Molecular Ecology (2003) 12, 1689–1702 doi: 10.1046/j.1365-294X.2003.01849.x© 2003 Blackwell Publishing LtdBlackwell Publishing Ltd.Microsatellite variation within and among North American lineages of Phragmites australisK. SALTONSTALL*Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA AbstractOver the past century, the spread of the common reed (Phragmites australis) has had adramatic impact on wetland communities across North America. Although native popula-tions of Phragmites persist, introduced invasive populations have dominated manysites and it is not clear if the two types can interbreed. This study compares patterns ofdifferentiation in 10 microsatellite loci among North American and European Phragmitesindividuals with results obtained from sequencing of noncoding chloroplast DNA. Threepopulation lineages (native, introduced and Gulf Coast) were previously identified inNorth America from chloroplast DNA and similar structuring was found in the nucleargenome. Each lineage was distinguished by unique alleles and allele combinations and theintroduced lineage was closely related to its hypothesized source population in Europe.Size homoplasy and diagnostic base substitutions distinguishing lineages were evident atseveral loci, further emphasizing that native, introduced and Gulf Coast North AmericanPhragmites lineages are genetically distinct. Gene flow between lineages was low andinvasive introduced populations do not represent a hybrid population type.Keywords: hybridization, invasive species, microsatellite DNA markers, Phragmites australis,population structureReceived 18 October 2002; revision received 18 February 2003; accepted 18 February 2003IntroductionExotic invasive species pose one of the greatest threats tospecies and habitat diversity today, second only to habitatloss (Wilcove et al. 1998). In addition to their impacts at thecommunity and ecosystems levels, such introductionspose a number of threats at the genetic level to closelyrelated species and locally adapted populations of thesame species. Perhaps most significant are the effects ofhybridization with closely related species (Anderson &Stebbins 1954; Lewontin & Birch 1966), which can quicklychange the genetic composition of native populations andcause loss of local adaptations (Anttila et al. 1998; Huxel1999). It may also stimulate invasiveness in introducedpopulations by increasing genetic variability, creatingfavourable gene combinations, masking deleterious alleles(Ellstrand & Scheirenbeck 2000; Lee 2002), and causingchanges in ploidy levels which often increases fitness(Soltis & Soltis 2000).In natural plant populations, microsatellites have greatpotential for helping to understand what determinespatterns of genetic variation, particularly when used inconcert with chloroplast DNA (cpDNA) markers. Theirutility has been demonstrated in studies of genetic diversity(Morand et al. 2002), mating systems (Durand et al. 2000),pollination biology (White et al. 2002) and seedling estab-lishment (Dow & Ashley 1996). Few studies have beencarried out using microsatellites in analysis of populationstructure of polyploid species. This is likely due to theproblems in analysing polyploid data as well as difficultiesin amplifying loci, possibly because of differences in theparental genomes of polyploids (Röder et al. 1995).An area of concern when using microsatellite frequenciesto estimate population parameters is size homoplasywhich can cause underestimation of the number of alleles,levels of heterozygosity and genetic diversity when onlyallele sizes are considered (reviewed in Estoup et al. 2002).A number of studies have demonstrated that microsatellitealleles of the same size can arise from mutation eventsCorrespondence: K. Saltonstall. *Present address: Horn PointLaboratory, University of Maryland Center for EnvironmentalScience, PO Box 775, Cambridge, MD 21613, USA. Fax:+1 410 221 8490; E-mail: [email protected] K. SALTONSTALL© 2003 Blackwell Publishing Ltd, Molecular Ecology, 12, 1689–1702which either interrupt repeat units or occur in the regionsflanking the repeat region. This has been shown to occurboth within (Angers & Bernatchez 1997; Viard et al. 1998)and among populations (Estoup et al. 1995; Viard et al. 1998)and closely related species (Peakall et al. 1998; van Oppenet al. 2000). One approach to minimizing the risk of mis-interpretation of genetic information is to characterize dif-ferent electromorphs by sequencing, particularly in cases inwhich other genetic data (e.g. chloroplast or mitochondrialsequences) suggest strong levels of genetic structuring thatis not being detected by microsatellite analysis.The common reed (Phragmites australis, hereafter Phrag-mites) has a worldwide distribution and is considerednative to North America. However, its distribution andabundance have increased dramatically over the past150 years in North America and it is considered a nuisancespecies in many regions. Phragmites is a perennial wetlandgrass that is tolerant of both freshwater and brackishconditions and typically forms a tall dense monoculture inthe systems that it invades. Its ability to readily colonizeopen habitat both by spread of seed and fragments ofrhizome material has undoubtedly contributed greatly tothe invasive spread of the species. Phragmites shows highvariation in ploidy levels throughout its distribution.Throughout the genus, the base chromosome number is12 (Tucker 1990). Although the diploid number (2n = 24)has never been reported in a natural population, a widerange of polyploid and aneuploid population types havebeen reported (reviewed in Clevering & Lissner 1999).Karyotypic studies of North American populationsindicate the presence of 3x, 4x, 6x and 8x plants, with 4xbeing the dominant chromosome number in modern daypopulations (Chambers et al. 1999).In this study, 10 microsatellite loci were used to assessthe genetic structure of Phragmites populations in NorthAmerica and Europe at the level of nuclear DNA. Recentevidence based on sequencing of cpDNA indicates that asingle nonnative lineage of Phragmites has been introducedto North America and is likely to be responsible for thedramatic spread of the species across North
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