Phylogenetics

Question 1

What is a phylogenetic tree?

Answer 1

The mathematical structure used to depict the evolutionary history of a group of organisms or genes

Question 2

What does phylogenetic trees show?

Answer 2

Shows historical relationships, not similarities

Question 3

What is systematics?

Answer 3

The discipline that focuses on inferring the phylogenetic relationships of organisms and creating classifications based on their evolutionary histories

Question 4

What is the hierarchical classification (from broad to specific)?

Answer 4

domain -> kingdom -> phylum -> class -> order -> family -> genus -> species

Question 5

What is a root?

Answer 5

The oldest point in the tree

Question 6

What is an internal branch?

Answer 6

Connects two nodes together

Question 7

What is an external branch?

Answer 7

Connects a tip (taxa) and a node

Question 8

What is a node?

Answer 8

Represents a branching point from the ancestral population

Question 9

What is a taxa?

Answer 9

It is a classification unit, representing a set or group of organisms

Question 10

What is a polytomy?

Answer 10

An internal node of a phylogenetic tree that is linked to three or more subtrees in a rooted tree or 4 or more subtrees in a unrooted tree

Question 11

What is a bifurcation?

Answer 11

An internal node that has exactly two descendants arising in a rooted tree and 3 descendants in an unrooted tree

Question 12

What is resolution?

Answer 12

the amount of information we get from sequence comparisons

Question 13

What does a hash mark mean in a phylogenetic tree?

Answer 13

represents a character shared by the groups to the right of the mark

Question 14

What is a sister group?

Answer 14

a single ancestral lineage gives rise to two daughter lineages

Question 15

What is the Newick standard?

Answer 15

((A,B,C), (D,E))

Question 16

What does the vertical axis mean in trees?

Answer 16

Cladograms: nothing
Chronograms: time
Phylograms: amount of change

Question 17

What does the horizontal axis mean in trees

Answer 17

nothing!!!

Question 18

What is the difference between a rooted tree and a unrooted tree?

Answer 18

A rooted tree attempts to identify when various species diverge from a common ancestor

Question 19

What are homologous characters?

Answer 19

characters present in a group of species due to shared ancestry

Question 20

What are analogous/homoplastic characters?

Answer 20

characters present in certain species that have evolved independently (convergent evolution)

Question 21

What are shared ancestral characters?

Answer 21

characters shared beyond a taxon we are trying to define

Question 22

What are shared derived characters?

Answer 22

evolutionary novelties unique to a particular clade
clade- a monophyletic group

Question 23

What is the differences between a monophyletic, polyphyletic, and paraphyletic groups?

Answer 23

Monophyly- based on shared derived characters
Paraphyly- based on shared ancestral characters
Polyphyly- based on convergent characters

Question 24

What are phylogenetic trees made out of, and what are some assumptions that are made?

Answer 24

Built from characters that can be morphological, behavioral, physiological, or molecular
Two assumptions: homologous and evolve independently from each other

Question 25

How is molecular data used in phylogenetic analyses?

Answer 25

DNA sequences are genetically inherited
Character identification is straightforward
Larger amount of phylogenetic information
Any groups of organisms can be compared
Different rates of evolution
mathematical modeling

Question 26

What is parsimony?

Answer 26

uses only characters/sites that are informative (have the same character in at least two different sequences)
The most parsimonious tree is the one with the smallest number of changes

Question 27

What are some challenges for phylogenetic inference?

Answer 27

• Phylogenies are hypotheses about gene/organism relationships that are constantly updated with new data
• Genes can be transferred horizontally
• Re-arrangements of genetic material can lead to false conclusions