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

作者：M. Elise Lauterbur, Maria Izabel A. Cavassim, Ariella Gladstein, Graham Gower, Nathaniel S. Pope, Georgia Tsambos, Jeff Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C. Haller, Ahmed Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obšteter, Vitor Antonio Corrêa Pavinato, Alice Pearson, David Peede, Manolo F. Perez, Murillo F. Rodrigues, Chris C. R. Smith, Jeffrey P. Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vázquez, Ryan K. Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A. Cartwright, Gregor Gorjanc, Ryan N. Gutenkunst, Jerome Kelleher, Andrew D. Kern, Aaron P. Ragsdale, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2022 · DOI：10.1101/2022.10.29.514266 · 被引用次数：10 · 研究领域：Evolution and Genetic Dynamics、Genomics and Phylogenetic Studies、Genetic Mapping and Diversity in Plants and Animals

Abstract Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of s...