Prediction and rate

Question 1

describe (a posteriori) analysis

Answer 1

• When a new phylogenetic tree is obtained, characters may be re-examined.
• may reveal important new information
  about the characters and the taxa
• For example, the initial hypothesis of homology of derived character states
  may be re-assessed if those characters exhibit homoplasy. Recall that:
  For a character with n states, the presence of ≥ n - 1 changes on the
  tree signals homoplasy.

Question 1

What is the predictive value of phylogenetic trees

Answer 1

1. phylogenetic trees are hypotheses
2. phylogenetic trees may be used as a
   framework for other studies.
3. Phylogenetic trees may be used to make
   predictions for future discoveries

Question 2

What are examples of characters that independently originated

Answer 2

1. Panda’s thumb in giant panda and red panda
2. Delayed implantation in bears and giant pandas
3. anal scent glands in mustellids and skunks

Question 3

Independent origins of similar traits (homoplasy) may give insight into

Answer 3

the conditions that led to their evolution (the adaptive circumstances under which they evolved)

Question 4

Are fast evolving homoplastic character or slow evolving homoplastic characters more useful for species identification

Answer 4

fast evolving homoplastic characters are more useful
for species identification (so the ones with more parsimony steps in the tree)

Question 5

describe studying character evolution via independent contrasts??

Answer 5

Independent contrasts summarize the amount of character change across each node in the tree, and can be used to estimate the rate of character change across a phylogeny.

Question 6

What is a method of estimating divergence times

Answer 6

• using molecular clocks

Question 7

What is the basis of the clock hypothesis

Answer 7

Molecular changes accumulate at a steady pace - Zuckerkandl and Pauling 1962

• this hypothesis implies that the amount of change accumulated by species since an event of interest could be used to date the event

Question 8

What is the neutral theory of molecular evolution

Answer 8

suggests that most nucleotide substitutions
and replacements in amino acid sequences
are neutral with respect to fitness.
Many of them are so-called silent-site
substitutions, mostly at the third codon
position; other substitutions are simply not
in coding regions of DNA.

If true, genetic drift should dominate at the
molecular level, and substitution rates
should approach the mutation rate.

Question 9

What is the typical values for substitution rates for mtDNA sequence divergence per million years

Answer 9

1-2%

–> such estimates depend on knowing the age of speciation events, either based on the fossil record or on the estimated age of major geological events

Question 10

For rates of sequence divergence, how does calibration using fossils work

Answer 10

• Uses the earliest reliable fossil records of a clade.
• The age of the fossil gives the minimum age of the clade.
• Allows upper bound to an estimate of rate of sequence divergence.
• The sister group of the clade should
  have the same minimum age.
• Some clades have a‘ghost lineage’
  prior to their first appearance in the
  fossil record. The ‘ghost lineage’ is
  inferred from the older fossils of their
  sister group, and is another predictive
  application of a phylogeny

Question 11

What is a major problem for molecular clocks

Answer 11

• groups do not always evolve at the same rate. If they did then branch lengths would be equal

–> one solution: apply methods that accommodate variation
in rates; e.g., ‘heterogeneous model’
or
“relaxed clocks”