Индивидуально ориентированная модель для имитации популяционно-генетических процессов у видов, населяющих одномерный ареал

Математическая биология и биоинформатика. 2014;9(2):438-452.

doi: 10.17537/2014.9.438.

1. Altukhov YuP. Genetic Processes in Populations. Moscow: Akademkniga; 2003 (in Russ.).
2. Etheridge A. Some Mathematical Models from Population Genetics. Springer; 2011. 119 p. doi: 10.1007/978-3-642-16632-7
3. Wright S. Evolution in Mendelian populations. Genetics. 1931;16:97-159.
4. Wright S. The genetical structure of population. Ann. Eugenics. 1951;15:323-354. doi: 10.1111/j.1469-1809.1949.tb02451.x
5. Kimura M. “Stepping stone” model of population. Ann. Rep. Nat. Ist. Genet. Mishima. 1953;3:63-65.
6. Kimura M, Weiss GH. The stepping stone model of population structure and decrease of genetic correlation with distance. Genetics. 1964;49:561-567.
7. Wright S. Isolation by distance. Genetics. 1943;28:114-138.
8. Maruyama T. Effective number of alleles in a subdivided population. Theor. Popul. Biol. 1970;1:273-306. doi: 10.1016/0040-5809(70)90047-X
9. Slatkin M. Inbreeding coefficients and coalescence times. Genet. Res. 1991;58:167-175. doi: 10.1017/S0016672300029827
10. Strobeck C. Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics. 1987;117:149-153.
11. Guillot G. On the inference of spatial structure from population genetics data. Bioinformatics. 2009;25:1796-180. doi: 10.1093/bioinformatics/btp267
12. Wilkins JF, Wakeley J. The Coalescent in a continuous, finite, linear population. Genetics. 2002;161:873-888.
13. Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992;132:583-589.
14. Bocquet-Appel JP, Bacro JN. Isolation by distance, trend surface analysis, and spatial autocorrelation. Human Biology. 1993;65:11-27.
15. Slatkin M, Maddison WP. Detecting isolation by distance using phylogenies of genes. Genetics. 1990;126:249-260.
16. Jensen JL, Bohonak AJ, Kelley ST. Isolation by distance, web service. BMC Genetics. 2005;6:13. doi: 10.1186/1471-2156-6-13
17. Carvajal-Rodríguez A. GENOMEPOP: A program to simulate genomes in populations. BMC Bioinformatics. 2008;9.
18. Laval G, Excoffier L. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics. 2004;20:2485-2487. doi: 10.1093/bioinformatics/bth264
19. Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA. Serial SimCoal: A population genetics model for data from multiple populations and points in time. Bioinformatics. 2005;21:1733-1734. doi: 10.1093/bioinformatics/bti154
20. Landguth EL, Cushman SA. CDPOP: A spatially-explicit cost distance population genetics program. Molecular Ecology Resources. 2010;10:156-161. doi: 10.1111/j.1755-0998.2009.02719.x
21. Strand AE, Niehaus JM. KERNELPOP, a spatially explicit population genetic simulation engine. Mol. Ecol. Notes. 2007;7:969-973. doi: 10.1111/j.1471-8286.2007.01832.x
22. Strand AE. Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. Mol. Ecol. Notes. V. 2002;2:373-376. doi: 10.1046/j.1471-8286.2002.00208.x
23. Balloux F. EASYPOP (version 1.7): a computer program for population genetics simulations. J. Hered. 2001;92:301-302. doi: 10.1093/jhered/92.3.301
24. Gomanenko GV, Kamaltynov RM, Kuzmenkova ZhV, Berenos K, Sherbakov DYu. Population Structure of the Baikalian Amphipod Gmelinoides fasciatus (Stebbing). Russian Journal of Genetics. 2005;41(8):907. doi: 10.1007/s11177-005-0179-5
