Chapter 6 Vocab

Question 1

Summary Statistics

Answer 1

A statistic that reduces complex data to a single value

Question 2

Genetic Distance

Answer 2

comparing the relatedness of populations or molecules. An increased values equals an increased evolutionary distance.

Question 3

Molecular distance

Answer 3

A measure of evolutionary change between 2 DNA sequences or haplotypes.

Question 4

Segregating Sites

Answer 4

The nucleotide sites that are variable within a set of sequences.

Question 5

Infinite Sites Model

Answer 5

A model of nucleotide diversity each muutation denotes a new allele formed.

Question 6

Pairwise

Answer 6

A comparison between two entities

Question 7

Mismatch distribution

Answer 7

The frequency of distribution of pairwise differences between a set of DNA sequences or haplotypes.

Question 8

Sequence Alignments

Answer 8

Putting 2 sets of sequences next to each other that have come from a common ancestor

Question 9

Hierarchial Population Structure

Answer 9

absence of random mating within a population accurately representing a meta and sub populations

Question 10

Principal Component Analysis

Answer 10

A type of multivariant analysis that allows multi-dimensional information to be displayed graphically

Question 11

Multivariate Analyses

Answer 11

Statistical methods that extract information multi dimensional data.

Question 12

Branches

Answer 12

Connections between nodes. Shows the relationships between taxa

Question 13

Taxa

Answer 13

nodes that share a recent common ancestor

Question 14

Cladogram

Answer 14

realitive recency of common ancestry

Question 15

Rooted Tree

Answer 15

All taxa have a common ancestor

Question 16

Unrooted Tree

Answer 16

No common ancestor between taxa

Question 17

Topology

Answer 17

Structure of a Tree

Question 18

Clade

Answer 18

An evolutionary branch where it shares a common ancestor

Question 19

Polytomy

Answer 19

An unresolved 3 (+) branches.

Question 20

Additive Trees

Answer 20

tree with branch lengths that depict the amount of change

Question 21

Ultrametric Tree

Answer 21

Tree with branches used to depict evolutionary time

Question 22

Monophyletic

Answer 22

group of lineages sharing a common ancestor

Question 23

Paraphyletic

Answer 23

group that shares a common ancestor but does not include all descendents

Question 24

Polyphyletic

Answer 24

a group of lineages that derive from many common ancestors. Mainly used for recombination

Question 25

Networks

Answer 25

a tree that represents an evolutionary relationship

Question 26

Distance Matrix

Answer 26

a table whose elements are distances between categories (often haplotypes or population) arrayed in rows and columns

Question 27

neighbor joining

Answer 27

A fast method for phylogentic reconstruction.

Question 28

Maximim likelhood

Answer 28

Best fit tree or graph. Most probable

Question 29

Maximum Parisomy

Answer 29

Selecting the tree from alternative trees that contain the least amount of steps between generations and taxa

Question 30

Bootstrap

Answer 30

A method of assessing how well supported an individual clades within a phylogeny

Question 31

Homoplasy

Answer 31

Did not inherit the character from a common ancestor but is identical to the common ancestor. Identity by state and convergent evolution.

Question 32

Coalescent Theory

Answer 32

Process estimating parameters of how they evolved. It takes present descendants and finding a common ancestor.

Question 33

Time to Most Recent Common Ancestor (TMRCA)

Answer 33

The estimated time since a set of sequences in a genealogy most recently shared an ancestor

Question 34

Gene Genealogy

Answer 34

Use of DNA evidence to determine the genetic relationship between individuals

Question 35

Mutation Dropping

Answer 35

Placing mutations on branches of trees to determine genetic relationships between individuals

Question 36

Neutrality tests

Answer 36

genetic varaition that has no effect on fitness

Question 37

Outlier analysis

Answer 37

Outlying observed value in the extremes of the distribution that can be regarded as significant

Question 38

Hard Sweep

Answer 38

A selective sweep that a single haplotype increases in frequency due to positive selection

Question 39

Selective Sweep

Answer 39

A rapid increase in frequecny of an advantagous allele and other variants linked to it

Question 40

Soft Sweep

Answer 40

A selective seep where positive selection acts on a standing variation

Question 41

Polygenic adaptation

Answer 41

Positive selection acting on standing variation in multiple variants within different genes

Question 42

Mc-Donald- Kreitman test

Answer 42

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!

Question 43

Hudson-Kreitman-Aguade Test (HKA)

Answer 43

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.

Question 44

Allele Frequency Spectrum

Answer 44

The spectrum of allele frequencies within a set of sequences

Question 45

Extended Haplotype Tests

Answer 45

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)

Question 46

Fluctuating Selection

Answer 46

Short bursts of positive selection and a long period of negative selection