Terminology and Units

Scope

In general we try to follow the terminology used by msprime when referring to parameters that will be used in setting up and implementing coalescent simulation, such as the per-site per-generation mutation rate, admixture proportions, and diploid effective population sizes.

Terminology

locus: a discrete sequence spanning 1 or more sites which may or may not include intra-locus recombination. Each locus is simulated independently in ipcoal, as if each is a distinct chromosome.

site: a single position on a chromosome/locus. Each simulated site on a locus has a genealogical tree, and one genealogical tree can represent the history for multiple linked sites that represent an interval on a locus between recombination events. Note: A simulated site has a genealogical tree history whether or not mutations/sequences are simulated.

genealogy: the true ancestry of a set of sampled gene copies at some location in the genome. In a simulation framework, the genealogy is known, but in the real world it is an unobservable variable that must be inferred from sequence variation.

gene tree: the inferred ancestry of a set of sampled gene copies at some location in the genome, based on a sequence alignment. In practice, gene trees rarely match the true genealogy exactly since there is often insufficient information (substitutions) within a small genomic region.

species tree: a demographic model describing the topology (ancestral relationships) and demographic parameters (e.g., Ne, divergence times, and admixture events) for one or more lineages.

substitution model: a parameterized Markov model for the mutational process. A mutation causes a change from one discrete state in the mutation model to another. The probability of changes depend on the current state, the per-site per-generation mutation rate ($\mu$), and the length of time over which a substitution can occur, repesented by the edges on a genealogy in units of generations.

Units

genealogical branch lengths: defined in number of generations.

gene tree branch lengths: Depends on the inference method. If using the default ML implementation in raxml-ng then gene tree branch lengths are in units of expected number of substitutions per site.

species tree branch lengths: defined in number of generations. Sometimes must be converted from coalescent units to generations, which requires only dividing by 2N if generation times are constant.

generation: the length of time from birth until reproduction. Under the Wright-Fisher process, which the coalescent approximates, generations do not overlap.

coalescent units: units of species tree branch lengths that describe the probability that n samples coalesce over a length of time. It is calculated as (time in generations) / 2Ne for diploid populations.

mutation rate: the expected number of mutations per site per generation.

recombination rate: the expected number of recombinations per site per generation.

admixture time: a time (absolute) or proportion along an edge (float between 0.0 and 1.0) defining the moment within an overlapping interval of two species tree edges that an admixture event occurred. (For example, if admixture time=0.5, the event happens at the midpoint of the overlap between the two branches).

admixture proportion: the proportion of the source population that migrates to the destination population backwards in time (use visualization and debugging methods to ensure the model is doing what you expect).