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What is phylogeny?
evolutionary history of a group of organisms
what is a phylogenetic tree?
shows ancestor-descendant relationships among populations or species
what is monophyletic group? called anything else?
- called clade/lineage
- -means an ancestor and all of its descendants forms this
Nodes of phylgenetic tree is?
- nodes: branching points
- branches: lines
- topology: branching pattern
what is sister taxa?
two taxa that are more closely related to each other than either is to a 3rd taxon
Monophyletic groups are?
clades that contain all of the descendants and their coommon ancestor
paraphyletic groups are?
do not include all of descendants of an ancestor
what are polyphyletic groups?
contain descendents of more than a single ancestor
what is hard polytomy?
lack of resolution
rooted tree means?
unique path from root
unrooted tree means?
degree of kinship, no evolutionary path
depicts relative recency of common ancestry among taxa
depicts amount of change between taxa along tree branches (# of substitutions)
depicts time of divergence of taxa
Newick (shorthand) format
text based representation of relationships
What is the differ between true and inferred trees?
true tree: actual phylogenetic history of a group, which can only be known in case of simulation studies
inferred tree: phylogenetic hypothesis generated from data from living or fossil organisms
what is the differ between quantitative and qualitative data?
quantitative: continuous data (ie. height/length)
- qualitative: discrete (2 or more values)
- if binary; 2 values
- if multistate, more htan 2 values
what are most molecular data?
- most molecular data are qualitative
- binary: presen/ absence of band, or gap in sequence
- multi state: nucleotide data (A, T, G, C, -)
nucleotide character data.
characters: position in nucleotide sequence
character states: nucleotide at position in nucleotide sequence, or gap
name the steps in phylogenetic analysis
- 1. produce data se- sequence or download sequences
- 2. multiple sequence alighment
- 3. build trees -choose method, run programs
- 4. assess the trees - bootstrapping
what is the most critical step in phylogenetic analysis?
what are the methods of tree reconstruction?
- max. parsimony
- distance method
- max likelihood
- bayesian inference
what is max. parsimony?
gen. scientific criterion for choosing among competing hypotheses that states that we should accept hypothesis that explains the data most simply and efficiently
most likely tree (best hypothesis) - the one with fewest number of change sto explain the data
- uses synapomorphies aone to estab. recent common ancestry
- relies solely on synapomorphies to define monophyletic clades (natural groups)
shared derived character; shared by more than one species or group
derived character that is unique to single species or group (unique derived character)
- non-homologous similarity
- resemblance not due to common ancestry
- evolved independently
what are the strengths and weaknesses of the tree.
- strength: simple, efficient alogrithms, good for morphological data
- weakness: cant correctfor multiple substitutions, long branch attraction
evolutionary distances (# of substitutions) are computed for all pairs of taxa
neighbor joining method, what are the strenghts and weaknesses?
- strengths: fast
- weak: performs poorly with divergent sequences
describe max. likelihood method.
- finds tree that max. prob. of observing the data
- under a given tree and specified model of character state changes
- aim: to find tree (among all possible trees) wtih highest L value
Learn how to calculate likelihood - slide 43. look at book.
strenghts and weakness for likelihood?
- strengths: explicit model of sequence evolution
- weak: computationally damanding
bayes's theorem. look at book
strength and weakness for bayes's theorem
- strength: consistent, efficient, less computationally damanding than ML
- weak: philosophical
trees derived from set of trees and summariez phylogenetic info of several treesi n a single tree
what is the most commonly used consensus tree?
what is strict consensus?
all ocnflucting branching patterns are collapsed
Bootstrap method. look at book.