Computer Simulations: Tools for Population and Evolutionary Genetics

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2012 Jan 11

PMID 22230817

Citations 95

Authors

Sean Hoban

Giorgio Bertorelle

Oscar E Gaggiotti

Affiliations

Soon will be listed here.

Abstract

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions.

Citing Articles

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Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.

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References

Servedio M . The evolution of premating isolation: local adaptation and natural and sexual selection against hybrids. Evolution. 2004; 58(5):913-24. DOI: 10.1111/j.0014-3820.2004.tb00425.x. View

Daetwyler H, Villanueva B, Woolliams J . Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One. 2008; 3(10):e3395. PMC: 2561058. DOI: 10.1371/journal.pone.0003395. View

Sellers T, Weaver T, Phillips B, Altmann M, Rich S . Environmental factors can confound identification of a major gene effect: results from a segregation analysis of a simulated population of lung cancer families. Genet Epidemiol. 1998; 15(3):251-62. DOI: 10.1002/(SICI)1098-2272(1998)15:3<251::AID-GEPI4>3.0.CO;2-7. View

Estoup A, Baird S, Ray N, Currat M, Cornuet J, Santos F . Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus. Mol Ecol Resour. 2011; 10(5):886-901. DOI: 10.1111/j.1755-0998.2010.02882.x. View

Carvajal-Rodriguez A . Simulation of genes and genomes forward in time. Curr Genomics. 2010; 11(1):58-61. PMC: 2851118. DOI: 10.2174/138920210790218007. View

Hellenthal G, Auton A, Falush D . Inferring human colonization history using a copying model. PLoS Genet. 2008; 4(5):e1000078. PMC: 2367454. DOI: 10.1371/journal.pgen.1000078. View

Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, Beeson K . Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009; 10(3):R32. PMC: 2691003. DOI: 10.1186/gb-2009-10-3-r32. View

Fagundes N, Ray N, Beaumont M, Neuenschwander S, Salzano F, Bonatto S . Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci U S A. 2007; 104(45):17614-9. PMC: 2077041. DOI: 10.1073/pnas.0708280104. View

Epperson B, McRae B, Scribner K, Cushman S, Rosenberg M, Fortin M . Utility of computer simulations in landscape genetics. Mol Ecol. 2010; 19(17):3549-64. DOI: 10.1111/j.1365-294X.2010.04678.x. View

10.

Carvajal-Rodriguez A . Simulation of genomes: a review. Curr Genomics. 2009; 9(3):155-9. PMC: 2679650. DOI: 10.2174/138920208784340759. View

11.

Ilves K, Huang W, Wares J, Hickerson M . Colonization and/or mitochondrial selective sweeps across the North Atlantic intertidal assemblage revealed by multi-taxa approximate Bayesian computation. Mol Ecol. 2010; 19(20):4505-19. DOI: 10.1111/j.1365-294X.2010.04790.x. View

12.

Chadeau-Hyam M, Hoggart C, OReilly P, Whittaker J, De Iorio M, Balding D . Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics. 2008; 9:364. PMC: 2542380. DOI: 10.1186/1471-2105-9-364. View

13.

Anderson C, Ramakrishnan U, Chan Y, Hadly E . Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics. 2004; 21(8):1733-4. DOI: 10.1093/bioinformatics/bti154. View

14.

Lohmueller K, Indap A, Schmidt S, Boyko A, Hernandez R, Hubisz M . Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008; 451(7181):994-7. PMC: 2923434. DOI: 10.1038/nature06611. View

15.

Landguth E, Cushman S, Murphy M, Luikart G . Relationships between migration rates and landscape resistance assessed using individual-based simulations. Mol Ecol Resour. 2011; 10(5):854-62. DOI: 10.1111/j.1755-0998.2010.02867.x. View

16.

Ficetola G, Bonin A, Miaud C . Population genetics reveals origin and number of founders in a biological invasion. Mol Ecol. 2008; 17(3):773-82. DOI: 10.1111/j.1365-294X.2007.03622.x. View

17.

Dudek S, Motsinger A, Velez D, Williams S, Ritchie M . Data simulation software for whole-genome association and other studies in human genetics. Pac Symp Biocomput. 2006; :499-510. View

18.

Liu Y, Athanasiadis G, Weale M . A survey of genetic simulation software for population and epidemiological studies. Hum Genomics. 2009; 3(1):79-86. PMC: 3525177. DOI: 10.1186/1479-7364-3-1-79. View

19.

Schneider S, Excoffier L . Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics. 1999; 152(3):1079-89. PMC: 1460660. DOI: 10.1093/genetics/152.3.1079. View

20.

Hardy O, Charbonnel N, Freville H, Heuertz M . Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics. 2003; 163(4):1467-82. PMC: 1462522. DOI: 10.1093/genetics/163.4.1467. View