Population history and seed dispersal in widespread Central American Begonia species (Begoniaceae) inferred from plastome-derived microsatellite markers

Botanical Journal of the Linnean Society

Volumn 171, Issue 1, 2013, Pages 260-276

  Twyford, Alex D ^a,b   Kidner, Catherine A ^a,b   Harrison, Nicola ^a,b,c   Ennos, Richard A ^b  

^a ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c EAST MALLING RESEARCH   (United Kingdom)

Author keywords

Dispersal limitation; Isthmus of Tehuantepec; Mexico; Phylogeography; Plastid microsatellites; Pleistocene climate change; Pleistocene refugia

Indexed keywords

ADAPTATION; BIOMARKER; DIVERGENCE; GENETIC STRUCTURE; PHYLOGEOGRAPHY; PLANT; POPULATION BOTTLENECK; POPULATION GENETICS; POPULATION MODELING; SEED DISPERSAL; SPECIES DIVERSITY;

CENTRAL AMERICA; ISTHMUS OF TEHUANTEPEC; MEXICO [NORTH AMERICA];

BEGONIA; BEGONIA HERACLEIFOLIA; BEGONIA NELUMBIIFOLIA; BEGONIACEAE;

EID: 84871255424     PISSN: 00244074     EISSN: 10958339     Source Type: Journal    
DOI: 10.1111/j.1095-8339.2012.01265.x     Document Type: Article

References (78)

