Simulation of molecular data under diverse evolutionary scenarios

PLoS Computational Biology

Volumn 8, Issue 5, 2012, Pages

  Arenas, Miguel ^a,b  

^a UNIVERSITY OF BERN   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DATA;

GENOMIC DNA;

AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA ANALYSIS; GENETIC RECOMBINATION; INDEL MUTATION; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS;

EID: 84863707192     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002495     Document Type: Article

References (91)

1. Peck SL, (2004) Simulation as experiment: a philosophical reassessment for biological modeling. Trends Ecol Evol 19: 530-534.
2. DeChaine EG, Martin AP, (2006) Using coalescent simulations to test the impact of quaternary climate cycles on divergence in an alpine plant-insect association. Evolution 60: 1004-1013.
3. Carvajal-Rodriguez A, Crandall KA, Posada D, (2006) Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol 23: 817-827.
4. Arenas M, Valiente G, Posada D, (2008) Characterization of reticulate networks based on the coalescent with recombination. Mol Biol Evol 25: 2517-2520.
5. Westesson O, Holmes I, (2009) Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput Biol 5: e1000318 doi:10.1371/journal.pcbi.1000318.
6. Hill WG, Robertson A, (1966) The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
7. Beaumont MA, Zhang W, Balding DJ, (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
8. Arenas M, Posada D, (2010) Coalescent simulation of intracodon recombination. Genetics 184: 429-437.
9. Ray N, Currat M, Foll M, Excoffier L, (2010) SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics 26: 2993-2994.
10. Excoffier L, Foll M, (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27: 1332-1334.
11. Yang Z, (2006) Computational molecular evolution Oxford University Press.
12. Fletcher W, Yang Z, (2009) INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 26: 1879-1888.
13. Carvajal-Rodriguez A, (2008) Simulation of genomes: a review. Curr Genomics 9: 155-159.
14. Carvajal-Rodriguez A, (2010) Simulation of genes and genomes forward in time. Curr Genomics 11: 58-61.
15. Liu Y, Athanasiadis G, Weale ME, (2008) A survey of genetic simulation software for population and epidemiological studies. Hum Genomics 3: 79-86.
16. Hoban S, Bertorelle G, Gaggiotti OE, (2012) Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 13: 110-122.
17. Arenas M, Posada D, (2012) Simulation of coding sequence evolution. In: Cannarozzi GM, Schneider A, editors. Codon evolution Oxford Oxford University Press pp. 126-132.
18. Carvajal-Rodriguez A, (2008) GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 9: 223.
19. Hernandez RD, (2008) A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24: 2786-2787.
20. Neuenschwander S, (2006) AQUASPLATCHE: a program to simulate genetic diversity in populations living in linear habitats. Mol Ecol Notes 6: 583-585.
21. Peng B, Kimmel M, (2005) simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21: 3686-3687.
22. Arbiza L, Patricio M, Dopazo H, Posada D, (2011) Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol 3: 896-908.
23. Anisimova M, Nielsen R, Yang Z, (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236.
24. Arenas M, Posada D, (2007) Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 8: 458.
25. Navascues M, Depaulis F, Emerson BC, (2010) Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol Ecol Resour 10: 760-772.
26. Rambaut A, Grassly NC, (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosciences 13: 235-238.
27. Strope CL, Abel K, Scott SD, Moriyama EN, (2009) Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol 26: 2581-2593.
28. Yang Z, (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13: 555-556.
29. Sipos B, Massingham T, Jordan GE, Goldman N, (2011) PhyloSim- Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics 12: 104.
30. Ihaka R, Gentleman R, (1996) R: a language for data analysis and graphics. J Comput Graph Stat 169: 299-314.
31. Biswas S, Akey J, (2006) Genomic insights into positive selection. Trends Genet 22: 437-446.
32. Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM, (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res 16: 980-989.
33. Ewing G, Hermisson J, (2010) MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26: 2064-2065.
34. Spencer CC, Coop G, (2004) SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
35. Arenas M, Posada D, (2010) The effect of recombination on the reconstruction of ancestral sequences. Genetics 184: 1133-1139.
36. Lemey P, Lott M, Martin DP, Moulton V, (2009) Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics 10: 126.
37. Durbin RM, Altshuler DL, Abecasis GR, Bentley DR, Chakravarti A, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
38. Marjoram P, Wall JD, (2006) Fast "coalescent" simulation. BMC Genet 7: 16.
39. McVean GA, Cardin NJ, (2005) Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci 360: 1387-1393.
40. Excoffier L, Foll M, Petit RJ, (2009) Genetic consequences of range expansions. Annu Rev Ecol Evol Syst 40: 481-501.
41. Arenas M, Ray N, Currat M, Excoffier L, (2012) Consequences of range contractions and range shifts on molecular diversity. Mol Biol Evol 29: 207-218.
42. Ray N, Excoffier L, (2010) A first step towards inferring levels of long-distance dispersal during past expansions. Mol Ecol Resour 10: 902-914.
43. Schierup MH, Hein J, (2000) Consequences of recombination on traditional phylogenetic analysis. Genetics 156: 879-891.
44. Arenas M, Posada D, (2010) Computational design of centralized HIV-1 genes. Curr HIV Res 8: 613-621.
45. Bozek K, Lengauer T, (2010) Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evol Biol 10: 186.
