Terms and Formulas

• mutation
• the alteration of a DNA sequence to produce a different form than the original

• random genetic drift/population size
• the random fluctuation in allele frequencies from generation to generation caused by chance events, such as sampling errors due to small population size, founder events and bottlenecks; population size specifies how fast genetic drift acts

effective population size

• migration/gene flow
• the movement of individuals or genes among populations; specifies the substructure and exchange rates of individuals among populations

• natural selection
• differential reproduction of different members of a species due to the variability in fitness among individuals or genotypes, leading to changes in allele frequencies over time

• real time
• measured in years

• coalescent time
• This is the generation time (τ) scaled by the population size (Ne), and is measured in units of generations/(individual/population) and is the average coalescent time for two lineages

generation time

If T is given as the TMRCA in the coalescent then the formula is T=t/Ne

If T is given as sequence divergence, then the formula is t=T/µ

• Pairwise nucleotide diversity (pi)
• estimate calculates the average genetic difference between all possible pairs of individuals within a population, providing a measure of the overall genetic variation within that group.

• sequence divergence
• defined by the proportion of nucleotide difference (p) between any two sequences (e.g., between an outgroup and ingroup sequence)

• fixation index
• the index of population differentiation do to genetic structure

average heterozygosity (genetic variation) among subpopulations

Average heterozygosity in the total population, regardless of locality from which they were drawn

• F_ST = 1 - (H_S/H_T)
• F_ST= 1/ (4 N_m +1)

• Hudson's test statistic for the null hypothesis that two sub-populations are not genetically differentiated.
• Uses sequence data

K_ST = 1 - (K_S/K_T)

The average number of differences between sequences within subpopulations

The average number of differences between sequences in the total population, regardless of the locality from where they were drawn

• d= k− s / 1+1/2+1/3+⋯+1n−1
• k is the average number of pairwise differences.
• s is the number of segregating sites.
• n is number of sequences being analyzed
• Taijima's D

Expected real time given expected population (Ne) and sample size (n)

• I_A = (V_o/Ve)-1
• Index of association
• if the individual is fully recombining, every locus is independent from each other

• Index of association
• Any value of I_A > 0 is some measure of clonality
• V_o is observed variance of the number of differences between two individuals over all loci
• V_e is expected sum of variance of the number of loci at which two individuals differ