metasim 1.0: an individual‐based environment for simulating population genetics of complex population dynamics
Abstract
metasim provides a flexible environment in which to perform individual‐based population genetic simulations. A wide range of landscape‐level dynamics, population structures, and within‐population demographies can be represented using the framework implemented in this software. In addition, temporal variation in all demographic characteristics can be simulated, both deterministically and stochastically. Such simulations can be used to produce null distributions of genotypes under realistic conditions. These genotypic data can then be used by a variety of analytical programs to develop null expectations of any population genetic statistic estimated from genotypic data.
Citing Literature
Number of times cited according to CrossRef: 32
- Christopher J. Katalinas, John D. Robinson, Allan E. Strand, Tanya Darden, Karl Brenkert, Michael R. Denson, Forecasting the genetic influences of red drum stock enhancement in South Carolina, Fisheries Management and Ecology, 10.1111/fme.12342, 26, 3, (224-235), (2019).
- Sean Hoban, Andria Dawson, John D. Robinson, Adam B. Smith, Allan E. Strand, Inference of biogeographic history by formally integrating distinct lines of evidence: genetic, environmental niche and fossil, Ecography, 10.1111/ecog.04327, 42, 12, (1991-2011), (2019).
- Craig A. McDougall, Amy B. Welsh, Thierry Gosselin, W. Gary Anderson, Patrick A. Nelson, Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens, PLOS ONE, 10.1371/journal.pone.0174269, 12, 3, (e0174269), (2017).
- Christian M. Parobek, Frederick I. Archer, Michelle E. DePrenger‐Levin, Sean M. Hoban, Libby Liggins, Allan E. Strand, skelesim: an extensible, general framework for population genetic simulation in R, Molecular Ecology Resources, 10.1111/1755-0998.12607, 17, 1, (101-109), (2016).
- Tanya L. Darden, John D. Robinson, Allan E. Strand, Michael R. Denson, Forecasting the Genetic Impacts of Net Pen Failures on Gulf of Mexico Cobia Populations Using Individual‐based Model Simulations, Journal of the World Aquaculture Society, 10.1111/jwas.12333, 48, 1, (20-34), (2016).
- Stacy A. Krueger‐Hadfield, Sean M. Hoban, The importance of effective sampling for exploring the population dynamics of haploid–diploid seaweeds, Journal of Phycology, 10.1111/jpy.12366, 52, 1, (1-9), (2016).
- Drew C. Wham, Todd C. LaJeunesse, Symbiodinium population genetics: testing for species boundaries and analysing samples with mixed genotypes, Molecular Ecology, 10.1111/mec.13623, 25, 12, (2699-2712), (2016).
- Jeffrey R. Row, Paul J. Wilson, Dennis L. Murray, The genetic underpinnings of population cyclicity: establishing expectations for the genetic anatomy of cycling populations, Oikos, 10.1111/oik.02736, 125, 11, (1617-1626), (2016).
- Marco Andrello, Stéphanie Manel, MetaPopGen: an r package to simulate population genetics in large size metapopulations, Molecular Ecology Resources, 10.1111/1755-0998.12371, 15, 5, (1153-1162), (2015).
- T. M. Bell, A. E. Strand, E. E. Sotka, The Adaptive Cline at LDH (Lactate Dehydrogenase) in Killifish Fundulus heteroclitus Remains Stationary After 40 Years of Warming Estuaries, Journal of Heredity, 10.1093/jhered/esu016, 105, 4, (566-571), (2014).
- Ю.С. Букин, Yu.S. Bukin, An Individual-Based Model to Simulate Genetic Processes in Populations of Species Inhabiting One-Dimensional Area, Математическая биология и биоинформатикаMathematical Biology and Bioinformatics, 10.17537/2014.9.438, 9, 2, (438-452), (2014).
- David A. Tallmon, Robin S. Waples, Dave Gregovich, Michael K. Schwartz, Detecting population recovery using gametic disequilibrium-based effective population size estimates, Conservation Genetics Resources, 10.1007/s12686-012-9689-3, 4, 4, (987-989), (2012).
- Sean Hoban, Giorgio Bertorelle, Oscar E. Gaggiotti, Computer simulations: tools for population and evolutionary genetics, Nature Reviews Genetics, 10.1038/nrg3130, 13, 2, (110-122), (2012).
- Béatrice M. Frank, John J. Piccolo, Philippe V. Baret, A review of ecological models for brown trout: towards a new demogenetic model, Ecology of Freshwater Fish, 10.1111/j.1600-0633.2011.00491.x, 20, 2, (167-198), (2011).
- Deukhwan Lee, Daniel A. Vasco, Predicting the Accuracy of Breeding Values Using High Density Genome Scans, Asian-Australasian Journal of Animal Sciences, 10.5713/ajas.2011.10163, 24, 2, (162-172), (2010).
- PER J. PALSBØLL, M. ZACHARIAH PEERY, MARTINE BÉRUBÉ, Detecting populations in the ‘ambiguous’ zone: kinship‐based estimation of population structure at low genetic divergence, Molecular Ecology Resources, 10.1111/j.1755-0998.2010.02887.x, 10, 5, (797-805), (2010).
