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Optimal sample sizes and allelic diversity in studies of the genetic variability of mycobiont and photobiont populations

Published online by Cambridge University Press:  16 December 2010

Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland. Email:


Population genetic studies of lichen-forming fungi and their algae require appropriate sampling schemes that ensure representative sampling of the genetic variability. One question is whether mycobiont and photobiont populations require different sampling strategies. Here, I applied rarefaction methods to a dataset containing three microsatellite loci of Lobaria pulmonaria and three microsatellite loci of its green-algal photobiont, Dictyochloropsis reticulata. I analysed the sample sizes required for 1) the number of individuals per population, 2) the number of individuals required across a landscape and 3) the number of populations. The analyses were performed separately for the mycobiont and photobiont loci to detect any differences in the accumulation of genetic diversity among the symbionts that would require different sampling schemes. About 20 individuals were sufficient at the population level; within landscapes, 300–400 samples and about 25–30 populations covered most of the allelic diversity. The results indicated that a slightly higher sampling effort was required for the photobiont than for the mycobiont. The optimal sampling strategy strongly depends on the research question, the spatial scale of investigation, and the type of analysis to be performed with the data.

Research Article
Copyright © British Lichen Society 2010

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Balding, D. J., Bishop, M. & Cannings, C. (2007) Handbook of Statistical Genetics. Chichester, UK: Wiley.CrossRefGoogle Scholar
Beerli, P. & Felsenstein, J. (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the United States of America 98: 45634568.CrossRefGoogle ScholarPubMed
Chao, A. (1984) Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265270.Google Scholar
Chao, A. (2005) Species richness estimation. In Encyclopedia of Statistical Sciences (Balakrishnan, N., Read, C. B. & Vidakovic, B., eds): 79097916. New York: Wiley.Google Scholar
Chao, A. & Lee, S. M. (1992) Estimating the number of classes via sample coverage. Journal of the American Statistical Association 87: 210217.CrossRefGoogle Scholar
Chung, M. Y., Nason, J. D. & Chung, M. G. (2005) Spatial genetic structure in populations of the terrestrial orchid Orchis cyclochila (Orchidaceae). Plant Systematics and Evolution 254: 209219.CrossRefGoogle Scholar
Dixon, C. J. (2006) A means of estimating the completeness of haplotype sampling using the Stirling probability distribution. Molecular Ecology Notes 6: 650652.CrossRefGoogle 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 (Fagaceaee). American Journal of Botany 92: 252261.CrossRefGoogle Scholar
Fitzpatrick, B. M. (2009) Power and sample size for nested analysis of molecular variance. Molecular Ecology 18: 39613966.CrossRefGoogle ScholarPubMed
Gotelli, N. J. & Colwell, R. K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4: 379391.CrossRefGoogle Scholar
Hewitt, G. M. (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58: 247276.CrossRefGoogle Scholar
Hewitt, G. M. (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907913.CrossRefGoogle ScholarPubMed
Hurlbert, S. H. (1971) The nonconcept of species diversity – critique and alternative parameters. Ecology 52: 577586.CrossRefGoogle Scholar
Jones, T. H., Vaillancourt, R. E. & Potts, B. M. (2006) Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forest. Molecular Ecology 16: 697707.CrossRefGoogle ScholarPubMed
Lättman, H., Lindblom, L., Mattsson, J. E., Milberg, P., Skage, M. & Ekman, S. (2009) Estimating the dispersal capacity of the rare lichen Cliostomum corrugatum. Biological Conservation 142: 18701878.CrossRefGoogle Scholar
Lindblom, L. (2009) Sample size and haplotype richness in population samples of the lichen-forming ascomycete Xanthoria parietina. Lichenologist 41: 529535.CrossRefGoogle Scholar
Lindblom, L. & Ekman, S. (2006) Genetic variation and population differentiation in the lichen-forming ascomycete Xanthoria parietina on the island Storfosna, central Norway. Molecular Ecology 15: 15451559.CrossRefGoogle ScholarPubMed