46. Yang Z, Nielsen R, Goldman N, Pedersen A-MK, (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
47. Posada D, Buckley TR, (2004) Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53: 793-808.
48. Sullivan J, Joyce P, (2005) Model selection in phylogenetics. Annu Rev Ecol Evol Syst 36: 445-466.
49. Luo A, Qiao H, Zhang Y, Shi W, Ho SY, et al. (2010) Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol 10: 242.
50. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
51. Kuhner MK, Felsenstein J, (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biol Evol 11: 459-468.
52. Posada D, (2002) Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol 19: 708-717.
53. Novembre J, Stephens M, (2008) Interpreting principal component analyses of spatial population genetic variation. Nat Genet 40: 646-649.
54. Novembre J, Stephens M, (2010) Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)]. Hum Biol 82: 469-470.
55. François O, Currat M, Ray N, Han E, Excoffier L, et al. (2010) Principal component analysis under population genetic models of range expansion and admixture. Mol Biol Evol 27: 1257-1268.
56. Cavalli-Sforza LL, Menozzi P, Piazza A, (1994) The history and geography of human genes Princeton, New Jersey Princeton University Press.
57. Excoffier L, Ray N, (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol Evol 23: 347-351.
58. Beaumont MA, (2010) Approximate Bayesian computation in evolution and ecology. Annu Rev Ecol Evol Syst 41: 379-405.
59. Wilson DJ, Gabriel E, Leatherbarrow AJ, Cheesbrough J, Gee S, et al. (2009) Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol Biol Evol 26: 385-397.
60. Laval G, Patin E, Barreiro LB, Quintana-Murci L, (2010) Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions. PLoS ONE 5: e10284 doi:10.1371/journal.pone.0010284.
61. Wang M, Kapralov MV, Anisimova M, (2011) Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco. BMC Evol Biol 11: 266.
62. Bastolla U, Porto M, Roman HE, Vendruscolo M, (2007) Structural approaches to sequence evolution Berlin, Heidelberg Springer.
63. Arenas M, Villaverde MC, Sussman F, (2009) Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach. J Comput Chem 30: 1229-1240.
64. Kryazhimskiy S, Plotkin JB, (2008) The population genetics of dN/dS. PLoS Genet 4: e1000304 doi:10.1371/journal.pgen.1000304.
65. Excoffier L, Novembre J, Schneider S, (2000) SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Heredity 91: 506-509.
66. Anderson CN, Ramakrishnan U, Chan YL, Hadly EA, (2005) Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21: 1733-1734.
67. Ramos-Onsins SE, Mitchell-Olds T, (2007) Mlcoalsim: multilocus coalescent simulations. Evol Bioinform Online 3: 41-44.
68. Grassly NC, Harvey PH, Holmes EC, (1999) Population dynamics of HIV-1 inferred from gene sequences. Genetics 151: 427-438.
69. Beiko RG, Charlebois RL, (2007) A simulation test bed for hypotheses of genome evolution. Bioinformatics 23: 825-831.
70. Hall BG, (2008) Simulating DNA coding sequence evolution with EvolveAGene 3. Mol Biol Evol 25: 688-695.
71. Cartwright RA, (2005) DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 21 (Suppl 3): iii31-38.
72. Rosenberg MS, (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Evol Bioinform Online 1: 81-83.
73. Gesell T, von Haeseler A, (2006) In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics 22: 716-722.
74. Stoye J, Evers D, Meyer F, (1998) Rose: generating sequence families. Bioinformatics 14: 157-163.
75. Varadarajan A, Bradley RK, Holmes IH, (2008) Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol 9: R147.
76. Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C, (2012) ALF-a simulation framework for genome evolution. Mol Biol Evol 29: 1115-1123.
77. Pang A, Smith AD, Nuin PA, Tillier ER, (2005) SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics 6: 236.
78. Arenas M, Patricio M, Posada D, Valiente G, (2010) Characterization of phylogenetic networks with NetTest. BMC Bioinformatics 11: 268.
79. Raup DM, Gould SJ, Schopf TJM, Simberloff DS, (1973) Stochastic models of phylogeny and the evolution of diversity. J Geol 81: 525-542.
80. Epperson BK, McRae BH, Scribner K, Cushman SA, Rosenberg MS, et al. (2010) Utility of computer simulations in landscape genetics. Mol Ecol 19: 3549-3564.
81. Peng B, Amos CI, Kimmel M, (2007) Forward-time simulations of human populations with complex diseases. PLoS Genet 3: e47 doi:10.1371/journal.pgen.0030047.
82. Calafell F, Grigorenko EL, Chikanian AA, Kidd KK, (2001) Haplotype evolution and linkage disequilibrium: a simulation study. Hum Hered 51: 85-96.
83. Jones TC, Laughlin TF, (2010) PopGen fishbowl: a free online simulation model of microevolutionary processes. Am Biol Teach 72: 100-103.
84. Coombs JA, Letcher BH, Nislow KH, (2010) Pedagog: software for simulating eco-evolutionary population dynamics. Mol Ecol Resour 10: 558-563.
85. Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M, (2008) Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178: 2417-2427.
86. Nordborg M, (2007) Coalescent theory. In: Balding DJ, Bishop M, Cannings C, editors. Handbook of statistical genetics. Third edition Chichester, UK John Wiley & Sons, Ltd pp. 843-877.
87. Wakeley J, (2008) Coalescent Theory: An Introduction Greenwood Village, Colorado Roberts and Company Publishers.
88. Slatkin M, (2001) Simulating genealogies of selected alleles in a population of variable size. Genet Res 78: 49-57.
89. Hudson RR, (1998) Island models and the coalescent process. Mol Ecol 7: 413-418.
90. Hudson RR, (1983) Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23: 183-201.
91. Hudson RR, Kaplan NL, (1988) The coalescent process in models with selection and recombination. Genetics 120: 831-840.