1. Ågren J, Schemske DW. 1991. Pollination by deceit in a Neotropical monoecious herb, Begonia involucrata. Biotropica 23: 235-241.
2. Antonelli A, Sanmartín I. 2011. Why are there so many plant species in the Neotropics? Taxon 60: 403-414.
3. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522.
4. Barrier E, Velasquillo L, Chavez M, Gaulon R. 1998. Neotectonic evolution of the Isthmus of Tehuantepec (southeastern Mexico). Tectonophysics 287: 77-96.
5. Bawa KS. 1992. Mating systems, genetic differentiation and speciation in tropical rain forest plants. Biotropica 24: 250-255.
6. Bermingham E, Moritz C. 1998. Comparative phylogeography: concepts and applications. Molecular Ecology 7: 367-369.
7. Bryson RW, García-Vázquez UO, Riddle BR. 2011. Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone. Journal of Biogeography 38: 1570-1584.
8. Burt-Utley K. 1985. A revision of Central American species of Begonia section Gireoudia (Begoniaceae). Tulane Studies in Zoology and Botany 25: 1-131.
9. Cárdenas ML, Gosling WD, Sherlock SC, Poole I, Pennington RT, Mothes P. 2011. The response of vegetation on the Andean flank in Western Amazonia to Pleistocene climate change. Science 331: 1055-1058.
10. Cardoso MA, Provan J, Powell W, Ferreira PCG, De Oliveira DE. 1998. High genetic differentiation among remnant populations of the endangered Caesalpinia echinata Lam. (Leguminosae-Caesalpinioideae). Molecular Ecology 7: 601-608.
11. Castoe TA, Daza JM, Smith EN, Sasa MM, Kuch U, Campbell JA, Chippindale PT, Parkinson CL. 2009. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. Journal of Biogeography 36: 88-103.
12. Cavers S, Navarro C, Lowe AJ. 2003. Chloroplast DNA phylogeography reveals colonization history of a Neotropical tree, Cedrela odorata L., in Mesoamerica. Molecular Ecology 12: 1451-1460.
13. Ceplitis ALF, Su Y, Lascoux M. 2005. Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology 14: 4221-4233.
14. Chan EY. 2009. Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery. Methods in Molecular Biology 578: 95-111.
15. Colinvaux PA, De Oliveira PE, Bush MB. 2002. Amazonian and Neotropical plant communities on glacial time-scales: the failure of the aridity and refuge hypothesis. Quaternary Science Reviews 19: 141-169.
16. Cornuet JM, Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
17. Corriveau JL, Coleman AW. 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany 75: 1443-1458.
18. Crawford NG. 2010. SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources 10: 556-557.
19. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research 36: e122.
20. Devitt TJ. 2006. Phylogeography of the western lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition. Molecular Ecology 15: 4387-4407.
21. Dewitte A, Twyford AD, Thomas DC, Kidner CA, Van Huylenbroeck J. 2011. The origin of diversity in Begonia: genome dynamism, population processes and phylogenetic patterns. In: Grillo O, Venora G, eds. The dynamical processes of biodiversity - case studies of evolution and spatial distribution. InTech, DOI: 10.5772/23789.
22. Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A. 2011. Geneious v5.4. Available at: http://www.geneious.com/ (Accessed 2 November 2011).
23. Duminil J, Hardy O, Petit R. 2009. Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure. BMC Evolutionary Biology 9: 177.
24. Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11: 2571-2581.
25. Ebert D, Peakall R. 2009. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and application to a wide array of plant species. Molecular Ecology Resources 9: 673-690.
26. Ennos RA. 1994. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72: 250-259.
27. Ennos RA, Sinclair WT, Hu X-S, Langdon A. 1999. Using organelle markers to elucidate the history, ecology and evolution of plant populations. In: Hollingsworth PM, Bateman RM, Gornall RJ, eds. Molecular systematics and plant evolution. London: Taylor & Francis, 1-19.
28. Ersts PJ. Internet. Geographic Distance Matrix Generator (version 1.2.3). American Museum of Natural History, Center for Biodiversity and Conservation. Available at: http://biodiversityinformatics.amnh.org/open_source/gdmg (Accessed 1 November 2011).
29. Escalante T, Rodríguez G, Cao N, Ebach M, Morrone J. 2007. Cladistic biogeographic analysis suggests an early Caribbean diversification in Mexico. Die Naturwissenschaften 94: 561-565.
30. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
31. Fazekas AJ, Steeves R, Newmaster SG. 2010. Improving sequencing quality from PCR products containing long mononucleotide repeats. BioTechniques 48: 277-285.
32. Fontaine C, Lovett PN, Sanou H, Maley J, Bouvet JM. 2004. Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers. Heredity 93: 639-648.
33. French GC. 2003. Conservation genetics of British Euphrasia L. PhD Thesis. University of Edinburgh and Royal Botanic Garden Edinburgh.
34. Frodin DG. 2004. History and concepts of big plant genera. Taxon 53: 753-776.
35. Goodall-Copestake W, Pérez-Espona S, Harris DJ, Hollingsworth PM. 2010. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biological Journal of the Linnean Society 101: 243-250.
36. Gutiérrez-Rodríguez C, Ornelas JF, Rodríguez-Gómez F. 2011. Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests. Molecular Phylogenetics and Evolution 61: 603-615.
37. Haffer J. 1969. Speciation in Amazonian forest birds. Science 165: 131-137.
38. Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59: 1633-1638.
39. Hewitt GM. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
40. Hoover S. 1979. Notes on the spatial distribution patterns for three Mexican species of Begonia. Phytologia 34: 107-132.
41. Hughes M, Hollingsworth PM. 2008. Population genetic divergence corresponds with species-level biodiversity patterns in the large genus Begonia. Molecular Ecology 17: 2643-2651.
