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Ó 2003 The American Genetic Association Journal of Heredity 2003:94(3):197–204 DOI: 10.1093/jhered/esg060 THE WILHELMINE E. KEY 2002 INVITATIONAL LECTURE Phylogeography, Haplotype Trees, and Invasive Plant Species B. A. SCHAAL, J. F. GASKIN, AND A. L. CAICEDO From the Department of Biology, Washington University, St. Louis, MO 63130 (Schaal and Caicedo) and USDA Agricultural Research Service, Northern Plains Agricultural Research Laboratory, 1500 N. Central Avenue, Sidney, MT 59270 (Gaskin). Address correspondence to Barbara A. Schaal at the address above. Barbara A. Schaal is Spencer T. Olin Professor of Biology at Washington University in St. Louis. She received her Ph.D. in population biology from Yale University and did postdoctoral work at the University of Georgia, and she was on the faculty at the University of Houston and Ohio State University before moving to Washington University in 1980. Dr. Schaal was president of the Botanical Society of America and has served as executive vice president of the Society for the Study of Evolution, for which she is currently president-elect. Additionally, she has served on editorial boards of numerous journals and was chair of the Department of Biology, Washington University. Dr Schaal currently serves as chair of the Scientific Advisory Council of the Center for Plant Conservation, chair of the NRC Committee on Agriculture, Biotechnology, Health and the Environment, and as a member of the board of trustees, Missouri chapter of The Nature Conservancy. She is a fellow of the American Association for the Advancement of Science, a John Simon Guggenheim Fellow, and a member of the U.S. National Academy of Sciences. Abstract The distribution of genetic variants in plant populations is strongly affected both by current patterns of microevolutionary forces, such as gene flow and selection, and by the phylogenetic history of populations and species. Understanding the interplay of shared history and current evolutionary events is particularly confounding in plants due to the reticulating nature of gene exchange between diverging lineages. Certain gene sequences provide historically ordered neutral molecular variation that can be converted to gene genealogies which trace the evolutionary relationships among haplotypes (alleles). Gene genealogies can be used to understand the evolution of specific DNA sequences and relate sequence variation to plant phenotype. For example, in a study of the RPS2 gene in Arabidopsis thaliana, resistant phenotypes clustered in one portion of the gene tree. The field of phylogeography examines the distribution of allele genealogies in an explicit geographical context and, when coupled with a nested clade analysis, can provide insight into historical processes such as range expansion, gene flow, and genetic drift. A phylogeographical approach offers insight into practical issues as well. Here we show how haplotype trees can address the origins of invasive plants, one of the greatest global threats to biodiversity. A study of the geographical diversity of haplotypes in invasive Phragmites populations in the United States indicates that invasiveness is due to the colonization and spread of distinct genotypes from Europe (Saltonstall 2002). Likewise, a phylogeographical analysis of Tamarix populations indicates that hybridization events between formerly isolated species of Eurasia have produced the most common genotype of the second-worst invasive plant species in the United States. 197 Journal of Heredity 2003:94(3) There have been numerous advances in the study of evolutionary biology over the past two decades. Clearly one of the most important developments has been the use of DNA sequences and markers for understanding both the patterns and processes of evolution. Associated with the application of molecular techniques have been both conceptual and analytical advances. At the population level, the use of DNA sequences to infer past evolutionary processes has been enhanced by John Avise’s concept of phylogeography, which examines the distribution of genealogical lineages of specific DNA sequences in a geographical context. Phylogeographic approaches offer a way of determining the types of contemporary and historical processes that have influenced the current geographic distribution of variation (Avise 2000). The separation of a single lineage into two separate lineages is perhaps the most interesting and critical stage of genetic divergence, since in some cases it is a prelude to speciation. In plants, lineage diversification has been particularly difficult to analyze because of the reticulating, hybridizing nature of plant species. Reconstructions of the genealogical relationships between genes through the use of haplotype networks or trees can be used to analyze evolutionary processes at the time of lineage separation. As lineages diverge, the assumptions of population genetics that apply to processes within populations no longer hold. Such assumptions include equilibrium between genetic drift and gene flow, an equilibrium only rarely observed in plants, if at