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Geonomics: Forward-time, spatially explicit, and arbitrarily complex landscape genomic simulations
Published in Molecular Biology and Evolution, 2022
Understanding the drivers of spatial patterns of genomic diversity has emerged as a major goal of evolutionary genetics. The flexibility of forward-time simulation makes it especially valuable for these efforts, allowing for the simulation of arbitrarily complex scenarios in a way that mimics how real populations evolve. Here, we present Geonomics, a Python package for performing complex, spatially explicit, landscape genomic simulations with full spatial pedigrees that dramatically reduces user workload yet remains customizable and extensible because it is embedded within a popular, general-purpose language. We show that Geonomics results are consistent with expectations for a variety of validation tests based on classic models in population genetics and then demonstrate its utility and flexibility with a trio of more complex simulation scenarios that feature polygenic selection, selection on multiple traits, simulation on complex landscapes, and nonstationary environmental change. We then discuss runtime, which is primarily sensitive to landscape raster size, memory usage, which is primarily sensitive to maximum population size and recombination rate, and other caveats related to the model’s methods for approximating recombination and movement. Taken together, our tests and demonstrations show that Geonomics provides an efficient and robust platform for population genomic simulations that capture complex spatial and evolutionary dynamics.
Recommended citation: Terasaki Hart, D. E., Bishop, A. P., & Wang, I. J. (2021). "Geonomics: forward-time, spatially explicit, and arbitrarily complex landscape genomic simulations." Molecular Biology and Evolution, 38(10), 4634-4646.
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teaching
2014 Spring Teaching 1
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title: “Climate Change and the Future of California” collection: teaching type: “Undergraduate course” permalink: /teaching/CCFC venue: “University of California, Berkeley, Dept. of Environmental Science, Policy, & Management” date: 2018-01-15 location: “Berkeley, CA, USA”
Teaching experience 2
Workshop, University 1, Department, 2015
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