1. bookVolume 67 (2018): Edizione 1 (February 2018)
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eISSN
2509-8934
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22 Feb 2016
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1 volta all'anno
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Inglese
access type Accesso libero

A regression approach to estimate the relative roles of pollen- versus seed-mediated gene flow under an isolation by distance model

Pubblicato online: 28 Jun 2018
Volume & Edizione: Volume 67 (2018) - Edizione 1 (February 2018)
Pagine: 41 - 50
Dettagli della rivista
License
Formato
Rivista
eISSN
2509-8934
Prima pubblicazione
22 Feb 2016
Frequenza di pubblicazione
1 volta all'anno
Lingue
Inglese
Abstract

In the present work, a new estimator to be known as rIBD is pro­posed. The proposed estimator indirectly quantifies the relati­ve role of gene flow mediated by pollen in relation to the gene flow mediated by seeds in hermaphrodite angiosperm species when an isolation by distance model is assumed. The proposed estimator complements the well-known estimator proposed by Ennos, which is appropriate for studies under the island model. In the present work, the proposed rIBD index was used to analyze microsatellite data from uni- and biparentally inherited genomes generated by simulations, as well as for the analysis of an empirical data set obtained from public databases of forest tree species. The differences in median values of the pro­posed rIBD index for simulated data using the Stepping Stone Model and Truncated Pareto Distribution Model coincided with the magnitude expected in terms of differences between levels of pollen and seed dispersion previously established in the simulations. In empirical data, the proposed rIBD index shows lower levels of gene flow by seed versus gene flow by pollen, the ratio between them being three times lower than the ratio obtained by the Ennos index estimated under the island model. From the analyses carried out, it is feasible to consider the rIBD index as a suitable estimator of the role of gene flow by seeds in relation to gene flow by pollen under iso­lation by distance.

Keywords

M, Austerlitz F, Elzinga J A, Teixeira S, Goudet J, Bernasconi G (2011) Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. He­redity 106: 13-24. https://doi.org/10.1038/hdy.2010.38 10.1038/hdy.2010.38318385920389310Apri DOISearch in Google Scholar

Charlesworth B (1998) Measures of divergence between populations and the ef­fect of forces that reduce variability. Mol Biol Evol 15: 538-543. https://doi.org/10.1093/oxfordjournals.molbev.a025953 10.1093/oxfordjournals.molbev.a0259539580982Apri DOISearch in Google Scholar

Cockerham CC (1973) Analysis of gene frequencies. Genetics 74: 679-700. Crawford T J (1984) The estimation of neighbourhood parameters for plant pop­ulations. Heredity 52(2): 273-283. https://doi.org/10.1038/hdy.1984.29 10.1038/hdy.1984.29Apri DOISearch in Google Scholar

Dainou K, Bizoux J, Doucet J, Mahy G, Hardy O J, Heuert M (2010) Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Mol Ecol 19: 4462-4477. https://doi.org/10.1111/j.1365-294x.2010.04831.x 10.1111/j.1365-294x.2010.04831.xApri DOISearch in Google Scholar

Ducousso A, Michaud H, Lumaret R (1993) Reproduction and gene flow in the genus Quercus L. Ann Sci Forest 50(11): 91-106. https://doi.org/10.1051/forest:19930708 10.1051/forest:19930708Apri DOISearch in Google Scholar

Dutech C, Sork V L, Irwin A J, Smouse P E, Davis F W (2005) Gene flow and fine-scale genetic structure in a wind-pollinated tree species, Quercus lobata (Fagaceae). Am J Bot 92(2): 252-261. https://doi.org/10.3732/ajb.92.2.252 10.3732/ajb.92.2.25221652402Apri DOISearch in Google Scholar

Ennos, R A (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72: 250-259. https://doi.org/10.1038/hdy.1994.35 10.1038/hdy.1994.35Apri DOISearch in Google Scholar