all. At the same time, the assumptions of cladistics are not valid at the time of lineage diversification. To apply, cladistic analysis lineages must be isolated and nonreticulating. Plants, of course, are notorious for their ability to hybridize even between lineages that have been separated over millions of years. Thus studies of gene genealogies are particularly important in plants, where below the species level mating is nearly always nonrandom, and where above the species level hybridization is frequent. Reconstructions of gene genealogies have great potential for advancing our understanding of plant evolution; they are a powerful tool that enables the testing of numerous population-level hypotheses and they provide insight into current processes that greatly affect biodiversity. Construction of Haplotype Trees The use of molecular-level data has become ubiquitous in intraspecific studies in the past two decades. However, molecular population-level studies in plants still remain much less common than similar studies in animals, primarily due to the difficulty of finding genetic markers with appropriate intraspecific levels of polymorphism (Schaal et al. 1998). Many plant studies have turned to genome-wide markers such as random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP), but these data cannot be historically ordered, which precludes the construction of gene trees. The dearth of studies has had a negative impact on the application of analytical tools available for ordered data that are otherwise common in animal intraspecific studies. This impact has been felt 198 especially in the field of phylogeography, where plant studies are far outnumbered by those in animals (Avise 2000; Cruzan and Templeton 2000). The last 5 years, however, have seen an increase in the identification of molecular markers in plants that present variation at the intraspecific level, in the nuclear genome (e.g., Gaskin and Schaal 2002; Olsen and Schaal 1999; Strand et al. 1997), and in the chloroplast (e.g., Maskas and Cruzan 2000) and mitochondrial genomes (e.g., Chiang et al. 2001). Thus the construction of intraspecific phylogenies for plant groups is becoming more common and important. Moreover, the use of these phylogenies is allowing us to understand in greater detail the historical and population processes that have governed the evolution of plants, especially those that greatly affect human affairs through agriculture or habitat degradation. The properties of genetic relationships at the population level have been reviewed extensively (Crandall et al. 1994; Posada and Crandall 2001; Templeton et al. 1992). The main aspects in which intraspecific genetic relationships differ from those between species are the following: 1. There is a lower amount of divergence between haplotypes. 2. Ancestral haplotypes usually remain within the species. 3. Single haplotypes can give rise to many others, leading to multifurcations. 4. There is a greater possibility of recombination creating homoplasious relationships (see Posada and Crandall 2001). Because of these four properties, networks, rather than the bifurcating trees used for between-species comparisons, are the most appropriate way to represent the relationships within a species. As the use of networks has proliferated in intraspecific studies, the terminology used to refer to them has grown slightly confusing. We adopt the terminology used by Posada and Crandall (2001). Within this classification scheme, a true gene genealogy is a representation of the relationship of all genes (at a particular locus) present in all individuals in a sample. To determine a gene genealogy, pedigree data of the individuals is necessary. This is the only way to determine the true relationship between genes borne by individuals with the same haplotype. Pedigree information is generally unavailable for most population samples; however, within a sample of genes from several individuals, we can generally distinguish the relationship betweens genes differing by mutations. Genes at a locus that differ by mutations are known as alleles or haplotypes. Thus the depiction of relationships between alleles or haplotypes within a species is known as a haplotype or allele tree or network. There are several methods for constructing the network relationship between haplotypes in a sample (reviewed by Posada and Crandall 2001). Determination of which method is appropriate is an area of active debate. We have generally found that in our datasets, which consist primarily of DNA sequences, the levels of divergence and homoplasy are low enough that the network can be built by hand following a maximum parsimony criterion of minimizing the number Schaal et al. of mutations between haplotypes. Network construction can also be greatly aided by TCS (Clement et al. 2000), a program that uses statistical parsimony to estimate relationships between haplotypes. Statistical parsimony was developed by Templeton et al. (1992) to allow the application of maximum parsimony to intraspecific phylogenies. Under statistical parsimony, the number of differences between haplotypes that are due to