Lecture 6 - Origins and Evolution of Life

Question 1

cladograms

Answer 1

shows tree topology where lengths do not mean anything

Question 2

ultrametric trees (time trees)

Answer 2

tips in trees are equidistant from roots but branch lengths could indicate time

Question 3

polytomy

Answer 3

internal node in a phylogenetic tree with more than 2 descendants

Question 4

phylogenetic analysis

Answer 4

• genes must be homologous
• aligned bps/a.a. residues must share positional homology
• multiple-sequence alignment must include positions that are informative for the method of analysis used
• single-gene alignments can be concatenated and analyzed

Question 5

concatenated alignment

Answer 5

combining different gene alignments to form “mega alignment”

Question 6

phylogenetic analysis methods

Answer 6

• clustering
• parsimony
• likelihood-based

Question 7

clustering

Answer 7

calculate estimated evolutionary distance between all pairs of distance

Question 8

pasimony

Answer 8

minimum number of character changes

Question 9

maximum likelihood

Answer 9

possible trees are compared and given a score (score is based on how likely the tree was evolved given a.a. or nucleotide sub possibilties)

Question 10

problems with trees

Answer 10

• long branch attraction

- homoplasy

Question 11

long branch attraction (LBA)

Answer 11

• groups together taxa that are at the end of long branches but are not related
• parsimony can be misleading if true tree had long branches
• ## “parallel changes exceed informative nonparallel changes”

Question 12

homoplasy

Answer 12

multiple mutations turn into convergence evolution and the tree can group it wrong

Question 13

clustering and parsimony are susceptible to LBA

Answer 13

• parsimony can be misleading if true tree had long branches

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Question 14

likelihood of phylogenetic tree

Answer 14

• likelihood of generating the observed data given that tree, where the tree compromises a topology and branch lengths
• measure of how well a model fits the data

Question 15

log-likelihood

Answer 15

natural logarithm of likelihood values are used to make calculations easier

Question 16

maximum likelihood

Answer 16

minimizes the amount of surprise at the observed data

Question 17

elements of likelihood models

Answer 17

• model of substitution

- phylogram

Question 18

model of substitution

Answer 18

• the assumptions regarding the process of sequence evaluation
• includes a substitution matrix

Question 19

phylogram

Answer 19

• the topology and branch lengths

- each tree will represent a different hypothesis regarding evolution

Question 20

simple nucleotide substitution models

Answer 20

usually GTR or simplifications of GTR

Question 21

model simplicity

Answer 21

simple models can cause problems if they are too simplistic

Question 22

simplifying assumptions

Answer 22

• independence of evolution
• equal rates of nucleotide substitution types
• reversibility substitutions
• BPS are the only types of mutations
• evolutionary process remain the same among different lineages

Question 23

3-domain TOL (Woese’s Hypothesis)

Answer 23

archaea is monophyletic, therefore eukaryotes may not be a sister clade

Question 24

2-domain TOL (eocyte hypothesis)

Answer 24

archaea is paraphyletic to eukaryotes

Question 25

3-d vs 2-d TOL

Answer 25

2D is inferred when overly simplistic assumptions are avoided, therefore archaea is not monophyletic