Kitchen, James and Allaby, Robin G.. (2012) The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations. PLoS ONE, Vol.7 (No.8). e43254. ISSN 1932-6203

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Abstract

Computational models of evolutionary processes are increasingly required to incorporate multiple and diverse sources of data. A popular feature to include in population genetics models is spatial extension, which reflects more accurately natural populations than does a mean field approach. However, such models necessarily violate the mean field assumptions of classical population genetics, as do natural populations in the real world. Recently, it has been questioned whether classical approaches are truly applicable to the real world. Individual based models (IBM) are a powerful and versatile approach to achieve integration in models. In this study an IBM was used to examine how populations of plants deviate from classical expectations under spatial extension. Populations of plants that used three different mating strategies were placed in a range of arena sizes giving crowded to sparse occupation densities. Using a measure of population density, the pollen communication distance (Pcd), the deviation exhibited by outbreeding populations differed from classical mean field expectations by less than 5% when Pcd was less than 1, and over this threshold value the deviation significantly increased. Populations with an intermediate mating strategy did not have such a threshold and deviated directly with increasing isolation between individuals. Populations with a selfing strategy were influenced more by the mating strategy than by increased isolation. In all cases pollen dispersal was more influential than seed dispersal. The IBM model showed that mean field calculations can be reasonably applied to natural outbreeding plant populations that occur at a density in which individuals are less than the average pollen dispersal distance from their neighbors.