a sequence of single mutations at each site, with 95% confidence, are calculated. This number is known as the limits of parsimony, and haplotypes differing by a greater number of mutations will not be connected, as their true relationship is more likely to be obscured by homoplasy (Templeton et al. 1992). All haplotypes within the limits of parsimony are connected, and the final network gives an immediate visual representation of mutations distinguishing any pair of alleles. A simple example of how to construct a haplotype tree and some of the types of information that can be obtained from this representation can be seen in a study of RPS2 variation in Arabidopsis thaliana (Caicedo et al. 1999). RPS2 is a gene involved in the recognition of a pathogenic bacterium, Pseudomonas syringae pv. tomato. Functional alleles of RPS2 confer resistance to strains of P. syringae pv. tomato that carry the avrRpt2 allele. RPS2 was sequenced in 17 accessions of A. thaliana and seven distinct haplotypes were found. In this case, a complete absence of homoplasy made it very easy to deduce the haplotype tree relating these alleles. Figure 1 shows the most parsimonious relationship between haplotypes. The tree is not rooted. Although rooting for an intraspecific tree is possible (discussed in Castelloe and Templeton 1994), in many cases rooting is unnecessary for the types of inferences that need to be made. Some studies that reconstruct population history will require rooting of an intraspecific tree. In the case of RPS2, we wanted to determine the relationships between resistant and susceptible alleles rather than a historical reconstruction. Among our sampled haplotypes, 36 polymorphic sites were found. The results showed varying degrees of divergence between RPS2 alleles in A. thaliana accessions. A significantly high level of amino acid replacement substitutions were found to cluster together on the tree, many leading to alternative alleles that still conferred resistance to P. syringae expressing avrRpt2. This indicated that certain nonsynonymous mutations did not alter the resistance functionality of the gene. An interesting finding was that all alleles found conferring resistance were closely related to each other. However, this cluster also included susceptible types. Susceptible alleles, on the other hand, could be widely divergent from the resistant haplotypes and each other. This example illustrates how haplotype trees can provide insight into the evolution of functional genes. Although it has not been exploited much in plants, further insights in functional gene evolution can be obtained by incorporating analytical techniques developed for intraspecific phylogenies. Haplotype trees in conjunction with phenotypic data and nested cladistic analysis (Templeton 1988; Templeton et al. 1987) can be used to deduce associations between sequence and phenotypic effect (Templeton 1995; Templeton and Phylogeography, Haplotype Trees, and Invasive Plant Species Figure 1. Haplotype of the RPS2 gene in A. thaliana. Conservative a.a. change, c; nonconservative a.a. change, nc. Sing 1993; Templeton et al. 1987, 1988, 1992). There is justifiable concern over the lack of correlation between neutral markers and the phenotype in question (Reed and Frankham 2001), though that concern should be diluted for genealogies that coalesce further into the past. As more functional genes are identified and sequenced, this type of analysis might become more useful, especially for agriculturally important traits. The most frequent use of haplotype trees so far has been to obtain information on historical processes. For example, a number of excellent studies have established the migration routes of important tree species from Pleistocene refugia in Europe (e.g., Lumaret et al. 2002; Petit et al. 2002; Taberlet et al. 1998). Other studies have documented the origin of important crops species (Olsen 2000) and examined the colonization and diversification of plant species in Asia (Ge et al. 2002; Huang et al. 2001). Below we discuss how haplotype trees and phylogeographic analyses have been used to examine the origin of invasive plants, one of the greatest threats to the biodiversity of the United States and other regions of the world. Invasive Species The invasion of introduced species into regions of the world has altered natural environments and severely threatened native biodiversity. In many cases the species introduced is noninvasive in its native land, while in other examples a species may have recently become invasive. The root causes of invasiveness are not clear and probably represent a different suite of traits for each species (e.g., Baker 1965; Williamson 1999). Causes can include intrinsic factors, such as high seed set, or extrinsic factors, such as a loss of competitors or herbivores. A less studied aspect of invasive species has been their underlying genetic structure. When a species is transferred to new region, multiple genotypes are often introduced, perhaps from different regions that are isolated, and thus genetic recombination and reassortment may be a factor affecting invasiveness. 