Phylogenetic tree of species available in the stdpopsim catalog, including the six species we published in the original release (Adrion et al., 2020, in blue), and 15 species that have since been added (in orange). Solid circles indicate species that have one (light grey) or more (dark grey) demographic models and recombination maps. Branch lengths were derived from the divergence times provided by TimeTree5 (Kumar et al., 2022). The horizontal bar below the tree indicates 500 million years (my).

Guidelines for dealing with missing parameters.

For each parameter, we provide a suggested course of action, and mention the main discrepancies between simulated data and real genomic data that could be caused by misspecification of that parameter.

The species parameters and demographic model used for Anopheles gambiae in the stdpopsim catalog. (A) The parameters associated with the genome build and species, including chromosome lengths, average recombination rates (per base per generation), and average mutation rates (per base per generation). (B) A graphical depiction of the demographic model, which consists of a single population whose size changes throughout the past 11,260 generations in 67 time intervals (note the log scale). The width at each point depicts the effective population size (Ne), with the horizontal bar at the bottom indicating the scale for Ne = 106. This figure is adapted from the data on the stdpopsim catalog documentation page (see Data availability) and plotted with POPdemog (Zhou et al., 2018).