Item Type:	Journal Article
Subjects:	Q Science > QK Botany
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Population genetics -- Mathematical models, Plant population genetics, Pollen -- Dispersal -- Mathematical models, Seeds -- Dispersal -- Mathematical models
Journal or Publication Title:	PLoS ONE
Publisher:	PLOS
ISSN:	1932-6203
Date:	August 2012
Volume:	Vol.7
Number:	No.8
Page Range:	e43254
Identification Number:	10.1371/journal.pone.0043254
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Leverhulme Trust (LT)
Grant number:	F/00215/BC (LT)
References:	1. Allaby RG (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany 61: 935–944. 2. Hardy GH (1908) Mendelian proportions in a mixed population. Science 28 (706): 49–50. 3. Wright S (1943) Isolation by distance. Genetics 28: 114–138. 4. Mayr E (1978) Review of Modes of Speciation by MJD White. Syst. Zool. 27: 478–482. 5. Templeton A (1980) The theory of speciation via the founder principle. Genetics 94: 1011–1038. 6. Garroway CJ, Bowman J, Wilson PJ (2011) Using a genetic network to parameterize a landscape resistance surface for fishers, Martes pennanti. Mol Ecol 20: 3978–3988. 7. Rasic G, Keyghobadi N (2011) From broadscale patterns to fine-scale processes: habitat structure influences genetic differentiation in the pitcher plant midge across multiple spatial scales. Molecular Ecology: doi: 10.1111/j.1365- 294X.2011.05280.x. 8. Jones KN, Reithel JS (2001) Pollinator-mediated selection on a flower colour polymorphism in experimental populations of Antirrhinum (Scophulariaceae). Am. J. Bot. 88: 447–454. 9. Levin DA, Kerster HW (1972) Assortative pollination for stature in Lythrum sativa. Evolution 27: 144–152. 10. Weis AE, Kossler TM (2004) Genetic variation in flowering time induces phonological assortative mating; quantitative genetic methods applied to Brassica rapa. Am. J. Bot. 91: 825–836. 11. Bomblies K, Yant L, Laitinen RA, Kim ST, Hollister JD, et al. (2010) Localscale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana. PLoS Genet 6: e1000890. 12. Baker HG (1955) Self-compatibility and establishment after ‘‘long-distance’’ dispersal. Evolution 9: 347–349. 13. Platt A, Horton M, Huang YS, Li Y, Anastasio AE, et al. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genet 6: e1000843. 14. Allaby RG, Fuller DQ, Brown TA (2008) The genetic expectations of a protracted model for the origins of domesticated crops. Proceedings of the National Academy of Sciences USA 105: 13982–13986. 15. Allaby RG, Brown TA, Fuller DQ (2010) A simulation of the effect of inbreeding on crop domestication genetics with comments on the integration of archaeobotany and genetics: a reply to Honne and Heun. Vegetation History and Archaeobotany 19: 151–158. 16. Cuddington KM, Yodzis P (2000) Diffusion-limited predator-prey dynamics in euclidean environments: An allometric individual-based model. Theoretical Population Biology 58: 259–278. 17. Wilson WG, McCauley E, De Roos AM (1995) Effect of dimensionality of Lotka_Volterra predator_prey dynamics: individual based simulation results. Bull. Math. Bio. 57: 507–526. 18. Wilson WG, De Roos AM, McCauley E (1993) Spatial instabilities within the diffusive Lotka-Volterra system: Individual-based simulation results. Theor. Popul. Biol. 43: 91–127. 19. McCauley E, Wilson WG, De Roos AM (1993) Dynamics of age-structured and spatially structured predator_prey interactions: Individual-based models and population-level formulations. Am. Nat. 142: 412–442. 20. De Roos AM, McCauley E, Wilson WG (1991) Mobility versus density-limited predator_prey dynamics on different spatial scales. Proc. R. Soc. Lond. B 246: 117–122. 21. Spear SF, Balkenhol N, Fortin MJ, McRae BH, Scribner K (2010) Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis. Mol Ecol 19: 3576–3591. 22. Kuparinen A, Schurr FM (2007) A flexible modelling framework linking the spatio-temporal dy- namics of plant genotypes and populations: Application to gene flow from transgenic forests. Ecological Modelling 202: 476–486. 23. Landguth EL, Cushman SA (2010) cdpop: A spatially explicit cost distance population genetics program. Mol Ecol Resour 10: 156–161. 24. Gavrilets S, Li H, Vose MD (1998) Rapid parapatric speciation on holey adaptive landscapes. Proc R. Soc. Lond 265: 1483–1489. 25. Rice WR (1984) Disruptive selection on habitat preference and the evolution of reproductive isolation: a simulation study. Evolution 38 (6): 1251–1260. 26. Savill NJ, Hogeweg P (1998) Spatially induced speciation prevents extinction: the evolution of dispersal distance in oscillatory predator-prey models. Proc R. Soc. Lond 265: 25–32. 27. Durret R, Buttel L, Harrison R (2000) Spatial models for hybrid zones. Heredity 84: 9–19. 28. Sadedin S, Hollander J, Panova M, Johannesson K, Gavrilets S (2009) Case studies and mathematical models of ecological speciation. 3: Ecotype formation in a Swedish snail. Molecular Ecology 18: 4006–4023. 29. Hartman PJ, Wetzel DP, Crowley PH, Westneat DF (2012) The impact of extrapair mating behavior on hybridization and genetic introgression. Theor Ecol 5: 219–229. 30. Doligez A, Baril C, Joly HI (1998) Fine-scale spatial genetic structure with nonuniform distribution of individuals. Genetics 148: 905–919. 31. Hartl DL, Clark AG (1997) Principles of Population Genetics. Sinauer Associates, Sunderland, Massachusetts, 141–144. 32. Finkel RA, Bentley JL (1974) Quad Trees: A Data Structure for Retrieval on Composite Keys. Acta Informatica 4 (1): 1–9. 33. Beckie HJ, Hall LM (2008) Simple to complex: Modeling crop pollen-mediated gene flow. Plant Science 175: 615–628. 34. Barrat MD, Wallace MJ, Anthony JM (2012) Characterization and cross application of novel microsatellite markers for a rare sedge, Lepidosperma Gibsonii (Cyoeraceae). American Journal of Botany 99(1): e14–e16. 35. King TL, Springmann JA, Young JA (2011) Tri- and tetra-nucleotide microsatellite DNA markers for assessing genetic diversity, population structure, and demographics in the Holmgren milk-vetch (Astragalus holmgreniorum). Conservation Genet Resour 4(1): 39–42. 36. Wo¨hrmann T, Guicking D, Khoshbakht K, Weising K (2011) Genetic variability in wild populations of Prunus divaricata Ledeb. in northern Iran evaluated by EST-SSR and genomic SSR marker analysis. Genet Resour Crop Evol 58: 115– 1167. 37. Millar MA, Byrne M, Barbour E (2012) Characterisation of eleven polymorphic microsatellite DNA markers for Australian sandalwood (Santalum spicatum) (R.Br.) A.DC. (Santalaceae). Conservation Genet Resour 4: 51–53. 38. Muir K, Byrne M, Barbour E, Cox MC, Fox JED (2007) High levels of outcrossing in a family trial of Western Australian Sandalwood (Santalum spicatum). Silvae Genetica 56: (5) 222–230. 39. Douaihy B, Vendramin GG, Boratynski A, Machon N, Bou Dagher-Kharrat M (2011) High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region. Aob Plants. plr003. 40. Allphin L, Windham MD, Harper KT (1998) Genetic diversity and gene flow in the endangered dwarf bear poppy, Arctomecon Humilis. American Journal of Botany 85(9): 1251–1261. 41. Restoux G, Silva DE, Sagnard F, Torre F, Klein E, et al. (2008) Life at the margin: the mating system of Mediterranean conifers. Web Ecol. 8: 94–102. 42. Karron JD, Thumser NM, Tucker R, Hessenauer AJ (1995) The influence of population density on outcrossing rates in Mimulus ringens. Heredity 75: 175–180. 43. Dering M, Chybicki I (2012) Assessment of genetic diversity in two-species oak seed stands and their progeny populations. Scandinavian Journal of Forest Research 27(1): 2–9. 44. Olivier A, Glaszmann JC, Lanaud C, Leroux GD (1998) Population structure, genetic diversity and host specificity of the parasitic weed Striga hermonthica (Scrophulariaceae) in Sahel. Plant Systematics and Evolution 209: 33–45. 45. Smith WG, Schall BA (1979) Isozyme variation in Desmodium nudiflorum. Biochemical Systematics and Ecology 7: 121–123. 46. Pritchard JK (2010) How we are evolving. Scientific American 303: (4)41–47. 47. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, et al. (2006) Positive Natural Selection in the Human Lineage. Science 312: 1614–1620. 48. Peng J, Ronin Y, Fahima T, Ro¨der MS, Li Y, et al. (2003) Domestication quantitative loci in Triticum dicoccoides, the progenitor of wheat. Proc. Natl. Acad. Sci. USA 100: 2489–2494. 49. Peleg Z, Fahima T, Korol AB, Abbo S, Saranga Y (2011) Genetic analysis of wheat domestication and evolution under domestication. J. Exp. Bot. 62: 5051– 5061.
URI:	http://wrap.warwick.ac.uk/id/eprint/52045

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