199 Journal of Heredity 2003:94(3) Figure 2. Haplotype network of two noncoding chloroplast regions from P. australis. Gray ovals represent haplotypes recovered. Small black squares represent inferred haplotypes not recovered in the sample. Each link between haplotypes corresponds to one mutational difference, with indels coded as single characters. Native North American haplotypes are indicated by brackets. The invasive haplotype M, which is discussed in the text, is in the large circle. If it is the duty of systematists and population biologists to apply their skills toward critical ecological problems, along with attaining fundamental knowledge of evolutionary events, then the current problem of plant species invasion warrants substantial attention. Invasion of nonnative species into natural areas ranks second behind only habitat destruction as the largest ecological disaster worldwide (Wilson 1997). Of the 972 plants and animals listed by the U.S. Endangered Species Act, approximately 400 are at risk primarily due to competition from and predation by nonnative species (Stein and Flack 1996). For these reasons, the control of selected invasives is becoming an integral part of ecosystem stewardship. Methods of controlling invasive plants include manual removal, fire, herbicides, biological control, and legislation concerning the importation and use of certain plant species. But control efforts often begin before there is a basic understanding of the invasion. Exactly which species is invading? What genotypes of the species are present in an invasion and where did they come from? Which other species, genera, and families are most closely related to the invasive species? Is there gene flow between the invasive and closely related native species? All of these questions can be addressed by molecular studies, and in particular by the construction of haplotype tress and phylogeographical analyses. Case Studies: Phylogeography of Plant Invasions Phragmites The common reed (Phragmites australis) is a tall (up to 4 m) perennial grass found in marshes and along river and lake edges. The species is cosmopolitan, but in the last 150 years it has expanded its distribution and increased its density dramatically in the United States. The success of this species was hypothesized to have been due to human-mediated disturbance and pollution, but an alternate explanation focuses on the introduction of an aggressive, cryptic, nonnative genotype. In an exemplary study, Saltonstall (2002) sequenced two 200 noncoding chloroplast regions of 345 plants worldwide, including herbarium samples collected before and after the range expansion in 1910. She found 27 haplotypes worldwide, and the older North American haplotypes were quite differentiated from those found in other parts of the world (Figure 2). A very common ancestral haplotype (M) was found throughout Europe and continental Asia. Before 1910, this haplotype M was detected just four times (6.4%) in the United States, and only along the coast of New England. Since 1960, this haplotype has expanded its range across the entire United States and is now the most widespread and common (61.5%) genotype found in North America. There has been a corresponding drop in diversity of the native P. australis genotypes during the last century. Saltonstall also broke down her samples into 20-year intervals for a portion of the New England area, illustrating the haplotype distribution pattern over time. From mapped distributions, one can conclude that haplotype M has found its way from port areas to more inland locations, becoming essentially the only genotype in the area as the native genotypes appear to become regionally extinct. This study illustrates how cryptic invaders can be just as devastating to native terrestrial communities as easily recognized invaders, and illustrates the utility of phylogeographic studies in elucidating historical evolutionary events. The presence of a cryptic invasion may indicate that this haplotype will be an eternal dominant of many wetland areas, or that populations will have to be genotyped as native or exotic prior to any control efforts. Polysiphonia A second phylogeographic study looked at an invasion of a red alga. Marine invasions are especially numerous due to the increase in ocean transport and the associated ballast water used by ships. The number of invasions may be underestimated because of the difficulty in distinguishing morphologically similar sibling species. The red alga Polysiphonia harveyi is considered exotic on the Atlantic coast of Europe, showing up in various locations there in the last two centuries, and conspecific populations are known from Atlantic North America and Japan. Typical of algal invasives, P. harveyi is eurythermal, weedy, and attaches to artificial substrata. McIvor et al. (2001) looked at rbcL sequence analysis, karyology, and interbreeding data from P. harveyi and various congeners in the Pacific and North Atlantic Oceans to determine how this species first got to the British Isles. Possible invasion origins included the Pacific Ocean near Japan, which contains specimens morphologically similar to