- BRYAN K. EPPERSON, BRAD H. MCRAE, KIM SCRIBNER, SAMUEL A. CUSHMAN, MICHAEL S. ROSENBERG, MARIE‐JOSÉE FORTIN, PATRICK M. A. JAMES, MELANIE MURPHY, STÉPHANIE MANEL, PIERRE LEGENDRE, MARK R. T. DALE, Utility of computer simulations in landscape genetics, Molecular Ecology, 10.1111/j.1365-294X.2010.04678.x, 19, 17, (3549-3564), (2010).
- DAVID A. TALLMON, DAVE GREGOVICH, ROBIN S. WAPLES, C. SCOTT BAKER, JENNIFER JACKSON, BARBARA L. TAYLOR, ERIC ARCHER, KAREN K. MARTIEN, FRED W. ALLENDORF, MICHAEL K. SCHWARTZ, When are genetic methods useful for estimating contemporary abundance and detecting population trends?, Molecular Ecology Resources, 10.1111/j.1755-0998.2010.02831.x, 10, 4, (684-692), (2010).
- J.-M. Okland, O. A. Haaland, H. J. Skaug, A method for defining management units based on genetically determined close relatives, ICES Journal of Marine Science, 10.1093/icesjms/fsp260, 67, 3, (551-558), (2009).
- GILLES GUILLOT, RAPHAËL LEBLOIS, AURÉLIE COULON, ALAIN C. FRANTZ, Statistical methods in spatial genetics, Molecular Ecology, 10.1111/j.1365-294X.2009.04410.x, 18, 23, (4734-4756), (2009).
- KAREN K. MARTIEN, DAVE GREGOVICH, MARK V. BRAVINGTON, ANDRÉ E. PUNT, ALLAN E. STRAND, DAVID A. TALLMON, BARBARA L. TAYLOR, tossm: an R package for assessing performance of genetic analytical methods in a management context, Molecular Ecology Resources, 10.1111/j.1755-0998.2009.02686.x, 9, 6, (1456-1459), (2009).
- Elizabeth L. Cushman, Nathaniel K. Jue, Allan E. Strand, Erik E. Sotka, Evaluating the demographic significance of genetic homogeneity using a coalescent-based simulation: a case study with gag (Mycteroperca microlepis), Canadian Journal of Fisheries and Aquatic Sciences, 10.1139/F09-140, 66, 10, (1821-1830), (2009).
- GENTILE FRANCESCO FICETOLA, AURELIE BONIN, CLAUDE MIAUD, Population genetics reveals origin and number of founders in a biological invasion, Molecular Ecology, 10.1111/j.1365-294X.2007.03622.x, 17, 3, (773-782), (2008).
- J. A. JACKSON, N. J. PATENAUDE, E. L. CARROLL, C. SCOTT BAKER, How few whales were there after whaling? Inference from contemporary mtDNA diversity, Molecular Ecology, 10.1111/j.1365-294X.2007.03497.x, 17, 1, (236-251), (2007).
- Anna Kuparinen, Frank M. Schurr, A flexible modelling framework linking the spatio-temporal dynamics of plant genotypes and populations: Application to gene flow from transgenic forests, Ecological Modelling, 10.1016/j.ecolmodel.2006.11.015, 202, 3-4, (476-486), (2007).
- Lawrence Barnthouse, Wayne Munns, Mary Sorensen, References, Population-Level Ecological Risk Assessment, 10.1201/9781420053333, (247-284), (2007).
- Cino Pertoldi, R. Bijlsma, Volker Loeschcke, Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges, Biodiversity and Conservation, 10.1007/s10531-007-9212-4, 16, 14, (4147-4163), (2007).
- ALLAN E. STRAND, JAMES M. NIEHAUS, kernelpop, a spatially explicit population genetic simulation engine, Molecular Ecology Notes, 10.1111/j.1471-8286.2007.01832.x, 7, 6, (969-973), (2007).
- Dario Gasbarra, Mikko J. Sillanpää, Elja Arjas, Backward simulation of ancestors of sampled individuals, Theoretical Population Biology, 10.1016/j.tpb.2004.08.003, 67, 2, (75-83), (2005).
- E. C. ANDERSON, K. K. DUNHAM, spip 1.0: a program for simulating pedigrees and genetic data in age‐structured populations, Molecular Ecology Notes, 10.1111/j.1471-8286.2005.00884.x, 5, 2, (459-461), (2005).
- E. C. ANDERSON, K. K. DUNHAM, spip 1.0: a program for simulating pedigrees and genetic data in age-structured populations, Molecular Ecology Notes, 10.1111/j.1471-8286.2004.00884.x, 0, 0, (070621074211209), (2004).
- C.‐H. Kuo, F. J. Janzen, bottlesim: a bottleneck simulation program for long‐lived species with overlapping generations, Molecular Ecology Notes, 10.1046/j.1471-8286.2003.00532.x, 3, 4, (669-673), (2003).




