Phylogenetics Flashcards
Phylogeny
the evolutionary history of a group of organisms (a summary of relatedness among groups)
Phylogenetic Tree
graphical summary of relatedness that describes the pattern among lineages
Taxon
A group of genetically related organisms (populations, species, families, etc)
Clade
a group of taxa derived from a common ancestor
Nodes on a phylogenetic trees are
branching points
What are tips/terminal nodes
the end points of branches where nothing else branches
Time moves from ____ to ___ on a phylogenetic tree
left to right
Polytomy
unresolved branching on a phylogenetic tree
Out-group
the taxon that is indisputably most distantly related to all other members
2 factors that make phenotypic similarity approach bad
convergence and reversals
Convergence is
unrelated groups evolve similar phenotypes independently
Reversals is
related taxa no long share a homologous trait found in a common ancestor (one of both taxa lose the trait)
Homologous trait
one that evolved originally in the same ancestor and were then passed on to all descendant taxa (ex: feathers on birds)
Convergence and reversals together are called
homoplasys
In terms of homoplasy convergence is a _____ and reversal is a _______
convergaence is a phenotypic similarityreversal is a dissimilarity (all among closely related taxa)
What is phenotypic noise
something that increases/decreases phenotypic similarity among taxa (ex: homoplasy)
On a graph of similarity to evolutionary relatedness the ideal slope is ____ and scattered plots are due to _____
1 , homoplasy
Plots above the ideal phone are ____ and plots below are ____
convergence, and reversals
T/F: it is accurate to make P-trees based on p-similarity alone
False- every error prone due to homoplasy
Cladistic analysis is
a more accurate way to draw P-trees
3 major factors needed to construct a phylogeny
1) homologous traits2) minimize homoplasy3) many independently evolving characters (to counter homoplasy “noise” )
2 major characters needed to construct a phylogeny
1) molecular data (DNA, RNA)2) Gross phenotypic data (bones, teeth, behavior)
Synapomorphies
shared derived characters (ex: hooves)
Cladistic Method
Identifies groups based on synapomorphies
The difference between synapomorphy and homologous trait
Homologous trait deals with any characteristic similarity between organisms from a common ancestor; synapomophy is sorta the same except the trait as changed so the ancestor doesnt have the same ones as the descendants
To start a P-tree we need an
out-group
In a P-tree the traits need to be polarized, whats does that mean?
arranged in chronological order.
Phylogenies are _____
hypotheses- the best fit with available data
In making a tree using molecular data, the base sequence used to determine all placement is…
the reference point
The reference point is..
the sequence of the out-group; the sequenced used to base all change
Major problems of producing homoplasy in molecular data are:
reversalsconvergencemultiple hitssaturation(only 4 bases to work with)
Another type of phylogenetic tree is a
genetic distance tree
Each vertical line in a genetic distance tree is…..
a common ancestor
Each horizontal line in a genetic distance tree is…
an evolving lineage
The length of each ___ line is proportional to its ______ from a common ancestor. It determines the number of ______ differences
length, genetic divergence, base pair differences
Using a genetic distance tree on HIV we can see that _____ increases over time and pays out as predicted by the _____ hypothesis
clonal diversity; escape hypothesis
Phylogenomics
Constructing P-trees based on whole genome sequences. (large sequences)
