Chapter 6 Vocab Flashcards
Summary Statistics
A statistic that reduces complex data to a single value
Genetic Distance
comparing the relatedness of populations or molecules. An increased values equals an increased evolutionary distance.
Molecular distance
A measure of evolutionary change between 2 DNA sequences or haplotypes.
Segregating Sites
The nucleotide sites that are variable within a set of sequences.
Infinite Sites Model
A model of nucleotide diversity each muutation denotes a new allele formed.
Pairwise
A comparison between two entities
Mismatch distribution
The frequency of distribution of pairwise differences between a set of DNA sequences or haplotypes.
Sequence Alignments
Putting 2 sets of sequences next to each other that have come from a common ancestor
Hierarchial Population Structure
absence of random mating within a population accurately representing a meta and sub populations
Principal Component Analysis
A type of multivariant analysis that allows multi-dimensional information to be displayed graphically
Multivariate Analyses
Statistical methods that extract information multi dimensional data.
Branches
Connections between nodes. Shows the relationships between taxa
Taxa
nodes that share a recent common ancestor
Cladogram
realitive recency of common ancestry
Rooted Tree
All taxa have a common ancestor
Unrooted Tree
No common ancestor between taxa
Topology
Structure of a Tree
Clade
An evolutionary branch where it shares a common ancestor
Polytomy
An unresolved 3 (+) branches.
Additive Trees
tree with branch lengths that depict the amount of change
Ultrametric Tree
Tree with branches used to depict evolutionary time
Monophyletic
group of lineages sharing a common ancestor
Paraphyletic
group that shares a common ancestor but does not include all descendents
Polyphyletic
a group of lineages that derive from many common ancestors. Mainly used for recombination
Networks
a tree that represents an evolutionary relationship
Distance Matrix
a table whose elements are distances between categories (often haplotypes or population) arrayed in rows and columns
neighbor joining
A fast method for phylogentic reconstruction.
Maximim likelhood
Best fit tree or graph. Most probable
Maximum Parisomy
Selecting the tree from alternative trees that contain the least amount of steps between generations and taxa
Bootstrap
A method of assessing how well supported an individual clades within a phylogeny
Homoplasy
Did not inherit the character from a common ancestor but is identical to the common ancestor. Identity by state and convergent evolution.
Coalescent Theory
Process estimating parameters of how they evolved. It takes present descendants and finding a common ancestor.
Time to Most Recent Common Ancestor (TMRCA)
The estimated time since a set of sequences in a genealogy most recently shared an ancestor
Gene Genealogy
Use of DNA evidence to determine the genetic relationship between individuals
Mutation Dropping
Placing mutations on branches of trees to determine genetic relationships between individuals
Neutrality tests
genetic varaition that has no effect on fitness
Outlier analysis
Outlying observed value in the extremes of the distribution that can be regarded as significant
Hard Sweep
A selective sweep that a single haplotype increases in frequency due to positive selection
Selective Sweep
A rapid increase in frequecny of an advantagous allele and other variants linked to it
Soft Sweep
A selective seep where positive selection acts on a standing variation
Polygenic adaptation
Positive selection acting on standing variation in multiple variants within different genes
Mc-Donald- Kreitman test
Compares amount of nonsynonymous and synonymous polymorphisms within a species, to the amount between species (humans vs humans) and (human vs chimps) Only one gene!
Hudson-Kreitman-Aguade Test (HKA)
A general form of a test, Compares at 2 or more loci. Compares to neutral allele. Can be genome wide. This test is harder because you need to know what allele is nuetral in order to have a succesful test.
Allele Frequency Spectrum
The spectrum of allele frequencies within a set of sequences
Extended Haplotype Tests
Measures the extent of himozygosity as a measure of haplotype diversity. If positive selection is present diversity over a region will be low (LD is high)
Fluctuating Selection
Short bursts of positive selection and a long period of negative selection