Lindblom, L. & Ekman, S. (2007) New evidence corroborates population differentiation in Xanthoria parietina. Lichenologist 39: 259271.CrossRefGoogle Scholar
Linde, C. C., Zhan, J. & McDonald, B. A. (2002) Population structure of Mycosphaerella graminicola: from lesions to continents. Phytopathology 92: 946955.CrossRefGoogle ScholarPubMed
Nordborg, M. (2001) Coalescent theory. In Handbook of Statistical Genetics (Balding, D. J., Bishop, M. J. & Cannings, C., eds): 179212. Chichester, UK: John Wiley & Sons, Inc.Google Scholar
Oksanen, J. (2005) Vegan: Community ecology package. R package version 1.6-7.: URL:∼jarioksa/.Google Scholar
Piercey-Normore, M. D. (2006) The lichen-forming ascomycete Evernia mesomorpha associates with multiple genotypes of Trebouxia jamesii. New Phytologist 169: 331344.CrossRefGoogle ScholarPubMed
Printzen, C., Ekman, S. & Tønsberg, T. (2003) Phylogeography of Cavernularia hultenii: evidence of slow genetic drift in a widely disjunct lichen. Molecular Ecology 12: 14731486.CrossRefGoogle Scholar
R Development Core Team (2008) R: a Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.Google ScholarPubMed
Templeton, A. R. (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7: 381397.CrossRefGoogle ScholarPubMed
Templeton, A. R. (2004) Statistical phylogeography: Methods of evaluating and minimizing inference errors. Molecular Ecology 13: 789809.CrossRefGoogle ScholarPubMed
Wagner, H. H., Holderegger, R., Werth, S., Gugerli, F., Hoebee, S. E. & Scheidegger, C. (2005) Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data. Genetics 169: 17391752.CrossRefGoogle ScholarPubMed
Walser, J. C., Sperisen, C., Soliva, M. & Scheidegger, C. (2003) Fungus-specific microsatellite primers of lichens: application for the assessment of genetic variation on different spatial scales in Lobaria pulmonaria. Fungal Genetics and Biology 40: 7282.CrossRefGoogle ScholarPubMed
Walser, J. C., Holderegger, R., Gugerli, F., Hoebee, S. E. & Scheidegger, C. (2005) Microsatellites reveal regional population differentiation and isolation in Lobaria pulmonaria, an epiphytic lichen. Molecular Ecology 14: 457467.CrossRefGoogle ScholarPubMed
Werth, S. (2010) Population genetics of lichen-forming fungi – a review. Lichenologist 42: 499519.CrossRefGoogle Scholar
Werth, S. & Sork, V. L. (2008) Local genetic structure in a North American epiphytic lichen, Ramalina menziesii (Ramalinaceae). American Journal of Botany 95: 568576.CrossRefGoogle Scholar
Werth, S. & Sork, V. L. (2010) Identity and genetic structure of the photobiont of the epiphytic lichen Ramalina menziesii on three oak species in southern California. American Journal of Botany 97: 821830.CrossRefGoogle ScholarPubMed
Werth, S., Wagner, H. H., Holderegger, R., Kalwij, J. M. & Scheidegger, C. (2006) Effect of disturbances on the genetic diversity of an old-forest associated lichen. Molecular Ecology 15: 911921.CrossRefGoogle ScholarPubMed
Werth, S., Gugerli, F., Holderegger, R., Wagner, H. H., Csencsics, D. & Scheidegger, C. (2007) Landscape-level gene flow in Lobaria pulmonaria, an epiphytic lichen. Molecular Ecology 16: 28072815.CrossRefGoogle ScholarPubMed
Widmer, I., Dal Grande, F., Cornejo, C. & Scheidegger, C. (2010) Highly variable microsatellite markers for the fungal and algal symbionts of the lichen Lobaria pulmonaria and challenges in developing biont-specific molecular markers for fungal associations. Fungal Biology 114: 538544.CrossRefGoogle ScholarPubMed
Wornik, S. & Grube, M. (2010) Joint dispersal does not imply maintenance of partnerships in lichen symbioses. Microbial Ecology 59: 150157.CrossRefGoogle Scholar
Yahr, R., Vilgalys, R. & DePriest, P. T. (2006) Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis. New Phytologist 171: 847860.CrossRefGoogle ScholarPubMed
Yamagishi, H., Tomimatsu, H. & Ohara, M. (2007) Fine-scale spatial genetic structure within continuous and fragmented populations of Trillium camschatcense. Journal of Heredity 98: 367372.CrossRefGoogle ScholarPubMed
Zoller, S., Lutzoni, F. & Scheidegger, C. (1999) Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation. Molecular Ecology 8: 20492059.CrossRefGoogle ScholarPubMed