Phylogenetic Trees

Question 1

Define Phylogeny

Answer 1

the evolutionary relationships among organisms

Question 2

Define sister taxa

Answer 2

are each others closest relatives

Question 3

Define polytomy

Answer 3

internal node that is linked to 3 or more branches

Question 4

Define monophyletic

Answer 4

clade contains the most recent common ancestor and all descendants

Question 5

Define paraphyletic

Answer 5

clade contains the most recent common ancestor and some but not all descendants

Question 6

Define polyphyletic

Answer 6

clade does not contain most recent common ancestor and contains some but not all descendants

Question 7

Define plesiomorphies

Answer 7

ancestral trait, evolutionary trait that is homologous within a particular group (find in the ancestor but maybe not descendants)

Question 8

Define apomorphies

Answer 8

derived trait/different form, a specialized trait or character that is unique to a group or species

Question 9

Define synapomorphies

Answer 9

shared derived trait, an apomorphy shared by two or more taxa, common between ancestor AND descendant

Question 10

Define homoplasy

Answer 10

similarity not due to descent, analogous traits

Question 11

The two types of homoplasy

Answer 11

1. convergence
2. reversal

Question 12

Define convergence

Answer 12

homoplasy, independent appearance of synapomorphies (due to environment similarity) ex. bird and bats wings

Question 13

Define reversal as homoplasy

Answer 13

a back mutation from a derived to an ancestral form (from T to A back to T)

Question 14

What is the danger of paralogs

Answer 14

in paralogs, if we only consider parts of the trees and not all, then danger could be that some species looking closer because only looking at part of the tree

Question 15

Dangers of analogous traits

Answer 15

analogous traits can make species look similar although it may not be due to descent

Question 16

Dangers of divergence

Answer 16

where species sharing a common ancestor become more distinct due to differential selection pressures, so could cause to think they are not related when they actually are

Question 17

What does UPGMA to draw trees assumes

Answer 17

assumes all rates are equal

Question 18

Explain the principle of parsimony (Occam’s razor)

Answer 18

trees are almost always drawn correctly if they have the smallest number of changes
occam’s razor = choose the explanation with the smallest number of elements

Question 19

What is parsimony score

Answer 19

number of character changes (mutations) along the evolutionary rate

Question 20

Explain maximum likelihood, alternative method

Answer 20

math model to determine probability of all possible trees and observing data under different models of evolution
is slow!

Question 21

Explain Bayesian inference as alternative method

Answer 21

creates local vs. global peaks
does “plane” of probabilities trying to get to global peak, problem is could get stuck on local peak which may not actually be the right answer. perform multiple times to ensure answer. done on a computer

Question 22

What is bootstrapping

Answer 22

a test or metric that uses random sampling with replacement and falls under the broader class of resampling methods, if get same result with replacement then confident in answer! Whichever result happens the most is the answer

Question 23

What 3 things should we do overall when drawing trees

Answer 23

1. use multiple approaches
2. include bootstrapping
3. include outgroup to root tree