Phylogenetics

Question 1

What is the definition of phylogeny?

Answer 1

Evolution of a lineage into branches

Question 2

What are nodes?

Answer 2

Points in a phylogeny where the lineage splits

Question 3

What are internal nodes?

Answer 3

Nodes located within the phylogeny representing ancestral populations or species that have long since disappeared

Question 4

What is a clade?

Answer 4

Single “branches” in the tree of life; each clade represents an organism and all of its elements

Question 5

What does studying phylogeny allow scientists to do?

Answer 5

Classify species based on their evolutionary history. It gives a relative order of all the changes in lineages

Question 6

What does it mean to be a monophyletic clade?

Answer 6

It is a group of organisms that form their own clade; an ancestor and all of its descendants

Question 7

What is a polyphyletic taxon?

Answer 7

It is a taxon that does not include the common ancestor of all the members of the taxon

Question 8

What are characters?

Answer 8

Heritable aspects of organisms that can be compared across taxa; can be used to determine relationships

Question 9

What do the taxa that have diverged from each other more recently represent?

Answer 9

It represents the fact that these taxa have more character states in common than the taxa that have diverged farther in the past

Question 10

What is a synapomorphy?

Answer 10

Derived form of a trait that is shared by a group of related species; evolved in the immediate common ancestor of a clade and were inherited by all the descendants.
AKA – changes in a character that arose in an ancestor that are
then shared by all the descendants of that common ancestor

Question 11

What is the outgroup?

Answer 11

The species used for comparison of one group with another species outside of the clade; must have a common ancestor at some point, such as carnivores and primates

Question 12

What is a homoplasy?

Answer 12

A character state similarity not due to shared decent, could be because of independent evolution of the same trait in two or more lineages

Question 13

Define convergent evolution.

Answer 13

Independent origin of similar traits in separate evolutionary lineages

Question 14

Define evolutionary reversal.

Answer 14

Reversion of a derived character state to a form resembling its ancestral state; character similarity in distantly related taxa resulting from reversal to an original state

Question 15

What is a parsimony?

Answer 15

A principle that guides the selection of alternative hypothesis; the alternative requiring the fewest assumptions or steps is usually best

Question 16

What is polytomy?

Answer 16

An internal node of a phylogeny with two or more branches

Question 17

How do fossils help in the creation of phylogenies?

Answer 17

They help determine some aspects of the timing of evolution, and provide constraints to a clade’s history

Question 18

Define horizontal gene transfer.

Answer 18

Transfer of genetic material–other than from parent to offspring–to another organism, sometimes a distantly related one, without reproduction; rather extensive amongst prokaryotes

Question 19

What is exaptation?

Answer 19

A trait that initially carries out one function and is later co-opted for a new function; the original function may or may not be retained

Question 20

How is purifying selection beneficial to a species?

Answer 20

It removes deleterious alleles from a population, and is a common form of stabilizing selection

Question 21

What is tree thinking?

Answer 21

The ability to conceptualize those relationships and make inferences from the trees

Question 22

What are synapomorphies important?

Answer 22

1. used to reconstruct evolutionary trees using
   one of the classic analytical methods of phylogenetics (termed cladistics)
2. useful for providing characters that define
   parts of the Tree of Life

Question 23

Every phylogeny is a ___ about the events that happened in the past

Answer 23

hypothesis

Question 24

Why are many phylogenetic hypothesis still uncertain?

Answer 24

1. vast number of possible topologies

2. homoplasies (convergent evolution) that obscure true relationships

Question 25

What are support values on the branches?

Answer 25

They show how supported each branch is...usually on a 0-1 or 0-100 scale, with 1 or 100 being the most highly supported; also gives an index of how strongly that topology is supported by the data that went into making the tree

Question 26

Define an adaptation.

Answer 26

A trait modified by selection that increases the ability of an individual to survive or reproduce compared to individuals without the trait

Question 27

What are two types of tests to study adaptation?

Answer 27

1. experiment on variation | 2. examine evolutionary history of change (comparative method)

Question 28

Convergent evolution and homoplasy offer strong evidence for ___.

Answer 28

adaptation

Question 29

What are examples of character types?

Answer 29

morphological, molecular, behavioral

Question 30

Phylogenetic characters should be:

Answer 30

1. heritable 2. slowly-evolving 3. homologous

Question 31

What is a paraphyletic group?

Answer 31

A group with an ancestor with some, but not all, of its descendants