Week 4: Phylogeography Flashcards
What is phylogeography?
the study of processes that influence the distribution of phylogenetic lineages
- relationship between species, space, and time
What are 3 historical evolutionary processes we might be interested in?
- dispersal
- founder effect
- vicariance
How did glaciation affect salmon phylogeography?
- ice melting made more rivers accessible, salmon slowly moved in (high site fidelity)
What is a pro/con to unipaternally inherited markers in phylogeography?
- simple lineage tracking
- single locus, sensitive to bottlenecks
What is a pro and con of using microsatellites in looking at evolutionary history?
- highly variable (lots of alleles)
- size homoplasy
What is a benefit of SNPs in looking at evolutionary history?
- many de novo markers - high resolution genome-wide
(technical challenges/cost are no longer limiting)
What does having more loci do for a phylogeography study?
shows finer scale evolutionary relationships
How many loci do we need for phylogeographic studies?
- depends on study context
- diminishing returns past 5000 loci
In phylogenetics, how do we use parsimony?
- The most likely phylogeny has the fewest individual mutations
- mutations that occur less often happened more recently
What is a molecular clock?
using sequence divergence to estimate evolutionary time, assuming mutation rates are constant
What are three reasons there is no universal molecular clock?
- different mechanisms of mutation have different rates
- different regions of the genome have different rates
- different species have different mutation rates (life history and generation time)
What is one application of molecular clocks?
- CALIBRATE WITH FOSSIL DATA
- checking if Darwin’s moth and that flower co-evolved – shows that co-evolution might predict species emergence
Name the three types of phylogenetic trees we need to know.
- rooted, scaled tree
- rooted, unscaled tree
- unrooted tree
Which phylogenetic tree displays the timing of divergence?
the scaled rooted tree
What is a distance-based tree?
- tree based on genetic ‘distance’ between taxa
- simplified method using individual sequences
What is a maximum parsimony tree?
- tree with minimum number of evolutionary changes
- assumes constant mutation rate between taxa, works best on closely related taxa
What is a maximum likelihood tree?
- tree that uses a specific evolutionary model to make observed data most probable (complex statistics)
What is a Bayesian phylogenetic tree?
trees made from Bayesian statistical models
For maximum likelihood phylogenetic trees, how are probabilities generated?
BOOTSTRAPPING
What do nodes measure in Bayesian phylogenetic models?
the posterior probabilities the tree is correct
What do phylogenetic trees measure?
lineage sorting
What variation do phylogenetic trees miss?
- fine-scale recent variation (gene specific)
- co-existence of ancestors and descendants
- rejoining of lineages
What is the coalescent?
- how alleles originated from a most recent common ancestor
- mathematical model generates backward lineages to see where alleles ‘coalesce’
- generates HAPLOTYPE NETWORKS
What is a haplotype network?
visible representations of networks of haplotypes
- size = frequency of haplotype
- length = number of mutations
