Topic 4: Phylogenetics

Question 1

Operational Taxonomic Unit (OTU)

Answer 1

“The entity” found at the end of a branch on a tree representing a species, genes, or genomes, “terminal node”

Question 2

What method is used to identify homologs?

Answer 2

BLAST, breaks sequences to 4-5 bps and compares them.

Question 3

What does a high score mean on a BLAST?

Answer 3

The higher the score the better the match.

Question 4

Problems with Trees?

Answer 4

• Long branch attraction

- Homoplasy

Question 5

How would you explore tree space? (3)

Answer 5

• parsimony analysis
• neighbour-Joining
• subtree pruning and redrafting

Question 6

Homologs are commonly divided in? (3)

Answer 6

Orthologs
Paralogs
Xenology

Question 7

Orthologs

Answer 7

diverged through speciation

Question 8

Paralogs

Answer 8

diverged through duplication

Question 9

Xenologs

Answer 9

diverged though lateral transfer

Question 10

Which method is considered more robust at creating a phylogeny and have the soundest statistical foundation?

Answer 10

maximum likelihood or Bayesian.

Question 11

Bootstrapping and jackknifing are used for?

Answer 11

assessing how well a constructed tree represents all of the data.

Question 12

How can phylogenetic analysis be used to detect recombination?

Answer 12

by comparing the tree for two portions of an alignment (L+R), the trees for the two partitions should be different.

Question 13

Concantenated Alignment

Answer 13

using more than one gene to create a tree, placing genes one after the other, aka “mega alignment”

Question 14

How would you root a tree?

Answer 14

root the tree with an “outgroup”, picking a branch that is suggested to be the oldest.

Question 15

Phylogenetic Congruence

Answer 15

shows that the topology of the tree of bacterial endosymbionts is identical to their overlapping host.

Question 16

Arbitrary root

Answer 16

picking a branch to represent the root

Question 17

Types of Measures of Support (2)

Answer 17

Bayesian Analysis (posterior probabilities) and
Bootstrap Probabilities represented as MP/ML
(Maximum Parsimony/Maximum Likelihood)

Question 18

What are some molecular phylogenetic methods used to infer the trees?

Answer 18

• parsimony
• distance
• maximum likelihood
• bayesian

Question 19

Steps in the construction of gene phylogenies:

Answer 19

1) choose gene(s) of interest
2) identify homologs
3) align sequences
4) calculate gene tree

Question 20

Evolutionary trees are considered _________?

Answer 20

Hypotheses

Question 21

What is Homoplasy?

Answer 21

Similarity in character states due to convergence and/or reversal appearing more than one place on a tree

Question 22

What are three problems associated with phylogenetic inference?

Answer 22

1) unequal rates
2) non-vertical evolution (LGT)
3) homoplasy

Question 23

Alignments are considered as _______?

Answer 23

Hypotheses

Question 24

What methods would you use to assess phylogenetic trees?

Answer 24

Bootstrapping/Jackknifing and Phylogenetic Congruence

Question 25

What is Long Branch Attraction?

Answer 25

a phenomenon in phylogenetic reconstruction methods group together OTUs that are at the end of long branches, whether or not the grouping is actually governed by their relatedness.