Demes: A standard format for demographic models

Graham Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin R. Thornton

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field. In particular, the important task of translating the model descriptions in published work into input suitable for population genetic simulators is labor intensive and error prone. We propose the Demes data model and file format, built on widely used technologies, to alleviate these issues. Demes provide a well-defined and unambiguous model of populations and their properties that is straightforward to implement in software, and a text file format that is designed for simplicity and clarity. We provide thoroughly tested implementations of Demes parsers in multiple languages including Python and C, and showcase initial support in several simulators and inference methods. An introduction to the file format and a detailed specification are available at https://popsim-consortium.github.io/demes-spec-docs/.

Original languageEnglish (US)
Article numberiyac131
JournalGenetics
Volume222
Issue number3
DOIs
StatePublished - Nov 2022

Keywords

  • demographic models
  • inference
  • simulation

ASJC Scopus subject areas

  • General Medicine

Fingerprint

Dive into the research topics of 'Demes: A standard format for demographic models'. Together they form a unique fingerprint.

Cite this