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Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris

Abstract

Habitat alteration, fragmentation and destruction as a consequence of human impact are a global phenomenon. Here we document changes in genetic variation in the marsh orchid Anacamptis palustris as a consequence of such habitat changes. We examined historical specimens that were collected during the nineteenth and early twentieth centuries, prior to the most recent massive habitat changes affecting this species. Sequences of a hypervariable region in the plastid DNA, located in the tRNALEU intron, from herbarium vouchers were compared with those from a near-exhaustive survey of the extant A. palustris populations on the Italian peninsula. It was found that private haplotypes and alleles found in small, extant populations were once widespread and more common in historic populations and that alleles, once present in historic populations, have gone extinct. In addition, genetic differentiation among populations has increased over time and haplotype frequencies significantly differ among historic and extant populations. These results document that human induced habitat changes have reduced genetic diversity and increased the importance of random genetic drift in this species. It is concluded that the analysis of herbarium specimens may provide important insights into changes of genetic diversity over time and may be critical for correct inference of the evolutionary history of rare and endangered species.

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References

  • Arditti J, Ghani AKA (2000) Tansley review No. 110—numerical and physical properties of orchid seeds and their biological implications. New Phytol 145:67–421

    Article  Google Scholar 

  • Bevilacqua P, Rossi-Doria M (1984) Lineamenti per una storia delle bonifiche in Italia dal ‘700 a oggi. Laterza, Roma-Bari

  • Cozzolino S, Cafasso D, Pellegrino G, Musacchio A, Widmer A (2003a) Fine-scale phylogeographical analysis of Mediterranean Anacamptis palustris (Orchidaceae) populations based on chloroplast minisatellite and microsatellite variation. Mol Ecol 12:2783–2792

    Article  CAS  Google Scholar 

  • Cozzolino S, Noce ME, Musacchio A, Widmer A (2003b) Variation at a chloroplast minisatellite locus reveals the signature of habitat fragmentation and genetic bottlenecks in the rare orchid Anacamptis palustris (Orchidaceae). Am J Bot 90:1681–1687

    Google Scholar 

  • Cozzolino S, Cafasso D, Pellegrino G, Musacchio A, Widmer A (2003c) Molecular evolution of a plastid tandem repeat locus in an orchid lineage. J Mol Evol 57:41–49

    Article  Google Scholar 

  • Cozzolino S, Cafasso D, Pellegrino G, Musacchio A, Widmer A (2004) Hypervariable plastid locus variation and intron evolution in the Anacamptis palustris lineage. Genome 47:999–1003

    PubMed  Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Drábková L, Kirschner J, Vlcek C (2002) Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Mol Biol Rep 20:161–175

    Google Scholar 

  • Ellegren H (1991) DNA typing of museum birds. Nature 354:113

    PubMed  Article  CAS  Google Scholar 

  • Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24:400–402

    PubMed  Article  CAS  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online

  • Fay M, Cowan RS (2001) Plastid microsatellites in Cypripedium calceolus (Orchidaceae): genetic fingerprints from herbarium specimens. Lindleyana 16:151–156

    Google Scholar 

  • Fréville H, Colas B, Ronfort J, Riba M, Olivieri I (1998) Predicting endemism from population structure of a widespread species: case study in Centaurea maculosa Lam. (Asteraceae). Conserv Biol 12:1269–1278

    Article  Google Scholar 

  • Gilbert MTP, Bandelt H, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541–544

    PubMed  Article  Google Scholar 

  • Glenn TC, Stephan W, Braun MJ (1999) Effects of population bottleneck on whooping crane mitochondrial DNA variation. Conserv Biol 13:1097–1107

    Article  Google Scholar 

  • Maunder M, Culham A, Bordeu A, Allainguillaume J, Wilkinson M (1999) Genetic diversity and pedigree for Sophora toromiro (Leguminosae): a tree extinct in the wild. Mol Ecol 8:725–738

    Article  Google Scholar 

  • Miller MP (1997) Tools for population genetic analyses (TFPGA) 1.3: a windows program for the analysis of allozyme and molecular population genetic data. Computer software distributed by the author

  • Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conversation. Proc Natl Acad Sci USA 100:4334–4339

    PubMed  Article  CAS  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nielsen EE, Hansen MM, Loeschcke V (1999) Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution 53:261–268

    Article  Google Scholar 

  • Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855

    Article  Google Scholar 

  • Pichler FB, Baker GS (2000) Loss of genetic diversity in the endemic Hector’s dolphin due to fisheries-related mortality. Proc R Soc B Biol Sci 267:97–102

    Article  CAS  Google Scholar 

  • Pons O, Petit RJ (1995) Estimation, variance and optimal sampling of gene diversity. 1. Haploid locus. Theor Appl Genet 90:462–470

    Article  Google Scholar 

  • Rosenbaum HC, Egan MG, Clapham PJ, Brownell RL Jr, Malik S, Brown MW, White BN, Walsh P, Desalle R (2000) Utility of North Atlantic right whale museum specimens for assessing changes in genetic diversity. Conserv Biol 14:1837–1842

    Article  Google Scholar 

  • Roy MS, Girman DJ, Taylor AC, Wayne RK (1994) The use of museum specimens to reconstruct the genetic variability and relationships of extinct populations. Experientia 50:551–557

    PubMed  Article  CAS  Google Scholar 

  • Saltonstall K (2002) Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc Natl Acad Sci USA 99:2445–2449

    PubMed  Article  CAS  Google Scholar 

  • Savolainen V, Cuénoud P, Spichiger R, Martinez MDP, Crèvecoeur M, Manen JF (1995) The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Syst Evol 197:87–98

    Article  CAS  Google Scholar 

  • Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants: problems and prospects. Mol Ecol 7:465–474

    Article  Google Scholar 

  • Taberlet P, Bouvet J (1992) Bear conservation genetic. Nature 358:197

    PubMed  Article  CAS  Google Scholar 

  • Tessier N, Bernatchez L (1999) Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.). Mol Ecol 8:169–179

    Article  Google Scholar 

  • Thomas WK, Pääbo S, Villablanca FX, Wilson AC (1990) Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. J Mol Evol 31:101–112

    PubMed  Article  CAS  Google Scholar 

  • Towne B, Devor EJ (1990) Effect of storage time and temperature on DNA extracted from whole blood samples. Hum Biol 62:301–306

    PubMed  CAS  Google Scholar 

  • Waples RB (1989) Temporal variation in allele frequencies: testing the right hypothesis. Evolution 43:1236–1251

    Article  Google Scholar 

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Acknowledgments

The authors thank the herbarium institutions (NAP, FI, ROMA, TO, Z/ZT) for providing access to their historic collections and for permitting sampling of specimens. In particular we thank the herbarium curators, namely M. Baltisberger, P. Cuccuini, L. Guglielmone, A. Millozza, and A. Santangelo for their invaluable help in specimen identification, label translation, and sample shipment. The authors also thank three anonymous reviewers for their comment that contributed to improve the MS. The present study was supported by the PRIN program of the Italian Ministry of the University and Scientific research and by a Swiss Federal Institute of Technology (ETH) grant to AW.

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Correspondence to Salvatore Cozzolino.

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Cozzolino, S., Cafasso, D., Pellegrino, G. et al. Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris . Conserv Genet 8, 629–639 (2007). https://doi.org/10.1007/s10592-006-9209-7

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Keywords

  • Anacamptis palustris
  • Plastid DNA
  • Herbarium specimens
  • Historic haplotype diversity
  • Temporal variation