Lecture 19 Flashcards
Outgroup
- lacks all characters that are seen in other branches
- character state is 0
Parsimony (2 concepts)
- methodological
- ontological
Methodological Parsimony
- Ockham’s Razor
- best hypothesis is simplest i.e. makes fewest assumptions
Ontological Parsimony
- 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
Determining proper tree
- 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
Automorphy
- only present in one clade
- not informative
- not used in analysis at end
- homoplasy on these trees is a characteristic that arises twice
Molecular Sequences
- 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
Parsimony in Cladistics
- 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
Why is there so much homoplasy in molecular data than in morphological data?
- 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
How many bp in human genome?
-3 billion
How do you estimate divergence times?
-fossil record
Unrooted Tree
- don’t know topology of relationships seen in the data
- used to give you a rather large scale map
Ordering States of Features for Analysis
- select features
- decide what are primitive and derived states for each feature
- generate data set
- application to cladogram inference
Polarity Assignment
- 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
When Building a Simple Cladogram
- 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
Inferring Trees
- Number of taxa and characters increases the complexity
- with number of taxa, number of possible trees increases fast
Phylogenetic Methods Used on Gene Sequence Data
- 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
Methods of Alignment and Inference
- Distance: use all differences
- Parsimony: use only synapomorphy (cladistic)
- look at picture in notes
Phylogenetic Trees
- 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
Value of DNA Sequence Phylogeny
- huge amount of data
- can bridge taxa that share no morphology
- can estimate divergence times
Are fossils necessary for phylogeny?
- 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