42. Hughes M, Hollingsworth PM, Miller AG. 2003. Population structure in the endemic Begonia of the Socotra archipelago. Biological Conservation 113: 277-284.
43. Jakobsson M, Säll T, Lind-Halldán C, Halldén C. 2007. Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. Theoretical and Applied Genetics 114: 223-235.
44. Jensen J, Bohonak A, Kelley S. 2005. Isolation by distance, web service. BMC Genetics 6: 13.
45. ST and its relatives do not measure differentiation. Molecular Ecology 17: 4015-4026.
46. Legro RAH, Doorenbos J. 1969. Chromosome numbers in Begonia. Netherlands Journal of Agricultural Science 17: 189-202.
47. Martins WS, Soares Lucas DC, de Souza Neves KF, Bertioli DJ. 2009. WebSat - a web software for microsatellite marker development. Bioinformation 3: 282-283.
48. Matolweni LO, Balkwill K, Mclellan T. 2000. Genetic diversity and gene flow in the morphologically variable, rare endemic Begonia dregei and Begonia homonyma (Begoniaceae). American Journal of Botany 87: 431-439.
49. Mayer C. 20062010. Phobos 3.3.11 Available at: http://www.rub.de/spezzoo/cm/cm_phobos.htm (Accessed 25 October 2011).
50. Mayr E, O'Hara RJ. 1986. The biogeographic evidence supporting the Pleistocene forest refuge hypothesis. Evolution 1: 55-67.
51. ST and related measures. Molecular Ecology Resources 11: 5-18.
52. Metcalfe SE, O'Hara SL, Caballero M, Davies SJ. 2000. Records of late Pleistocene-Holocene climatic change in Mexico - a review. Quaternary Science Reviews 19: 699-721.
53. Micheneau C, Duffy KJ, Smith RJ, Stevens LJ, Stout JC, Civeyrel L, Cowan RS, Fay MF. 2010. Plastid microsatellites for the study of genetic variability in the widespread Cephalanthera longifolia, C.damasonium and C.rubra (Neottieae, Orchidaceae), and cross-amplification in other Cephalanthera species. Botanical Journal of the Linnean Society 163: 181-193.
54. Morrone JJ. 2006. Biogeographic areas and transition zones of Latin America and the Caribbean islands based on panbiogeographic and cladistic analyses of the entomofauna. Annual Review of Entomology 51: 467-494.
55. Mulcahy DG, Morrill BH, Mendelson JR. 2006. Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec. Journal of Biogeography 33: 1889-1904.
56. Myers N, Mittermeier RA, Mittermeier CG, de Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
57. Nei M, Maruyama T, Chakraborty R. 1975. The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
58. Ornelas JF, Ruiz-Sánchez E, Sosa V. 2010. Phylogeography of Podocarpus matudae (Podocarpaceae): pre-Quaternary relicts in northern Mesoamerican cloud forests. Journal of Biogeography 37: 2384-2396.
59. Petit RJ, Aguinagalde I, de Beaulieu J-L, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Müller-Starck G, Demesure-Musch B, Palmé A, Martín JP, Rendell S, Vendramin GG. 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
60. Poelchau M, Hamrick J. 2012a. Comparative phylogeography of three common Neotropical tree species. Journal of Biogeography DOI: 10.1111/j.1365-2699.2011.02599.x.
61. Poelchau M, Hamrick J. 2012b. Palaeodistribution modeling does not support disjunct Pleistocene refugia in several Central American plant taxa. Journal of Biogeography DOI: 10.1111/j.1365-2699.2011.02648.x.
62. Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245.
63. Prance GT. 1987. Biogeography of Neotropical plants. In: Whitmore TC, Prance GT, eds. Biogeography and Quaternary history in tropical America. Oxford: Clarendon Press, 46-65.
64. Provan J, Powell W, Hollingsworth PM. 2001. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends in Ecology and Evolution 16: 142-147.
65. Provan J, Soranzo N, Wilson NJ, Goldstein DB, Powell W. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153: 943-947.
66. Quinn JF, Harrison SP. 1988. Effects of habitat fragmentation and isolation on species richness: evidence from biogeographic patterns. Oecologia 75: 132-140.
67. Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM. 2001. Rapid diversification of a species-rich genus of Neotropical rain forest trees. Science 293: 2242-2245.
68. Rousset F. 1997. Genetic Differentiation and Estimation of Gene Flow from F-Statistics Under Isolation by Distance. Genetics 145: 1219-1228.
69. Schuelke M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233-234.
70. Sullivan J, Arellano E, Rogers DS. 2000. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. American Naturalist 155: 755-768.
71. Teacher AGF, Griffiths DJ. 2011. HapStar: automated haplotype network layout and visualization. Molecular Ecology Resources 11: 151-153.
72. Thomas DC, Hughes M, Phutthai T, Ardi WH, Rajbhandary S, Rubite R, Twyford AD, Richardson JE. 2011. West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago. Journal of Biogeography 39: 98-113.
73. Toledo VM. 1982. Pleistocene changes of vegetation in tropical Mexico. In: Prance GT, ed. Biological diversification in the Tropics: Proceedings of the Fifth International Symposium of the Association for Tropical Biology, Caracas. New York: Columbia University Press, 93-111.
74. Vallone PM, Butler JM. 2004. AutoDimer: a screening tool for primer-dimer and hairpin structures. BioTechniques 37: 226-231.
75. Vendramin GG, Fady B, González-Martínez SC, Hu FS, Scotti I, Sebastiani F, Soto Á, Petit RJ. 2008. Genetically depauperate but widespread: the case of an emblematic Mediterranean pine. Evolution 62: 680-688.
76. Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R. 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology 19: 100-114.
77. Worth JRP, Marthick JR, Jordan GJ, Vaillancourt RE. 2011. Low but structured chloroplast diversity in Atherosperma moschatum (Atherospermataceae) suggests bottlenecks in response to the Pleistocene glacial. Annals of Botany 108: 1247-1256.
78. Wright SI, Nano N, Foxe JP, Dar VN. 2008. Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis. Genetics Research 90: 119-128.