Phylogenetic Data Analysis

Question 1

Define topology

Answer 1

Relative branching order in a phylogenetic tree

Question 2

What is a bifurcating node?

Answer 2

A node that only has two immediate descendents

Question 3

What is another name for a node that is bifurcating?

Answer 3

Dichotomous

Question 4

What is a multifurcating node?

Answer 4

If it has more than two immediate descendent lineages

Question 5

What is another name for a multifurcating node?

Answer 5

Polytomous

Question 6

True or false, in a cladogram branch lengths have no meaning?

Answer 6

True

Question 7

Define tree balance

Answer 7

A measure of the degree of symmetry of a rooted phylogenetic tree. It serves as an indication of the pattern of speciation events in the group of taxa under study

Or

The degree to which sister groups contain the same number of tips

Question 8

What is a clade?

Answer 8

A group of organisms that includes a single ancestor and all of its descendents

Question 9

List three problems with phylogenetic tree construction

Answer 9

1) Hybridisation and gene flow
2) Gene tree versus species tree
3) How do you define a species

Question 10

What is the Newick format?

Answer 10

It is a standard format to write phylogenetic trees in text.

The pattern of the parentheses indicated topology.

Each pair of parentheses enclose all members of a monophyletic group

Always ends in a semicolon

Question 11

Define genetics

Answer 11

Functional effect of specific genes, as well as their evolution and mutations

Question 12

Define genomics

Answer 12

Large stretches of DNA (coding and non-coding

the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes.

Question 13

What is a polymorphic site?

Answer 13

A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population

Question 14

What is a parsimony-informative site?

Answer 14

It contains at least two types of nucleotides (or amino acids), and at least two of them occur with a minimum frequency of two

Question 15

When was the human genome project completed?

Answer 15

2003 (it cost $2.7 billion and took 13 years)

Question 16

How long does it take to sequence a human genome today?

Answer 16

It takes 2 days and costs under $10,000

Question 17

What is NGS

Answer 17

Next Generation Sequencing

Question 18

What is a tree?

Answer 18

To be considered a tree the diagram has to be directed (time moves in one direction along each branch) and acyclic (the lineages that diverge never subsequently meet)

Question 19

What is the root of a tree?

Answer 19

A special node that marks the point where time enters the diagram

Question 20

What are sister groups/taxa?

Answer 20

Two descendants of a single node

Question 21

What is phylogenetic inference?

Answer 21

The reconstruction of phylogenetic trees

Question 22

What is an unrooted tree?

Answer 22

A tree without a root and, thus, without a specified time axis

Question 23

What is a cladogram?

Answer 23

A tree diagram that communicates the topology but not the branch lengths. It provides all the information needed to determine the degree of evolutionary relatedness between taxa

Question 24

What is a gene tree?

Answer 24

The history of a set of homologous recombinational genes

Question 25

Define merging

Answer 25

A way of simplifying a tree by representing a clade with a single terminal

Question 26

Define phylogenetics

Answer 26

The field of study concerned with inferring the evolutionary relationships of living and extinct taxa

Question 27

What is a phylogram?

Answer 27

A tree in which branch lengths are drawn proportional to the amount of change attributed to the branch

Question 28

Explain what is meant by ‘polymorphic’

Answer 28

Having two or more states within a single population o taxon

Question 29

Define pruning

Answer 29

The process of removing terminals/clades from a phylogenetic tree without changing the implied relationships of the remaining terminals