chapter 7- phylogeny

Question 1

phylogeny

Answer 1

A hypothesis of ancestor descendent relationships.

Question 2

Phylogenetics

Answer 2

the study of ancestor descendent relationships. The objective of phylogeneticists is to construct phylogenies

Question 3

Phylogenetic tree

Answer 3

a graphical summary of a phylogeny

Question 4

All life forms are related by common ancestry and descent. The construction of phylogenies provides explanations of the ———– seen in the natural world.

Answer 4

diversity

Question 5

Phylogenies can be based on ——– data, ———– data, ——– data or all three. Today, phylogenies are usually constructed using ———-

Answer 5

morphological, physiological, and molecular,

DNA sequence data

Question 6

We use —— to construct phylogenies. A ——- is any attribute of an organism that can provide us with insights into history (shared ancestry).

Answer 6

characters

character

Question 7

In molecular phylogenies, characters are typically ———— in a gene sequence, and each position can possess four CHARACTER STATES: A,C, G, or T

Answer 7

nucleotide positions

Question 8

Plesiomorphy

Answer 8

refers to the ancestral character state

Question 9

Apomorphy

Answer 9

a character state different than the ancestral state, or DERIVED STATE

Question 10

Synapomorphy

Answer 10

a derived character state (apomorphy) that is SHARED by two or more taxa due to inheritance from a common ancestor: these character states are phylogenetically informative using the parsimony or cladistic criterion

Question 11

Autapomorphy

Answer 11

a uniquely derived character state

Question 12

Monophyletic

Answer 12

a group that includes ALL of the descendants of a common ancestor. Monophyletic groups are also known as CLADES

Question 13

Non Monophyletic

Answer 13

Any case that does not satisfy the above, such as:
Paraphyletic
Polyphyletic

Question 14

Paraphyletic

Answer 14

A group that includes some, but not all of the descendants of a common ancestor

Question 15

Polyphyletic

Answer 15

assemblages of taxa that have been erroneously grouped on the basis of homoplasious characters (eg “vultures”) -we will return to this

Question 16

Homology

Answer 16

A character state that is shared between two DNA sequences or taxa may be so because they inherited it from a common ancestor, or it is HOMOLOGOUS (a homology/ synapomorphy)

Question 17

homoplasy

Answer 17

the shared character might occur because they were evolved independently, in which case they are called a HOMOPLASY

Question 18

Why can Homoplasy Occur

Answer 18

• parallel evolution
• convergent evolution
• secondary loss

Question 19

parallel evolution

Answer 19

independent evolution of a similar feature from the same ancestral condition

Question 20

convergent evolution

Answer 20

independent evolution of the same feature from different ancestral condition

Question 21

secondary loss

Answer 21

revision to ancestral condition

Question 22

Homoplasy results in ————, polyphyletic groupings

such as “vultures”

Answer 22

erroneous

Question 23

what happened with the old world vulture and new world vulture ?

Answer 23

• they were thought to be from the same common ancestor due to morphological similarities, both looked similar, ate dead animals
• through further research, molecular data it was shown that they don’t come from common ancestors
• new world vulture common ancestor storks and their relatives
• old world vulture common ancestor birds of preys

Question 24

relationship b/w new world vulture and old work vulture

Answer 24

polyphyletic - grouped together due to mistake, was believed to be derived independently

Question 25

Vultures are a—————-. New world and old world

vultures provide an example of homoplasy resulting from ———————–.

Answer 25

polyphyletic group- grouped together due to a mistake, as a result of homoplasy
convergent evolution - independent evolution of similar feature from different ancestral condition

Question 26

Three Spine Stickle Back

Answer 26

• 3 spine stickle back species pairs have evolved independently in coastal lakes of British Columbia
• Lake A have 3 spine stickle back , independently evolved similar feature from same ancestral condition : marine ancestors
• Lake B have 3 spine stickle back : independently evolved similar feature from same ancestral condition : marine ancestors

Question 27

Mutation can cause ————

Answer 27

synapomorphies

Question 28

———– can remove synapomorphies

Answer 28

reversals (back -mutations)

Question 29

We use ————— to construct phylogenetic trees and to identify groups that are monophyletic; synapomorphies are ———————

Answer 29

homologous characters (synapomorphies)
phylogenetically informative

Question 30

We want to avoid using ——————– to construct phylogenies

Answer 30

homoplasious characters

Question 31

The Principle of Parsimony

Answer 31

• simple explanations are preferred over more complicated ones.
• In terms of phylogenetic trees, less evolutionary steps are better than more steps to explain relationships. The tree with the least number of steps is the most parsimonious.

Question 32

The parsimony method ———- the total number of evolutionary changes required to explain relationships

Answer 32

minimizes

Question 33

outgroup

Answer 33

• When constructing a phylogeny for a group of organisms, we need to employ an outgroup, which is not part of the group of interest (the ingroup), but also not too distantly related to it.
• The outgroup is used to polarize the character states, or infer change. The character state possessed by the outgroup is defined a priori as ancestral (pleisiomorphic)

Question 34

Bootstrap Method

Answer 34

• Assessing Confidence in Phylogeny
• Computational technique for estimating the confidence level of a phylogenetic hypothesis
• Randomly generates new data sets from the original set (1000 replicates is most common)
• Computes the number of times that a particular grouping (or branch) appeared in the tree

Question 35

Taxonomic groups can be

Answer 35

Monophyletic – contain all descendants of a common ancestor
Paraphyletic – contain some but not all descendants of a common ancestor, or polyphyletic (erroneous homoplasious groupings)

Question 36

The goal of ——— is to only recognize monophyletic groups as valid taxa, but traditional taxonomy has not always done this

Answer 36

cladistic taxonomy

Question 37

Cladistics

Answer 37

the use of parsimony to construct evolutionary relationships

Question 38

cladistic taxonomy is equal to

Answer 38

= evolutionary taxonomy

Question 39

Coevolution

Answer 39

• The process where evolutionary changes in the traits of one species drives evolutionary changes in the traits of another species. Coevolution can involve predators and prey, hosts and parasites, and mutualisms, such as aphids and their endosymbiotic bacteria (above).
• Coevolution can result in co-speciation.