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Expanding the stdpo...
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Lauterbur, M. EliseUniv Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
(author)
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
- Article/chapterEnglish2023
Publisher, publication year, extent ...
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eLife Sciences Publications Ltd,2023
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-508060
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-508060URI
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https://doi.org/10.7554/eLife.84874DOI
Supplementary language notes
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Language:English
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Summary in:English
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Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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.
Subject headings and genre
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Cavassim, Maria Izabel A.Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA
(author)
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Gladstein, Ariella L.Embark Vet Inc, Boston, MA USA
(author)
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Gower, GrahamUniv Copenhagen, Globe Inst, Sect Mol Ecol & Evolut, Copenhagen, Denmark
(author)
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Pope, Nathaniel S.Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Tsambos, GeorgiaUniv Melbourne, Sch Math & Stat, Melbourne, Australia
(author)
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Adrion, JeffreyAncestry DNA, San Francisco, CA USA
(author)
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Belsare, SaurabhUniv Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Biddanda, Arjun54Gene Inc, Washington, DC USA
(author)
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Caudill, VictoriaUniv Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Cury, JeanUniv Paris Saclay, CNRS, INRIA, Lab Interdisciplinaire Sci Numer, Orsay, France
(author)
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Echevarria, IgnacioUniv Glasgow, Sch Life Sci, Glasgow, Scotland
(author)
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Haller, Benjamin C.Cornell Univ, Dept Computat Biol, Ithaca, NY USA
(author)
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Hasan, Ahmed R.Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada.;Univ Toronto Mississauga, Dept Biol, Mississauga, ON, Canada
(author)
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Huang, XinUniv Vienna, Dept Evolutionary Anthropol, Vienna, Austria.;Univ Vienna, Human Evolut & Archaeol Sci HEAS, Vienna, Austria
(author)
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Iasi, Leonardo Nicola MartinMax Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany
(author)
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Noskova, EkaterinaITMO Univ, Comp Technol Lab, St Petersburg, Russia
(author)
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Obsteter, JanaAgr Inst Slovenia, Dept Anim Sci, Ljubljana, Slovenia
(author)
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Pavinato, Vitor Antonio CorreaOhio State Univ, Entomol Dept, Wooster, OH USA
(author)
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Pearson, AliceUniv Cambridge, Dept Genet, Cambridge, England.;Univ Cambridge, Dept Zool, Cambridge, England
(author)
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Peede, DavidBrown Univ, Dept Ecol Evolut & Organismal Biol, Providence, RI USA.;Brown Univ, Ctr Computat Mol Biol, Providence, RI USA
(author)
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Perez, Manolo F.Univ Fed Sao Carlos, Dept Genet & Evolut, Sao Carlos, Brazil
(author)
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Rodrigues, Murillo F.Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Smith, Chris C. R.Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Spence, Jeffrey P.Stanford Univ, Dept Genet, Sch Med, Stanford, CA USA
(author)
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Teterina, AnastasiaUniv Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Tittes, SilasUniv Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Unneberg, PerUppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab(Swepub:uu)perun990
(author)
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Vazquez, Juan ManuelUniv Calif Berkeley, Dept Integrat Biol, Berkeley, CA USA
(author)
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Waples, Ryan K.Univ Washington, Dept Biostat, Seattle, WA USA
(author)
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Wohns, Anthony WilderBroad Inst MIT & Harvard, Cambridge, MA USA
(author)
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Wong, YanUniv Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England
(author)
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Baumdicker, FranzEberhard Karls Univ Tubingen, Cluster Excellence Controlling Microbes Fight Infe, Tubingen, Germany
(author)
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Cartwright, Reed A.Arizona State Univ, Sch Life Sci, Tempe, AZ USA.;Arizona State Univ, Biodesign Inst, Tempe, AZ USA
(author)
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Gorjanc, GregorUniv Edinburgh, Roslin Inst, Edinburgh, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh, Scotland
(author)
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Gutenkunst, Ryan N.Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ USA
(author)
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Kelleher, JeromeUniv Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England
(author)
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Kern, Andrew D.Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA
(author)
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Ragsdale, Aaron P.Univ Wisconsin Madison, Dept Integrat Biol, Madison, WI USA
(author)
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Ralph, Peter L.Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.;Univ Oregon, Dept Math, Eugene, OR USA
(author)
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Schrider, Daniel R.Univ North Carolina Chapel Hill, Dept Genet, Chapel Hill, NC USA
(author)
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Gronau, IlanReichman Univ, Efi Arazi Sch Comp Sci, Herzliyya, Israel
(author)
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Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USAUniv Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA
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Lauterbur, M. El ...
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Cavassim, Maria ...
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Gladstein, Ariel ...
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Gower, Graham
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Pope, Nathaniel ...
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Tsambos, Georgia
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Adrion, Jeffrey
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Belsare, Saurabh
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Biddanda, Arjun
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Caudill, Victori ...
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Cury, Jean
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Echevarria, Igna ...
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Haller, Benjamin ...
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Hasan, Ahmed R.
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Huang, Xin
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Iasi, Leonardo N ...
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Noskova, Ekateri ...
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Obsteter, Jana
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Pavinato, Vitor ...
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Pearson, Alice
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Peede, David
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Perez, Manolo F.
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Rodrigues, Muril ...
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Smith, Chris C. ...
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Spence, Jeffrey ...
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Teterina, Anasta ...
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Tittes, Silas
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Unneberg, Per
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Vazquez, Juan Ma ...
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Waples, Ryan K.
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Wohns, Anthony W ...
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Wong, Yan
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Baumdicker, Fran ...
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Cartwright, Reed ...
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Gorjanc, Gregor
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Gutenkunst, Ryan ...
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Kelleher, Jerome
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Kern, Andrew D.
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Ralph, Peter L.
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Schrider, Daniel ...
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