Table 1:

Glossary

Term	Explanation
Allele frequency spectrum	The distribution of polymorphisms which occur in given numbers of copies in the sample.
Ancestral recombination graph	A way to represent and model recombination events in a coalescent tree. A recombination event corresponds to a split of a lineage (when looking backward in time), where the ‘chromosome’ or the currently considered segment is split into a left and right subsegment. From this event onward (i.e. further backward in time) the two sub-segments have their own evolutionary history.
Balancing selection	A form of natural or artificial selection that favors the long-term maintenance of polymorphisms, of multiple alleles or haplotypes
Coalescent simulation	A method of simulating the genetic variability observable in a sample of genes or ‘chromosomes’. The coalescent is a binary tree where nodes represent the merger of ancestral lineages (i.e. edges, the length of which is proportional to time). Mutations occur according to a Poisson distribution ‘along the edges’. Any mutational event changes the ground state (wild-type allele) of some new site in all chromosomes which belong to the subtree under the current edge.
Demography	Generic term referring to any change of population size or population structure (panmictic or subpopulations with or without migration) in the evolutionary history of a population or species.
Directional selection	A form of natural or artificial selection that favors a single allele, haplotype or genotype.
Forward-in-time simulation	Type of computer simulation where the simulation runs from one (historical) generation to the next in natural direction of time
Generalized coalescent	Coalescent with nodes of degree k ≥ 3.
Heterozygosity	The probability that a pair of homologous alleles is nonidentical (neither by descent nor by state).
Hitchhiking mapping	Procedure by which the mutations which are causative for an adaptive phenotypic change are mapped to specific regions in the genome by examining features of the chromosomal profile of genetic diversity.
Linkage disequilibrium	The nonrandom association of alleles at two (or more) linked loci.
Random binary tree	A directed, acyclic graph with vertices of degree three. Randomness refers to the random merger of edges (or arbitrary labeling).
Recessive beneficial mutation	In diploid organisms: the mutation has a selective advantage only if it occurs in homozygous state
Selective sweep	The rapid fixation of an advantageous allele in a population and the concomitant reduction of genetic diversity.
Soft sweep	Selective sweep from standing variation; i.e. the advantageous allele is not introduced as a single copy at the onset of the sweep but present in multiple copies.
Tajima's D	A summary statistic based on the number of polymorphisms observable in a sample of (homologous) sequences and the average number of differences in pairwise comparisons from this sample. Under neutrality and constant population size this statistic is expected to be zero. Deviations from zero are expected under nonneutral evolution and/or demographic changes.
Time reversibility	Property of many quantities occurring in evolutionary studies. In particular, equilibria, for instance the mutation-drift equilibrium, in neutrally evolving populations can be obtained by considering the evolutionary process forward in time or backward in time.
Wright–Fisher model	Mathematical model to describe the change of allele frequencies from one generation to the next. Typical evolutionary forces which change allele frequencies include selection, mutation and genetic drift. While the change in allele frequency induced by the former two is modeled deterministically, the change due to drift is modeled by binomial (in case of two alleles) or multinomial (in case of multiple alleles) sampling.