Chapter 5

Question 1

Wrote The Principles of Numerical Taxonomy,

Answer 1

obert Sokal and Peter Sneath

Question 2

Essentially assessed overall similarity and Often referred to as Phenetics

Answer 2

Numerical Taximony

Question 3

• Intellectual successor to NT

* Count pairwise differences between species

Answer 3

Genetic Distance Based Method

Question 4

Slowed American acceptance and set up a battle between pheneticists and cladists that continued until the 1980’s
• Goal: develop an objective taxonomy and a method for phylogenetic reconstruction

Answer 4

Willi Hennig

Question 5

find the tree with the minimum amount of homoplasy (convergences, reversals, parallelisms)
fewest evolutionary changes

Answer 5

maximum parsimony

Question 6

Phylogenetic Analysis Using Parsimony

Answer 6

PAUP* (Swofford)

Question 7

very fast tree-searching algorithms

Answer 7

TNT (Goloboff)

Question 8

Rarely do you get just one most parsimonious tree

• What do you do when each of these is equally likely?

Answer 8

Consensus Trees

Question 9

only those nodes found in all most parsimonious trees represented

Answer 9

Strict consensus

Question 10

nodes found in greater than 50% of trees represented

Answer 10

Majority Rule consensus

Question 11

Sampling with replacement

Answer 11

Bootstrap analysis - about 75% is good

Question 12

in tree support what is the ultimate test?

Answer 12

congruence

Congruence - does the tree in one analysis match the tree of another?

Question 13

Transitions

Answer 13

purines (AG) or

pyrimidines (CT) - easier

Question 14

Transversions

Answer 14

urines and pyrimidines (AT, AC, GT, GC) =harder

Question 15

• Simplest based on transmission codes

Answer 15

= Neighbor Joining - doesn’t assume equal rates of DNA sequence evolution

Question 16

• Third position based on transmission codes

Answer 16

easiest - least likely to alter amino acid •

Question 17

First - based on transmission codes

Answer 17

middle, second - hardest

Question 18

calculates the tree that best fits the data and model

Answer 18

Maximum Likelihood

Question 19

Runs numerous simulations of the data to maximize probability for the tree (Markov Chain Monte Carlo)

Answer 19

Bayesian Analysis

Question 20

Maximum likihood uses

Answer 20

bootstrap

Question 21

Bayesian Analysis

Answer 21

posterior probabilities, close to a statistic, but tend to overestimate support

Question 22

based originally on a fixed rate of change

Answer 22

Molecular clocks

Question 23

alter rates along branches

Answer 23

• BEAST: Relaxed clock – requires fossil

Question 24

Show us that basing a taxonomy means difficult changes

• 2 examples – horses and tetrapods

Answer 24

Fossils and Phylogeny

Question 25

Vertebrates to Land

Answer 25

Without fossils, this would be confusing
• Major changes to shoulder, pelvis, ear, skull, etc.
• Well known and studied
• A group of lobe-finned fishes lost dorsal fins, lost connection of pectoral to skull, gained digits, gained connection of pelvic girdle to vertebrae, etc.

Question 26

Very common fossil, long known- fish

Answer 26

Eusthenopteron

Question 27

Recent fossil, no dorsal fin-fish

Answer 27

Panderichthys

Question 28

Gills as adult, no dorsal fin, but with wrists and a cervical vertebra Verdict: ? Fishapod?

Answer 28

Tiktaalik

Question 29

use phylogeography to understand what

Answer 29

continental drift

Question 30

Who proposed Continental Drift

Answer 30

Alfred Wegener

Question 31

movement

Answer 31

dispersal

Question 32

sepration due to geological processes

Answer 32

Vicariance

Question 33

Phylogenetic Independent Contrasts

Answer 33

( A-B ) divided by branch length