Phylogenetics (More Complicated) Flashcards
(19 cards)
why are we doing all this again
phylogenetics has a ton of ambiguities that we want to resolve
what can we include in phylogenies
extant organisms DNA, morphology, and sometimes we can experiment with them
fossil record
synapomorphies
derived traits evolved only once, and define a shared ancestor and monophyletic group
ex. wings on insects
homoplasies
traits that look like synapomorphies, but are not monophyletic
evolutionary reversal
multiple losses of a recently derived trait
a single nucleotide substitution is an easily reversed trait
convergent evolution
independent origins of a superficially shared trait
ex. bipedalism in birds and humans
incomplete lineage sorting
multiple alleles are maintained in sister lineages, and randomly lost in non-monophyletic patterns, a.k.a we say what we want about species but the alleles are gonna go where they want, and die out when they want to
incomplete lineage sorting is especially common during
rapid genetic diversification
maximum parsimony
can help resolve ambiguous phylogenies
distinguishing synapomorphy from homoplasy
use more data!! more traits, genes, and species
speed of gene evolution/distance of species to use may be based on the age of the tree
extremely long branches are
hard to resolve due to a build-up of homoplasies
maximum likelihood method for tree building
allows for different substitution rates (depending on nucleotides, and codon positions) and evolutionary reversal
Bayesian inference method for tree building
similar to maximum likelihood and also allows input of prior info i.e. the fossil record
why use advanced methods?
more realistic models of evolution, based on substitution rates
can generate estimations for branch lengths
trees can include statistical support for each node, i.e. how confident we are about it - adds nuance
bootstrapping
used in maximum parsimony
randomly discard some of the data, re-estimate the phylogeny, and do it over and over again to gain confidence
introgression
alleles from one species mix into another species, through hybridization and horizontal gene transfer
making phylogenies with introgressions
look at how gene trees are physically related to each other on the chromosome
sweeps - example
stickleback populations can be high-plated (ancestral) or low-plated (only aquatic)
the phylogenetic tree would look different if a mutation causing low-plating did a sweep through the population vs. persisted at low frequency in the standing genetic variation
gene trees show the second option is true - the mutation sequence is the same wherever it arises, showing it is the same mutation just changing in frequency
reasons to reconstruct evolutionary history
- how we got to our current extant species
- source of infectious disease outbreaks
- convergent evolution -> which traits are more likely to be adaptive
- co-evolution can show important biological interactions (ex. XY sex determination is consistently correlated with female-biased sex ratio)
