Conservation Genetics

, Volume 12, Issue 4, pp 1027–1033 | Cite as

Remnant native Phragmites australis maintains genetic diversity despite multiple threats

  • Kristin Saltonstall
Research Article


Over the past century, an increasing number of species have been negatively impacted by anthropogenic factors such as habitat disturbance and introduced species. One such plant, Phragmites australis subsp. americanus is a perennial emergent grass found in tidal and inland marshes of the Atlantic coast of the United States. While rarely dominant, it grows in mixed communities and across much of this area its distribution has been reduced dramatically, likely due to eutrophication and the invasion of conspecific P. australis introduced from Europe. In this study, two noncoding cpDNA markers and six microsatellite loci were used to characterize genetic diversity among 58 remnant native P. australis stands from North Carolina to Maine. Five chloroplast DNA haplotypes were identified along with 42 multilocus genotypes. Bayesian exploration detected no population structure (e.g., optimal K = 1), indicating that these individuals form a single population. The analysis also detected no presence of hybrids of native and introduced P. australis in the samples, despite the close proximity of individuals to each other in many cases. These results suggest that the genetic composition of native P. australis across the region remains homogeneous and pure, providing managers with justification for its conservation and a potentially large source of germplasm for use in restoration activities.


Common reed Conservation Hybridization Marsh Native Invasive species Restoration 



Thanks to Dr. Eldredge Bermingham and Dr. Oris Sanjur for financial support and use of laboratory facilities. I also thank Adam Lambert, Michael League, William McAvoy, Robert E. Meadows, Thomas Mozdzer, Thomas J. Rawinski, Ron Rosza, and Alice Wellford for assistance with sample collections and field identifications of native P. australis populations. Jefferson S. Hall and two anonymous reviewers provided comments on earlier versions of the manuscript.