Epperson B K, Mcrae B H, Scribner K, Cushman S A, Rosenberg M S, Fortin M J, James P M, Murphy M, Manel S, Legendre P, Dale M R (2010) Utility of com­puter simulations in landscape genetics. Mol Ecol 19: 3549-3564. https://doi.org/10.1111/j.1365-294x.2010.04678.x 10.1111/j.1365-294x.2010.04678.xApri DOISearch in Google Scholar

Epperson, B K (1993) Spatial and spatial-time correlations in systems of subpop­ulations with genetic drift and migration. Genetics 133: 711-727. 10.1093/genetics/133.3.71112053548454211Search in Google Scholar

Epperson, B K (2007) Plant dispersal, neighbourhood size and isolation by dis­tance. Mol Ecol 16: 3854-3865. https://doi.org/10.1111/j.1365-294x.2007.03434.x 10.1111/j.1365-294x.2007.03434.xApri DOISearch in Google Scholar

Gerlach G, Jueterbock A, Kraemer P, Deppermann J, Harmand P (2010) Calcula­tions of population differentiation based on GST and D: Forget GST but not all of statistics! Mol Ecol 19(18): 3845-3852. 10.1111/j.1365-294X.2010.04784.x20735737Search in Google Scholar

Grivet D, Deguilloux M F, Petit R J, Sork V L (2006) Contrasting patterns of histori­cal colonization in white oaks (Quercus spp.) in California and Europe. Mol Ecol 15: 4085-4093. https://doi.org/10.1111/j.1365-294x.2006.03083.x 10.1111/j.1365-294x.2006.03083.xApri DOISearch in Google Scholar

Grivet D, Sork V L, Westfall R D, Davis F W (2008) Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genet­ic approach to conservation planning. Mol Ecol 17: 139-156. https://doi.org/10.1111/j.1365-294x.2007.03498.x 10.1111/j.1365-294x.2007.03498.xApri DOISearch in Google Scholar

Gugger P F, Ikegami M, Sork V L (2013a) Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quer­cus lobata Née. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g645d 10.5061/dryad.g645dApri DOISearch in Google Scholar

Gugger P F, Ikegami M, Sork V L (2013b) Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus loba­ta Née. Mol Ecol 22(13): 3598-3612. https://doi.org/10.1111/mec.12317 10.1111/mec.1231723802553Apri DOISearch in Google Scholar

Hedrick P W (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313-318. https://doi.org/10.1111/j.1558-5646.1999.tb03767.x 10.1111/j.1558-5646.1999.tb03767.x28565409Apri DOISearch in Google Scholar

Heller R, Siegismund H R (2009) Relationship between three measures of genet­ic differentiation GST, DEST and G’ST: How wrong have we been? Mol Ecol 18(10): 2080-2083. https://doi.org/10.1111/j.1365-294x.2009.04185.x 10.1111/j.1365-294X.2009.04185.x19645078Search in Google Scholar

Holsinger K E, Weir B S (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet 10:639-650. https://doi.org/10.1038/nrg2611 10.1038/nrg2611468748619687804Search in Google Scholar

Hu X, Ennos R A (1997) On estimation of the ratio of pollen to seed flow among plant populations. Heredity 79: 541-552. https://doi.org/10.1038/sj.hdy.6882080 10.1038/sj.hdy.6882080Apri DOISearch in Google Scholar

Hu X, Ennos R A (1999) Impacts of seed and pollen flow on population genetic structure for plant genomes with three contrasting modes of inheritance. Genetics 152: 441-450. 10.1093/genetics/152.1.441146059210224273Search in Google Scholar

Jakobsson M, Edge M D, Rosenberg N A (2013) The relationship between FST and the frequency, https://doi.org/10.1534/genetics.112.144758 10.1534/genetics.112.144758356774023172852Apri DOISearch in Google Scholar

Jenkins D G, Carey M, Czerniewska J, Fletcher J, Hether T, Jones A, Knight S, Knox J, Long T, Mannino M, McGuire M, Riffle A, Segelsky S, Shappell L, Sterner A, Strickler T, Tursi R (2010) A meta-analysis of isolation by distance: relic or ref­erence standard for landscape genetics? Ecography 33: 315-320. https://doi.org/10.1111/j.1600-0587.2010.06285.x 10.1111/j.1600-0587.2010.06285.xApri DOISearch in Google Scholar