the invasive, or from the eastern coast of North America. Alternatively the North American specimens may have been the result of an introduction from the Pacific. Six rbcL haplotypes were identified, all interfertile and similar in chromosome number, with the four most divergent haplotypes observed in Japan. One of the other two haplotypes was distributed on the eastern and western coasts of North America and in New Zealand, and the last haplotype was found exclusively on the Atlantic coast of Europe and Nova Scotia. The inability to match putative invasive haplotypes Schaal et al. with native haplotypes might have been solved with more intensive sampling, but the utility of sequence markers that vary at the population level is still clear. Once again we see that cryptic species and genotypes can make it difficult to estimate the magnitude and number of invasions without the use of molecular systematic and phylogeographic analyses. Tamarix Several species of the genus Tamarix L. (common name saltcedar or tamarisk, family Tamaricaceae) are, as a group, considered one of the worst plant invasions in the United States, exceeded only by purple loosestrife (Lythrum salicaria) (Stein and Flack 1996). Tamarix is an Old World genus of approximately 54 shrub and tree species found in salty, dry, or riparian habitats. Eight to 12 species were brought to the United States from southern Europe or Asia in the 1800s to be used for shade and erosion control (Baum 1967), and a subset of these species has taken over more than 600,000 riparian and wetland hectares (Brotherson and Field 1987). This invasion is expanding by 18,000 hectares/year (Di Tomaso 1998) throughout the western United States, including major river systems and national parks. In the United States, Tamarix escaped nearly all of its biological enemies (DeLoach et al. 2000) and has proven difficult to control on a large scale by either manual or chemical methods. Researchers at the U.S. Department of Agriculture (Agricultural Research Service) are currently searching for and testing candidate biological control insects as an alternative means of suppressing this invasion (DeLoach and Tracy 1997; DeLoach et al. 2000). Initial biological control tests of the saltcedar leaf beetle (Diorhabda elongata) show differential survival on what appear to be a single species of Tamarix collected from different regions of the United States and grown in common garden plots (DeLoach and Tracy 1997), perhaps suggesting that certain genotypes are more resistant to control agents. Many species of Tamarix are widespread in Eurasia (Baum 1978), and it is unlikely that all of the genotypes of any one species were imported to the United States. For these reasons, biological control researchers wanted to know how many genotypes are represented in the U.S. invasion, and to what degree we can pinpoint their Eurasian origins. The most dominant U.S. Tamarix invasion consists of two morphologically similar species: T. chinensis, native to China, Mongolia, and Japan; and T. ramosissima, which is widespread from eastern Turkey to Korea (Baum 1978). The ranges of these two species putatively overlap for approximately 4,200 km across China and Korea. A total of 269 vouchered DNA samples of Tamarix were collected from the western U.S. (155 plants) and Eurasian native populations of T. chinensis and T. ramosissima (114 plants), with one to eight individuals per population (Gaskin and Schaal 2002). An intron of the phosphoenolpyruvate carboxylase gene, approximately 900 bases in length, was sequenced, and this contained 144 variable sites in the species investigated. Phylogeography, Haplotype Trees, and Invasive Plant Species A total of 58 haplotypes were found among the 269 individuals (a total of 538 alleles). All populations except one in China (T. chinensis) had more than one haplotype represented, and some had up to 11 different haplotypes in six plants. The four haplotypes common to the United States and Asia were used to manually construct a maximum parsimony gene genealogy or minimum spanning network (Figure 3), which represents the mutational relationships among the haplotypes. In the native Eurasian range, by far the most common genotypic combinations were 1/1 and 2/2, which belong to T. ramosissima and T. chinensis, respectively (Figure 3). In contrast, within the U.S. invasion these genotypes were the second and third most common. The most common genotype in the United States was 1/2, a morphologically cryptic hybrid of T. ramosissima and T. chinensis which was not detected in Eurasia. Even though both species are putatively found all across China (Baum 1978), the 1/1 genotype was found exclusively west of central China and the 2/2 genotype exclusively east of central China (Figure 3). In Asia there are no known physical barriers between the two species except their putative edaphic affinities (Baum 1978), and in the United States the T. chinensis (2/2) and T. ramosissima (1/1) genotypes were found growing together in five populations as close as 2 m from each other on disturbed homogenous soil. Haplotype 12 was the third most common in the United