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

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

Lauterbur, M. Elise (författare): Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA

Cavassim, Maria Izabel A. (författare): Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA

Gladstein, Ariella L. (författare): Embark Vet Inc, Boston, MA USA

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Gower, Graham (författare): Univ Copenhagen, Globe Inst, Sect Mol Ecol & Evolut, Copenhagen, Denmark

Pope, Nathaniel S. (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Tsambos, Georgia (författare): Univ Melbourne, Sch Math & Stat, Melbourne, Australia

Adrion, Jeffrey (författare): Ancestry DNA, San Francisco, CA USA

Belsare, Saurabh (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Biddanda, Arjun (författare): 54Gene Inc, Washington, DC USA

Caudill, Victoria (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Cury, Jean (författare): Univ Paris Saclay, CNRS, INRIA, Lab Interdisciplinaire Sci Numer, Orsay, France

Echevarria, Ignacio (författare): Univ Glasgow, Sch Life Sci, Glasgow, Scotland

Haller, Benjamin C. (författare): Cornell Univ, Dept Computat Biol, Ithaca, NY USA

Hasan, Ahmed R. (författare): Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada.;Univ Toronto Mississauga, Dept Biol, Mississauga, ON, Canada

Huang, Xin (författare): Univ Vienna, Dept Evolutionary Anthropol, Vienna, Austria.;Univ Vienna, Human Evolut & Archaeol Sci HEAS, Vienna, Austria

Iasi, Leonardo Nicola Martin (författare): Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany

Noskova, Ekaterina (författare): ITMO Univ, Comp Technol Lab, St Petersburg, Russia

Obsteter, Jana (författare): Agr Inst Slovenia, Dept Anim Sci, Ljubljana, Slovenia

Pavinato, Vitor Antonio Correa (författare): Ohio State Univ, Entomol Dept, Wooster, OH USA

Pearson, Alice (författare): Univ Cambridge, Dept Genet, Cambridge, England.;Univ Cambridge, Dept Zool, Cambridge, England

Peede, David (författare): Brown Univ, Dept Ecol Evolut & Organismal Biol, Providence, RI USA.;Brown Univ, Ctr Computat Mol Biol, Providence, RI USA

Perez, Manolo F. (författare): Univ Fed Sao Carlos, Dept Genet & Evolut, Sao Carlos, Brazil

Rodrigues, Murillo F. (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Smith, Chris C. R. (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Spence, Jeffrey P. (författare): Stanford Univ, Dept Genet, Sch Med, Stanford, CA USA

Teterina, Anastasia (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Tittes, Silas (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Unneberg, Per (författare): Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab

Vazquez, Juan Manuel (författare): Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA USA

Waples, Ryan K. (författare): Univ Washington, Dept Biostat, Seattle, WA USA

Wohns, Anthony Wilder (författare): Broad Inst MIT & Harvard, Cambridge, MA USA

Wong, Yan (författare): Univ Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England

Baumdicker, Franz (författare): Eberhard Karls Univ Tubingen, Cluster Excellence Controlling Microbes Fight Infe, Tubingen, Germany

Cartwright, Reed A. (författare): Arizona State Univ, Sch Life Sci, Tempe, AZ USA.;Arizona State Univ, Biodesign Inst, Tempe, AZ USA

Gorjanc, Gregor (författare): Univ Edinburgh, Roslin Inst, Edinburgh, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh, Scotland

Gutenkunst, Ryan N. (författare): Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ USA

Kelleher, Jerome (författare): Univ Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England

Kern, Andrew D. (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA

Ragsdale, Aaron P. (författare): Univ Wisconsin Madison, Dept Integrat Biol, Madison, WI USA

Ralph, Peter L. (författare): Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.;Univ Oregon, Dept Math, Eugene, OR USA

Schrider, Daniel R. (författare): Univ North Carolina Chapel Hill, Dept Genet, Chapel Hill, NC USA

Gronau, Ilan (författare): Reichman Univ, Efi Arazi Sch Comp Sci, Herzliyya, Israel

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eLife Sciences Publications Ltd, 2023
2023
Engelska.
Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 12

Relaterad länk:: https://doi.org/10.7...; visa fler...; https://uu.diva-port... (primary) (Raw object); https://urn.kb.se/re...; https://doi.org/10.7...; visa färre...

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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 datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and 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 species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

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Av författaren/redakt...: Lauterbur, M. El ...; Cavassim, Maria ...; Gladstein, Ariel ...; Gower, Graham; Pope, Nathaniel ...; Tsambos, Georgia; visa fler...; Adrion, Jeffrey; Belsare, Saurabh; Biddanda, Arjun; Caudill, Victori ...; Cury, Jean; Echevarria, Igna ...; Haller, Benjamin ...; Hasan, Ahmed R.; Huang, Xin; Iasi, Leonardo N ...; Noskova, Ekateri ...; Obsteter, Jana; Pavinato, Vitor ...; Pearson, Alice; Peede, David; Perez, Manolo F.; Rodrigues, Muril ...; Smith, Chris C. ...; Spence, Jeffrey ...; Teterina, Anasta ...; Tittes, Silas; Unneberg, Per; Vazquez, Juan Ma ...; Waples, Ryan K.; Wohns, Anthony W ...; Wong, Yan; Baumdicker, Fran ...; Cartwright, Reed ...; Gorjanc, Gregor; Gutenkunst, Ryan ...; Kelleher, Jerome; Kern, Andrew D.; Ragsdale, Aaron ...; Ralph, Peter L.; Schrider, Daniel ...; Gronau, Ilan; visa färre...

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

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