Phylogenetics Midterm Flashcards
Character
any feature of an organism that can be defined by its states
Homoplasy
A character that transitions into and out of a given state on a phylogeny (due to being under strong selection, etc.)
Synapomorphy
A shared, derived character
Plesiomorphy
The ancestral character state for a particular clade
Apomorphy
A specialized of derived character state
Autapomorphy
A derived character state that is restricted to one taxon in a particular data set
Polyphyletic group
A type of non-monophyletic group in which the group does not include the most recent common ancestor of all members of that group
Paraphyletic
A type of non-monophyletic group that contains the most recent common ancestor byt not all descendants of that ancestor
Differences between phylogram, chronograph, cladogram
phylogram - proportional branch lengths.
chrono - scaled with time
clado - just relatedness
2 main things make a phylogenetic tree
Direction and Acyclic (unidirectional)
What is MAXIMUM PARSIMONY
Minimize the number of character state transitions needed to explain the data.
Tree with the smallest number of changes (fewest steps, shortest tree) is favored
What’s an examples of parsimony INFORMATIVE
Autapomorphies. Nothing else has them
Explain the CONSISTENCY INDEX (CI)
Number of character states -1 divided by number of state changes on the tree
Be able to write in Newick format and then draw tree from it
n/a
What is it called when all tips are extant?
Ultrametric
Issues with parsimony
- The probability of novel mutations on particularly long branches may draw them together (analogous)
- When they are long enough, adding more data will only push toward the wrong answer more often (balance)
Steps of a Heuristic search
- Stepwise addition. make a tree
- swap branches, in various way and at various points.
- repeat multiple starting points
- shortest tree is winner
What are “islands” in this context?
local optimas
How to avoid local optimas
continued swapping, explore other tree space, additions
Indel
insertions or deletions in the genetic code of an individual(s)
Jukes and Cantor Nucleotide Substitution Model
All substitutions occur at the same rate,
Define MAXIMUM LIKELIHOOD
Finding a tree that has the highest probability of giving rise to the observed data
Steps to get MAXIMUM LIKELIHOOD
- make a tree
- Determine the likelihood of each site
- Likelihoods of each site in the matrix are multiplied
- The program optimizes parameters and branch lengths by repeating prior steps to find the where the likelihood is maximized
- Tree space is searched to find the maximum likelihood tree
What’s bootstrapping?
Randomly resampling characters / columns with replacement to get a population of the same size
Non-parametic bootstrapping
- Get your best tree
- Randomize reweigh characters
- Repeat 10,000 times
- Make a new best tree
- Get majority rule/strict consensus trees
Steps in Bayesian Markov chain monte carlo (MCMC)
- Set Priors
- Propose a tree and set of parameters
- Calculate the likelihood of the tree
- Calculate the acceptance ratio (incorporating Hastings ratio)
- If ratio is 1.0, accept the move
- If ratio is < 1.0, accept the move with a probability equal to the acceptance ratio
Run chain until stationarity is reached - Begin recording sampled values with a given frequency (eg every 1000 steps) to build up an estimate of the posterior
- AT THE END - summarize the post-burnin trees and parameters, this set represents your posterior distribution.
Results of MCMC, heuristic search, and boostrapping
MCMC- collection of trees sampled from the posterior probability distribution
Huer - best tree and associated parameter estimates
Boot - Estimated confidence in each node
Fossils are often treated as the ______ stem age
minimum
Penalized likelihood
basically cuts computing time down.
3 claims must be made about stated fossils
- age
- diagnosis
- stem or crown calibrated
3 types of molecular clocks. list and define.
Strict- fewer parameters bc only the internal branches are free to vary in length, but not the tips
Correlated relaxed - Rates vary continuously across the tree, and are inherited from their ancestral branches
Uncorrelated relaxed - Rates vary continuously across the tree, but there is no autocorrelation of rates
What is meant by “lineage birth” and “lineage death”?
birth - speciation event
death - extinction
What are ghost lineages?
Nodes that are “hidden” by extinction
Evidence morphologically or even molecularly, but no physical evidence
Diversification ________ through time
decreases
2 approaches to understanding rate evolution
- BAMM -> rates are generally constant, and only rarely jump to new, possibly quite different, values
- ClaDS -> Rates change frequently, but the magnitude of change from ancestral values is constrained by a probability distribution
Draw an apopmorphy
na
Draw a homoplasy
na
Draw an autapomorphy
na
Draw a plesiomorphic triait
na
draw a monphyletic group
na
