are polyphyletic groups?

Answer 8

include only some distantly related descendants of a common ancestor and doesn’t include the most recent common ancestor of them all

Question 9

What determines branching points on a phylogenetic tree?

Answer 9

defined by shared derived characteristics, either molecular (genetic) or morphological (phenotypic)

Question 10

What can happen to derived characteristics?

Answer 10

they can be lost over generations

Question 11

How to determine monophyletic groups?

Answer 11

comparing homologous characteristics

Question 12

What are homologous characteristics?

Answer 12

similar traits inherited from a last common ancestor

Question 13

What is convergent evolution?

Answer 13

a general term for the repeated evolution of similar traits

Question 14

What could be a reason for characters not being homologous

Answer 14

convergent evolution

Question 15

Two types of convergent evolution

Answer 15

analogy and homoplasy

Question 16

What is analogy?

Answer 16

similar functional traits due to convergent evolution, not inherited from the last common ancestor

Question 17

Analogous traits

Answer 17

not homologous at the level of convergence

Question 18

What is Homoplasy?

Answer 18

repeated evolution of the same state of the same character on a phylogenetic tree
-this can be considered a type of homology because there is a path of common ancestry though it shows independent evolution so some argue its not homology

Question 19

Morphological phylogenies

Answer 19

first a morphological matrix is built to record the presence/absence of compared traits, this matrix is used to infer a phylogeny

Question 20

Molecular phylogenetic

Answer 20

-bases on molecular characters are reconstructed
-molecules are sampled and sequences
-sequences are aligned using computer algorithms to make a molecular character matrix
-alignment is used to infer phylogeny

Question 21

Variation in molecular sequences

Answer 21

some molecular sequences evolve faster than others

some sequences are more consistent while others have more sites that can vary

Question 22

Suitability of molecular sequences

Answer 22

different rates of mutation mean different MS will be suitable for different levels of phylogenetic analysis

Question 23

Uses of histone H4 in phylogeny

Answer 23

Histone H4 could be informative about very deep divergences such as species in different kingdoms (e.g plants and animals)

Question 24

Evolution of DNA

Answer 24

Non-coding DNA sequences generally evolve faster than protein-coding

Nucleotides evolve faster than the corresponding amino acids

The 3rd position base in a codon is usually the fastest because it is least likely to effect amino acid coded for

Question 25

Phylogenetic inference methods

Answer 25

compare the possible trees against the optimal criteria to see which is the best and most likely

Question 26

Two main types of phylogenetic inference:

Answer 26

maximum parsimony maximum likelihood

Question 27

What is Maximum Parsimony?

Answer 27

the best tree is the one which requires the lowest number of changes (e.g least number of base substitutions)

Question 28

What is maximum likelihood?

Answer 28

the best tree is the one that is most likely to have produced the data given a model of evolution -incoroporates evolutionary models

Question 29

What are evolutionary models?

Answer 29

models of the probability of different evolutionary events such as DNA substitution models which model the probability of mutation or substitution from one base to another

Question 30

Jukes and Cantor model

Answer 30

assumes that the probability of any nucleotide changing to any other is equal

Question 31

Variation in gene phylogenies

Answer 31

different genes can imply different phylogenies the best tree suggested by one gene may contrast the best tree suggested by another

Question 32

Why do genes suggest different phylogenies?

Answer 32

due to gene duplication or subsequent divergence

Question 33

What is Divergence?

Answer 33

means to split apart or move away from one another two species evolving further away from their common ancestor

Question 34

Two types of homologous genes

Answer 34

orthologous paralogous

Question 35

Orthologous genes

Answer 35

have shared ancestry due to inheritance following a speciation event (diverge after speciation)

Question 36

Paralogous genes

Answer 36

result from gene duplication, found in more than one copy in the genome. copies can diverge within the genome that carries them and evolve new functions

Question 37

Paralogous and Orthologous genes recording patterns of speciation

Answer 37

Orthologous record this more accurately than paralogous because paralogous genes show complex patterns of presence, absence and similarly among species

Question 38

What is Horizontal gene transfer?

Answer 38

a process which can lead to gene trees which don't precisely match species trees it is the transfer of genes between co-existing species not through common decent (e.g plasmids and viral replication)

Question 39

Problems with horizontal gene transfer

Answer 39

can lead to rapid and wide transfer of genes so patterns of presence and similarity in genes that have been horizontally transferred may not accurately record speciation