Phylogeny 1 Flashcards
what are the levels we see in nature (4)
- 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
phylogeny (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
what does the branching point on a phylogeny tree represent
- a speciation event
what do phylogeny trees tell us (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
most recent common ancestor (2)
- abbreviation
- definition
- MRCA
- the ancestor that is most recent and common between two groups of organisms
monophyletic group
- a clade that includes an ancestor and all of its descendants
sister groups
- pairs of closest relatives; the tips of the MCRA
why is it common to show mammals at the far right or far bottom of phylogenetic trees?
- 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
what does the left to right sequence or top to bottom sequence mean in a phylogenetic tree?
- nothing, not advancement or recency
- each branch point is symmetrical
how do biologists reconstruct phylogeny (4)
- synapomorphy
- parsimony
- likelihood
- bootstrap
derived trait
- mutations that are new within any given group
synapomorphy (2)
- a traits that is shared AND derived within a group
- can be used as evidence for monophyly
parsimony (2)
- 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
outgroup (2)
- a separate, but related group to the group that we are studying
- information about this group can root the phylogenetic tree
root of the tree
- sets the direction of time
- difficult to determine when data from outgroups are unavailable
model
- simplified machine that is thought to behave similarly to the real world to predict expected observations
statistical methods and phylogeny trees (2)
- 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
what is the “likelihood of the tree” (3)
- prob(observed | this tree)
- can be used to evaluate different trees to decide which is the better hypothesis tree
- maximizes likelihood
what is the recipe for reconstructing phylogeny?
- examine possible hypotheses (trees)
- assess each against the observations
- choose the tree that best satisfies your criterion
how do we put error bars or confidence limits on a phylogenetic tree
- with familiar statistics: the higher the variance, the lower the confidence
bootstrapping
- 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