States, found throughout the invasion, and it differed from haplotype 1 by 14 mutations, and was found only once in Eurasia in a homozygous plant (genotype 12/12) in Azerbaijan. The 2/12 genotype, found only in the United States, may be another novel hybrid (though perhaps a very rare one) given the disjunct native range of the haplotypes (China and Azerbaijan, respectively). Haplotype 7 was the only other T. ramosissima or T. chinensis haplotype common to the United States and Eurasia. It differs from haplotype 1 by five mutations, and was found in only one population in Idaho. In Eurasia it was found in the Republics of Georgia, Turkmenistan, and Kazakstan. The smallest native region that contained all of the detected T. ramosissima haplotypes common to Eurasia and the United States (1, 7, and 12) consists of the Republics of Georgia and Azerbaijan. Designating the native range of invasive genotypes has practical applications for biological control agent searches involving pest species with a widespread native distribution, but would require more extensive sampling than was provided in this study. These data, taken in total, indicate little if any hybridization among T. ramosissima and T. chinensis in their native range, even though their ranges putatively overlap. The 1/2 genotype may certainly occur in these areas, but given the 4200 km overlap of the two species’ ranges, it was surprising not to find T. ramosissima haplotypes in the eastern half of China, where they putatively exist. In contrast, there was extensive hybridization among two of the invasive Tamarix species within the United States. The 1/2 genotype, representing a T. chinensis 3 T. ramosissima hybrid, was the most common plant found in the invasion, ranging from 201 Journal of Heredity 2003:94(3) Figure 3. Distribution maps and network for haplotypes of T. ramosissima and T. chinensis common to the United States and Asia. Each link between haplotypes corresponds to one mutational difference. Oklahoma to Washington to California. Less extensive hybrids exist in the invasion, involving combinations of T. ramosissima and T. chinensis with other invasive species such as T. parviflora and T. gallica. The abundance of cryptic hybrids helps explain why identification of species in the United States using morphology has been, and will continue to be, problematic. 202 What do these results mean for the biological control of Tamarix? An effective and safe control agent should have high host specificity, the result of a shared evolutionary history. The hybrid Tamarix genotypes of the United States may be as little as 200 years old (Horton 1964) and thus have essentially no shared evolutionary history with any genotypespecific predators or diseases. The presence of a successful Schaal et al. novel hybrid in the U.S. invasion may potentially confound biological control results, depending on the control agent’s level of host specificity. Moreover, the results reported here allowed the circumscription of a native area that contains all detected T. ramosissima haplotypes common to both the United States and Eurasia, information that may help focus future biological control agent searches. The widespread presence of hybrid Tamarix in its introduced range serves as an additional warning for how continued accidental or intentional importation of plant species can unexpectedly alter the genotypic composition of naturalized populations and potentially contribute to the ecological devastation caused by exotic species invasion. Conclusion Haplotype trees and phylogeographic analysis have provided insights into many areas of evolutionary biology and holds promise for addressing practical issues as well. The studies of invasive plants discussed here are the beginning of a new understanding of the genetic structure of invasive plants. The scenarios of invasions constructed from morphological analysis can be misleading and it is clear that in some critical examples, the identity of the invasive plant has been poorly or incorrectly characterized. In fact, the ability to control an invasive plant may rely on understanding its origin and genetic structure. As more genetic data are forthcoming, we hope that some general patterns will emerge for the evolutionary history of invasive plant species. Such an understanding will increase our ability to confront and control the ongoing ecological disasters created by nonnative plants. Acknowledgments This lecture was delivered at the 2002 American Genetic Association Annual Symposium on Molecular Evolutionary Genetics, which was organized by Dr. Philip Hedrick and held at Arizona State University, Tempe, AZ, March 22–24, 2002. The paper was supported by grants from the National Science Foundation and U.S. Department of Agriculture, and by a Guggenheim Fellowship (to B.A.S.). J.F.G. was also supported by an EPA STAR Fellowship, the National Geographic Society, and the Mellon Foundation’s support of Missouri Botanical Garden graduate students. Phylogeography, Haplotype Trees, and Invasive Plant Species Caicedo AL, Schaal BA, and Kunkel BN, 1999. 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