Jost L (2008) GST and its relatives do not measure differentiation. Molecular Ecology 17(18): 4015-4026. https://doi.org/10.1111/j.1365-294x.2008.03887.x 10.1111/j.1365-294x.2008.03887.x19238703Apri DOISearch in Google Scholar

Jost L, Archer F, Flanagan S, Gaggiotti O, Hoban S, Latch E (2018) Differentiation measures for conservation genetics. Evolutionary Applications 1-10. https://doi.org/10.1111/eva.12590 10.1111/eva.12590605018330026802Apri DOISearch in Google Scholar

Kimura M (1953) “Stepping stone” model of population. Annu Rep Natio Inst Genet. 3: 62-63. Kimura M, Weiss G H (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49: 561-576. Search in Google Scholar

Leblois R, Beeravolu C R, Rousset F (2012) IBDSim version 2.0 User manual.Search in Google Scholar

Leblois R, Estoup A, Rousset F (2003) Influence of mutational and sampling fac­tors on the estimation of demographic parameters in a “continuous” popu­lation under isolation by distance. Mol Biol Evol 20(4): 491-502. https://doi.org/10.1093/molbev/msg034 10.1093/molbev/msg03412654930Apri DOISearch in Google Scholar

Leblois R, Estoup A, Rousset F (2008) IBDSim: a computer program to simulate genotypic data under isolation by distance. Mol Ecol Res 9(1): 107-109. https://doi.org/10.1111/j.1755-0998.2008.02417.x 10.1111/j.1755-0998.2008.02417.x21564573Apri DOISearch in Google Scholar

Leblois R, Rousset F, Estoup A (2004) Influence of spatial and temporal heteroge­neities on the estimation of demographic parameters in a continuous pop­ulation using individual microsatellite data. Genetics 166: 1081-1092. https://doi.org/10.1534/genetics.166.2.1081 10.1534/genetics.166.2.1081147072615020488Apri DOISearch in Google Scholar

Leng L, Zhang D X (2013) Time matters: Some interesting properties of the pop­ulation differentiation measures GST and D overlooked in the equilibrium perspective. Journal of Systematics and Evolution 51(1): 44-60. https://doi.org/10.1111/j.1759-6831.2012.00231.x 10.1111/j.1759-6831.2012.00231.xApri DOISearch in Google Scholar

Luximon N, Petit E J, Broquet T (2014) Performance of individual vs. group sam­pling for inferring dispersal under isolation-by-distance. Mol Ecol Res 14(4): 745-752. https://doi.org/10.1111/1755-0998.12224 10.1111/1755-0998.1222424400787Apri DOISearch in Google Scholar

Meirmans P G, Hedrick P W (2011) Assessing population structure: FST and relat­ed measures. Molecular Ecology Resources 11(1): 5-18. https://doi.org/10.1111/j.1755-0998.2010.02927.x 10.1111/j.1755-0998.2010.02927.x21429096Apri DOISearch in Google Scholar

Ndiade-Bourobou D, Hardy O J, Favreau B, Moussavou H, Nzengue E, Mignot A, Bouvet J M (2010) Long-distance seed and pollen dispersal inferred from spatial genetic structure in the very low-density rainforest tree, Baillonella toxisperma Pierre, in Central Africa. Mol Ecol 19: 4949-4962. https://doi.org/10.1111/j.1365-294x.2010.04864.x 10.1111/j.1365-294x.2010.04864.xApri DOISearch in Google Scholar

Neigel J E (1997) A comparison of alternative strategies for estimating gene flow from genetic markers. Annu Rev Ecol Evol Syst 28: 105-128. https://doi.org/10.1146/annurev.ecolsys.28.1.105 10.1146/annurev.ecolsys.28.1.105Apri DOISearch in Google Scholar

Nielsen R, Slatkin M (2013) An introduction to Population Genetics. Theory and Applications. Sinauer Associates, Inc. Publishers. Sunderland, Massachusetts U.S.A. https://doi.org/10.1086/673812 10.1086/673812Apri DOISearch in Google Scholar