25. Peretolchina TE, Bukin YuS, Sitnikova TYa, Sherbakov DYu. Genetic Differentiation of the Endemic Baikalian Mollusk Baicalia carinata (Mollusca: Caenogastropoda). Russian Journal of Genetics. 2007;43(12):1400 doi: 10.1134/S1022795407120095
26. Mashiko K, Kamaltynov RM, Sherbakov DYu, Mori-no H. Genetic separation of gammarid (Eulimnogammarus cyaneus) populations by localized topographic changes in ancient Lake Baikal. Archive Hydrobiology. 1997;139(3):379-387.
27. Mashiko K, Kamaltynov RM, Morino H, Sherbakov DYu. Genetic differentiation among gammarid (Eulimnogammarus cyaneus) populations in Lake Baikal, East Siberia. Archive Hydrobiology. 2000;148(2):249-261.
28. Nevado B, Mautner S, Sturmbauer C, Verheyen E. Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species. Mol Ecol. 2013;22(15):3933-3948. doi: 10.1111/mec.12374
29. Duftner N, Sefc KM, Koblmüller S, Nevado B, Verheyen E, Phiri H, Sturmbauer C. Distinct population structure in a phenotypically homogeneous rock-dwelling cichlid fish from Lake Tanganyika. Mol Ecol. 2006;15(9):2381-2395. doi: 10.1111/j.1365-294X.2006.02949.x
30. Kelly RP, Palumbi SR. Genetic Structure Among 50 Species of the northeastern pacific rocky intertidal community. PLoS ONE. 2010;5:e8594. doi: 10.1371/journal.pone.0008594
31. Semovski SV, Bukin YuS, Sherbakov DYu. Speciation in one-dimensional population: adaptive dynamics and neutral molecular evolution. Investigated in Russia. 2002;125e:1397-1402. http://www.sci-journal.ru/articles/2002/125e.pdf (accessed 01 November 2014).
32. Semovski SV, Bukin YuS, Sherbakov DYu. Speciation and neutral molecular evolution in one-dimensional closed population. Int. J. of Modern Physics. 2003;14(7): 973-983. doi: 10.1142/S012918310300511X
33. Bukin JuS, Pudovkina TA, Sherbakov DJu, Sitnikova TYa. Genetic flows in a structured one-dimensional population: simulation and real data on Baikalian polychaetes M. Godlewskii. In Silico Biology. 2007;7(3):277-284.
34. Svirezhev IuM., Logofet DO. Stability of Biological Communities. Mir Publishers; 1983. 319 p.
35. Doebeli M, Dieckmann U. Speciation along environmental gradients. Nature. 2003;421:259-264. doi: 10.1038/nature01274
36. Doebeli M, Dieckmann U. Evolutionary branching and sympatric speciation caused by different types of ecological interactions. Am. Nat. 2000;156:77-101. doi: 10.1086/303417
37. Kondrashov AS. Multilocus model of sympatric speciation III. Computer simulations. Theor. Pop. Biol. 1986;29:1-15. doi: 10.1016/0040-5809(86)90002-X
38. Dieckmann U, Doebeli M, Metz JAJ, Tautz D. Adaptive Speciation. Cambridge University Press; 2004. 445 p. doi: 10.1017/CBO9781139342179
39. Semovski SV, Verheyen E, Sherbakov DY. Simulating the evolution of neutrally evolving sequences in a population under environmental changes. Ecological Modelling. 2004;176:99-107. doi: 10.1016/j.ecolmodel.2003.07.013
40. Semovski SV, Bukin YuS, Sherbakov DYu. Models of Sympatric Speciation under Variable Environmental Conditions. Sibirskii Ekologicheskii Zhurnal (Siberian Ecological Journal). 2004;5:621-627 (in Russ.).
41. Tikhonov AN, Samarskii AA. Uravneniia matematicheskoi fiziki (Equations of Mathematical Physics). M.: Nauka, 1977. 735 p. (in Russ.).
42. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution. 2011;28:2731-2739. doi: 10.1093/molbev/msr121
43. Kumar S, Stecher G, Peterson D, Tamura K. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics. 2012;28:2685-2686. doi: 10.1093/bioinformatics/bts507