Phylogeny 1

Question 1

what are the levels we see in nature (4)

Answer 1

• individuals organisms with variation in phenotype and genotype
• individuals come together to form an interbreeding population
• multiple populations with occasional genetic exchange form a species
• there are multiple species with their own populations with different phenotypes and genotypes

Question 2

phylogeny (2)

Answer 2

• genetic history of life and genetic descent, including genes, genomes and species
• it broadly and approximately takes the form of a tree of branching lineages where species lineages descend, speciate, and go extinct

Question 3

what does the branching point on a phylogeny tree represent

Answer 3

• a speciation event

Question 4

what do phylogeny trees tell us (4)

Answer 4

• tells a story of species lineages descending and dividing through time
• it shows ancestral lines
• it shows relationships and implies how closely related species are
• it shows clades within clades/classification

Question 5

most recent common ancestor (2)

• abbreviation
• definition

Answer 5

• MRCA

- the ancestor that is most recent and common between two groups of organisms

Question 6

monophyletic group

Answer 6

• a clade that includes an ancestor and all of its descendants

Question 7

sister groups

Answer 7

• pairs of closest relatives; the tips of the MCRA

Question 8

why is it common to show mammals at the far right or far bottom of phylogenetic trees?

Answer 8

• mammals are the greatest focus of our attention and it is easiest to tell our story if we draw the tree with ourselves at the right or bottom

Question 9

what does the left to right sequence or top to bottom sequence mean in a phylogenetic tree?

Answer 9

• nothing, not advancement or recency

- each branch point is symmetrical

Question 10

how do biologists reconstruct phylogeny (4)

Answer 10

• synapomorphy
• parsimony
• likelihood
• bootstrap

Question 11

derived trait

Answer 11

• mutations that are new within any given group

Question 12

synapomorphy (2)

Answer 12

• a traits that is shared AND derived within a group

- can be used as evidence for monophyly

Question 13

parsimony (2)

Answer 13

• the simplest explanation that can explain the data is to be preferred; the tree with the fewest number of character changes is likely the right one
• minimizes changes

Question 14

outgroup (2)

Answer 14

• a separate, but related group to the group that we are studying
• information about this group can root the phylogenetic tree

Question 15

root of the tree

Answer 15

• sets the direction of time

- difficult to determine when data from outgroups are unavailable

Question 16

model

Answer 16

• simplified machine that is thought to behave similarly to the real world to predict expected observations

Question 17

statistical methods and phylogeny trees (2)

Answer 17

• simulate nucleotide patterns on a hypothesized tree given actual observed data
• calculate the probability that observed nucleotide patterns would have evolved if the hypothetical tree was true

Question 18

what is the “likelihood of the tree” (3)

Answer 18

• prob(observed | this tree)
• can be used to evaluate different trees to decide which is the better hypothesis tree
• maximizes likelihood

Question 19

what is the recipe for reconstructing phylogeny?

Answer 19

1. examine possible hypotheses (trees)
2. assess each against the observations
3. choose the tree that best satisfies your criterion

Question 20

how do we put error bars or confidence limits on a phylogenetic tree

Answer 20

• with familiar statistics: the higher the variance, the lower the confidence

Question 21

bootstrapping

Answer 21

• one method to measure “variance” in phylogenetic data; steps:
  1. randomly sample the data getting a “resampled matrix” and use that resample to infer a tree by redoing analysis
  2. repeat many times and see how similar the trees are
  3. if the data has low variance, each sample will yield the same tree and we will have confidence in our inferred clades