Oddou-Muratorio S, Petit R J, Le Guerroue B, Guesnet D, Demesure B (2001) Pol­len- versus seed-mediated gene flow in a scattered forest tree species. Evo­lution 55(6): 1123-1135. https://doi.org/10.1554/0014-3820(2001)055[1123:pvsmgf]2.0.co;2 10.1554/0014-3820(2001)055[1123:pvsmgf]2.0.co;2Apri DOISearch in Google Scholar

Rousset F (1997) Genetic differentiation and estimation of gene flow from F-sta­tistics under isolation by distance. Genetics 145: 1219-1228. 10.1093/genetics/145.4.1219Search in Google Scholar

Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Res 8: 103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x 10.1111/j.1471-8286.2007.01931.xSearch in Google Scholar

Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236: 787-792. https://doi.org/10.1126/science.3576198 10.1126/.3576198Apri DOISearch in Google Scholar

Sork V L, Davis F W, Westfall R, Flint A, Ikegami M, Wang H, Grivet D (2010) Gene movement and genetic association with regional climate gradients in Cali­fornia valley oak (Quercus lobata Née) in the face of climate change. Mol Ecol 19: 3806-3823. https://doi.org/10.1111/j.1365-294x.2010.04726.x 10.1111/j.1365-294x.2010.04726.xApri DOISearch in Google Scholar

Sork V L, Nason J, Campbell D R, Fernandez J F (1999) Landscape approaches to historical and contemporary gene flow in plants. Trends Ecol Evol 14(6): 219-224. https://doi.org/10.1016/s0169-5347(98)01585-7 10.1016/s0169-5347(98)01585-7Apri DOISearch in Google Scholar

Tero N, Aspi J, Siikamäki P, Jäkäläniemi A (2005) Local genetic population struc­ture in an endangered plant species, Silene tatarica (Caryophyllaceae). He­redity 94: 478-487. https://doi.org/10.1038/sj.hdy.6800642 10.1038/sj.hdy.6800642Apri DOISearch in Google Scholar

van Strien M J, Holderegger R, Van Heck H J (2015) Isolation-by-distance in land­scapes: considerations for landscape genetics. Heredity 114: 27-37. https://doi.org/10.1038/hdy.2014.62 10.1038/hdy.2014.62481560125052412Apri DOISearch in Google Scholar

Weiss G H, Kimura M (1965) A mathematical analysis of the stepping stone mod­el of genetic correlation. Appl Probab 2: 129-149. https://doi.org/10.2307/3211879 10.2307/3211879Apri DOISearch in Google Scholar

Whitlock M C (2011). G’ST and D do not replace FST. Molecular Ecology 20(6): 1083-1091. https://doi.org/10.1111/j.1365-294x.2010.04996.x 10.1111/j.1365-294x.2010.04996.x21375616Apri DOISearch in Google Scholar

Whitlock M C, McCauley D E (1999) Indirect measures of gene flow and migra­tion: FST ≠ 1/(4Nm+1). Heredity 82: 117-125. https://doi.org/10.1038/sj.hdy.6884960 10.1038/sj.hdy.688496010098262Apri DOISearch in Google Scholar

Wright S (1943) Isolation by distance. Genetics 28: 114-138. 10.1093/genetics/28.2.114120919617247074Search in Google Scholar

Wright S (1946) Isolation by distance under diverse systems of mating. Genetics 31: 39-59. 10.1093/genetics/31.1.39120931521009706Search in Google Scholar

Wright S (1969) Evolution and the genetics of population Vol. 2 The theory of gene frequencies. University of Chicago Press, Chicago. https://doi.org/10.1126/science.168.3932.722 10.1126/.168.3932.722Apri DOISearch in Google Scholar

Wright, S (1951) The genetical structure of populations. Annals of Eugenics 15: 323-354. https://doi.org/10.1111/j.1469-1809.1949.tb02451.x10.1111/j.1469-1809.1949.tb02451.x24540312Apri DOISearch in Google Scholar

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