Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson AZ 85719, USA
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles CA, USA
Embark Veterinary, Inc., Boston MA 02111, USA
Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
Institute of Ecology and Evolution, University of Oregon, Eugene OR 97402, USA
School of Mathematics and Statistics, University of Melbourne, Australia
AncestryDNA, San Francisco CA 94107, USA
54Gene, Inc., Washington DC 20005, USA
Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, UMR 9015 Orsay, France
School of Life Sciences, University of Glasgow, Glasgow, UK
Department of Computational Biology, Cornell University, Ithaca NY, USA
Department of Cell and Systems Biology, University of Toronto, Toronto ON, Canada
Department of Biology, University of Toronto Mississauga, Mississauga ON, Canada
Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Computer Technologies Laboratory, ITMO University, St Petersburg, Russia
Agricultural Institute of Slovenia, Department of Animal Science, Ljubljana, Slovenia
Entomology Department, The Ohio State University, Wooster OH, USA
Department of Genetics, University of Cambridge, Cambridge, UK
Department of Zoology, University of Cambridge, Cambridge, UK
Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence RI, USA
Center for Computational Molecular Biology, Brown University, Providence RI, USA
Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos 13565905, Brazil
Department of Genetics, Stanford University School of Medicine, Stanford CA 94305, USA
Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, SE-752 37 Uppsala, Sweden
Department of Integrative Biology, University of California, Berkeley, Berkeley CA, USA
Department of Biostatistics, University of Washington, Seattle WA, USA
Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
Cluster of Excellence - Controlling Microbes to Fight Infections, Eberhard Karls Universität Tübingen, Tübingen, Baden-Württemberg, Germany
School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe AZ, USA
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
Department of Molecular and Cellular Biology, University of Arizona, Tucson AZ 85721, USA
Department of Integrative Biology, University of Wisconsin-Madison, Madison WI, USA
Department of Mathematics, University of Oregon, Eugene OR 97402, USA
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC 27599, USA
Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel

Figures and data

Phylogenetic tree of species available in the stdpopsim catalog, including the six species we published in the original release (Adrion et al., 2020 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 (*N_e*), with the horizontal bar at the bottom indicating the scale for *N_e* = 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).

Figures and data

Guidelines for dealing with missing parameters.