Lecture #4: Using Phylogenies

Question 1

LO #1: Describe the basic procedures for building a phylogenetic tree

Answer 1

1. select taxa of interest (ingroup)
2. include one or more outgroups
3. collect data (observations)
4. assemble into a data matrix
5. select a method of inference (parsimony or statistical methods) ((using unrooted trees))
6. root the unrooted tree using the outgroup to produce the phylogeny

Question 2

LO #2: Explain why unrooted trees are used when building phylogenies

Answer 2

we use unrooted trees b/c the math is better and it makes for very realistic trees (3UN vs 15R for 4 taxa)

Question 3

LO #3: Contrast ingroup and outgroup

Answer 3

ingroup: the set of organisms under study
outgroup: taxon that is closely related to the ingroup as much as possible, but not be part of it; based on prior knowledge

Question 4

LO #4: Trace the evolution of a trait on the phylogenetic tree

Answer 4

ex: how did flightless birds evolve? – believe that they are a monophyletic group and that the lost of flight only happened one time

Question 5

LO #5: Provides examples of how phylogeny is used to inform conservation biology and forensics

Answer 5

conservation biology: giraffes
- different lineages of giraffes, not just one type. so who do you save? what’s your reasoning? –> look at the phylogeny

forensics: HIV at the dentist
- Kimberly Bergalis was a virgin so how? Because the dentist she went to had it and other patients under him contracted the virus and it can be traced back with a phylogeny

Question 6

concept of building phylogeny: a group of organisms is inferred from their _________

Answer 6

characteristics

Question 7

concept of building phylogeny: need to collect _____ (through 3 things)

Answer 7

data

1. morphology
2. genetics
3. behavior

Question 8

concept of building phylogeny: trees are 1. ________ that can be tested by adding more data, taxa w/ 2. _________ _____

Answer 8

1. hypotheses

2. analytical methods

Question 9

the set of organisms under study

Answer 9

ingroups

Question 10

taxon that is closely related to the ingroup as much as possible, but not be part of it; based on prior knowledge

Answer 10

outgroup

Question 11

a hypothesis of homology; all characters are assumed to be homologous

Answer 11

data matrix

Question 12

the best tree is the one w/ the fewest number of character changes

Answer 12

parsimony

Question 13

rooted –> unrooted

Answer 13

1. take away the root branch
2. root node gone
3. shuffle