Lecture 19

Question 1

Outgroup

Answer 1

• lacks all characters that are seen in other branches

- character state is 0

Question 2

Parsimony (2 concepts)

Answer 2

• methodological

- ontological

Question 3

Methodological Parsimony

Answer 3

• Ockham’s Razor

- best hypothesis is simplest i.e. makes fewest assumptions

Question 4

Ontological Parsimony

Answer 4

• nature prefers the simplest course of evolution (not necessarily true; what if nature doesn’t always prefer the fewest number of changes? homoplasies do exist-computers let you know how many exist in each tree)
• thus the best tree requires the fewest changes i.e. the fewest homoplasies

Question 5

Determining proper tree

Answer 5

• add more characters
• the longer the think is the less likely it is to be right
• want fewest number of informative steps
• want to find tree with shortest length, and reduce number of homoplasies

Question 6

Automorphy

Answer 6

• only present in one clade
• not informative
• not used in analysis at end
• homoplasy on these trees is a characteristic that arises twice

Question 7

Molecular Sequences

Answer 7

• loses relationship with extinct things but gains ability to see relationship between very different organisms like ears of corn or mushrooms as opposed to doing it morphologically
• genes don’t care about morphology
• don’t have to have any morphological characters in common to get relatedness

Question 8

Parsimony in Cladistics

Answer 8

• use only synaptomorphies
• character present in only one lineage not used in cladistics
• lose some data when you do it cladistically
• will use different data set depending on what method of analysis you use

Question 9

Why is there so much homoplasy in molecular data than in morphological data?

Answer 9

• mutation doesn’t always cause a morphological change
• more fundamental reason: only four possible bases for each position so you need a lot of sequence when you’re using this method because the homoplasy rate is so high

Question 10

How many bp in human genome?

Answer 10

-3 billion

Question 11

How do you estimate divergence times?

Answer 11

-fossil record

Question 12

Unrooted Tree

Answer 12

• don’t know topology of relationships seen in the data

- used to give you a rather large scale map

Question 13

Ordering States of Features for Analysis

Answer 13

1. select features
2. decide what are primitive and derived states for each feature
3. generate data set
4. application to cladogram inference

Question 14

Polarity Assignment

Answer 14

• Has to be determined empirically, as in examples; fossil data can help
• states can be assigned numbers for easy analysis
• e.g. 0 for primitive state, 1 for derived. If a second derived state exists can be called 2.
• with that, a table of taxa and character states can be prepared

Question 15

When Building a Simple Cladogram

Answer 15

• 0 means trait is absent 1 means trait is present

- computer doesn’t build a tree from the data it matches the data to all possible trees

Question 16

Inferring Trees

Answer 16

• Number of taxa and characters increases the complexity

- with number of taxa, number of possible trees increases fast

Question 17

Phylogenetic Methods Used on Gene Sequence Data

Answer 17

• lots of data
• need homologous genes from different taxa e.g. ribosomal genes-universal
• evolves by substitution of bases
• first step sequence genes
• second step align gene sequence from taxa
• third step apply tree algorithms can use a few distinct methods

Question 18

Methods of Alignment and Inference

Answer 18

• Distance: use all differences
• Parsimony: use only synapomorphy (cladistic)
• look at picture in notes

Question 19

Phylogenetic Trees

Answer 19

• not all are cladograms
• in molecular phylogeny what are called “distance trees” also are used
• branch length scan differ (a reflection of evolutionary rate along the branch)
• evolution of genes does not necessarily have a uniform rate

Question 20

Value of DNA Sequence Phylogeny

Answer 20

• huge amount of data
• can bridge taxa that share no morphology
• can estimate divergence times

Question 21

Are fossils necessary for phylogeny?

Answer 21

• fossils rarely yield DNA, so have almost no record of extinct genomes
• fossils also don’t contain as much morphology as live organisms
• however phylogenies made exclusively from life organisms or from DNA lack any trace of extinct lineages
• this means that extinc experiments not related to living forms are lost
• it also means that transitional and basal taxa that would tell us about evolution of major new features is lost
• fossils also give us the crucial dimension of time
• there are lineages that lack any fossil record. For phylogenies can only be built from live organisms
• Finally, DNA phylogenies offer a feature not available in any other way. That is relating completely unlike organisms into a tree