  1. Ayres DR, Smith DL, Zaremba K, Klohr S, Strong DR (2004) Spread of exotic cordgrasses and hybrids (Spartina sp.) in the tidal marshes of San Francisco Bay, California, USA. Biol Invasions 6:221–231CrossRefGoogle Scholar
  2. Barbará T, Palma-Silva C, Paggi GM et al (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 16:3759–3767PubMedCrossRefGoogle Scholar
  3. Boecklen WJ, Howard DJ (1997) Analysis of hybrid zones: numbers of markers and power of resolution. Ecology 78:2611–2616CrossRefGoogle Scholar
  4. Doyle JJ, Dickson EE (1987) Preservation of plant samples for DNA restriction endonuclease analysis. Taxon 36:715–722CrossRefGoogle Scholar
  5. Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implications for plant conservation. Annu Rev Ecol Syst 24:217–242CrossRefGoogle Scholar
  6. Ellstrand NC, Schierenbeck KA (2000) Hybridization as a stimulus for the evolution of invasiveness in plants. Proc Natl Acad Sci USA 97:7043–7050PubMedCrossRefGoogle Scholar
  7. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  8. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  9. Gedan KB, Silliman BR (2009) Patterns of salt marsh loss within coastal regions of North America: presettlement to present. In: Silliman BR, Grosholz ED, Bertness MD (eds) Human impacts on salt marshes: a global perspective. University of California Press, Berkeley, pp 253–266Google Scholar
  10. Goudet J (2002) FSTAT, a program to estimate and test gene diversities and fixation indices. J Hered 86:485–486Google Scholar
  11. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B 351:1291–1298CrossRefGoogle Scholar
  12. Holderegger R, Kamm U, Gugerli F (2006) Adaptive vs neutral genetic diversity: implications for landscape genetics. Landsc Ecol 21:797–807CrossRefGoogle Scholar
  13. Hufford KM, Mazer SJ (2003) Plant ecotypes: genetic differentiation in the age of ecological restoration. Trends Ecol Evol 18:147–155CrossRefGoogle Scholar
  14. League MT, Colbert EP, Seliskar DM, Gallagher JL (2006) Rhizome growth dynamics of native and exotic haplotypes of Phragmites australis (common reed). Estuar Coasts 29:269–276CrossRefGoogle Scholar
  15. Lynch M (1991) The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45:622–629CrossRefGoogle Scholar
  16. Marchant CJ (1967) Evolution in Spartina (Gramineae). II. Chromosomes, basic relationships and the problem of Spartina × townsendii agg. Bot J Linn Soc 60:381–409Google Scholar
  17. Meadows RE (2006) Aboveground competition between native and introduced Phragmites in two tidal marsh basins in Delaware. MS thesis, Department of Biology, Delaware State UniversityGoogle Scholar
  18. Meadows RE, Saltonstall K (2007) Distribution of native and introduced Phragmites australis in freshwater and oligohaline tidal marshes of the Delmarva Peninsula and southern New Jersey. J Torrey Bot Soc 134:99–107CrossRefGoogle Scholar
  19. Meyerson LA, Viola DV, Brown RN (2010) Hybridization of invasive Phragmites australis with a native subspecies in North America. Biol Invasions 12:103–111Google Scholar
  20. Niering WA, Warren RS, Weymouth CG (1977) Our dynamic tidal marshes: vegetation changes as revealed by peat analysis. Conn Arbor Bull 12:22Google Scholar
  21. Novak SJ, Mack RN (2005) Genetic bottlenecks in alien plant species. In: Sax DF, Stachowicz JJ, Gaines SD (eds) Species invasions: insights into ecology, evolution, and biogeography. Sinauer Associates Inc, Sunderland, pp 201–228Google Scholar
  22. Orson R (1999) A paleoecological assessment of Phragmites australis in New England tidal marshes: changes in plant community structure during the last millenium. Biol Invasions 1:149–158CrossRefGoogle Scholar
  23. Packett CR, Chambers RM (2006) Distribution and nutrient status of haplotypes of the marsh grass Phragmites australis along the Rappahannock River in Virginia. Estuar Coasts 29:1222–1225Google Scholar
  24. Paetkau D, Slades R, Burdens M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13:55–65PubMedCrossRefGoogle Scholar
  25. Paul J, Vachon N, Garroway CJ, Freeland JR (2010) Molecular data provide strong evidence of natural hybridization between native and introduced lineages of Phragmites australis in North America. Biol Invasions 12:2967–2773Google Scholar
  26. Pemberton JM, Slate J, Bancroft DR, Barrett JA (1995) Non-amplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252PubMedCrossRefGoogle Scholar
  27. Piry S, Alapetite A, Cornuet JM et al (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539PubMedCrossRefGoogle Scholar
  28. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  29. Raicu P, Staicu S, Stoian V, Roman T (1972) The Phragmites communis Trin. chromosome complement in the Danube delta. Hydrobiologia 39:83–89CrossRefGoogle Scholar
  30. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201PubMedCrossRefGoogle Scholar
  31. Saltonstall K (2001) A set of primers for amplification of noncoding regions of chloroplast DNA in the grasses. Mol Ecol Notes 1:76–78CrossRefGoogle Scholar
  32. Saltonstall K (2002) Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc Natl Acad Sci USA 99:2445–2449PubMedCrossRefGoogle Scholar
  33. Saltonstall K (2003a) Genetic variation among North American populations of Phragmites australis: implications for management. Estuaries 26:444–451CrossRefGoogle Scholar
  34. Saltonstall K (2003b) Microsatellite variation within and among North American lineages of Phragmites australis. Mol Ecol 12:1689–1702PubMedCrossRefGoogle Scholar
  35. Saltonstall K, Stevenson JC (2007) The effect of nutrients on seedling growth of native and introduced Phragmites australis. Aquat Bot 86:331–336CrossRefGoogle Scholar
  36. Saltonstall K, Peterson PM, Soreng RJ (2004) Recognition of Phragmites australis subsp. americanus (Poaceae: Arundinoideae) in North America: evidence from morphological and genetic analyses. SIDA 21:683–692Google Scholar
  37. Saltonstall K, Glennon K, Barnett A, Hunter RB, Hunter K (2007) Comparison of morphological variation indicative of ploidy level in Phragmites australis (Poaceae) from eastern North America. Rhodora 109:415–429CrossRefGoogle Scholar
  38. Saltonstall K, Lambert A, Meyerson LA (2010) Genetics and reproduction of common (Phragmites australis) and giant reed (Arundo donax). Invasive Plant Sci Manag 3:495–505CrossRefGoogle Scholar
  39. Seehausen O (2004) Hybridization and adaptive radiation. Trends Ecol Evol 19:198–207PubMedCrossRefGoogle Scholar
  40. Silliman BR, Bertness MD (2004) Shoreline development drives invasion of Phragmites australis and the loss of plant diversity on New England salt marshes. Conserv Biol 18:1424–1434CrossRefGoogle Scholar
  41. Stebbins GL (1959) The role of hybridization in evolution. Proc Am Philos Soc 103:231–251Google Scholar
  42. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109PubMedCrossRefGoogle Scholar
  43. Vähä J-P, Primmer CR (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15:63–72PubMedCrossRefGoogle Scholar
  44. Vasquez EA, Glenn EP, Brown JJ, Guntenspergen GR, Nelson SC (2005) Salt tolerance underlies the cryptic invasion of North American salt marshes by an introduced haplotype of the common reed Phragmites australis (Poaceae). Mar Ecol Prog Ser 298:1–8CrossRefGoogle Scholar
  45. Vilà C, Walker C, Sundqvist A-K et al (2003) Combined use of maternal, paternal and bi-parental genetic markers for the identification of hybrids. Heredity 90:17–24PubMedCrossRefGoogle Scholar
  46. Vitousek PM, Mooney HA, Lubchenco J, Melillo JM (1997) Human domination of earth’s ecosystems. Science 277:494–499CrossRefGoogle Scholar
  47. Wilcove DS, Rothstein D, Dubow J, Phillips A, Losos E (1998) Quantifying threats to imperiled species in the United States. Bioscience 48:607–615CrossRefGoogle Scholar
  48. Zedler JB, Kercher S (2004) Causes and consequences of invasive plants in wetlands: opportunities, opportunists, and outcomes. Crit Rev Plant Sci 23:431–452CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Smithsonian Tropical Research InstitutePanamáRepublic of Panamá

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