Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae)

Spartina x townsendii arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced Spartina alterniflora, native to the eastern seaboard of North America. Duplication of the hybrid genome gave rise to Spartina anglica, a vigorous allopolyploid involved in natural and artificial invasions on several continents. This system allows investigation of the early evolutionary changes that accompany stabilization of new allopolyploid species. Because allopolyploidy may be a genomic shock, eliciting retroelement insertional activity, we examined whether retrotransposons present in the parental species have been activated in the genome of S. anglica. For this purpose we used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposons-microsatellite amplified polymorphism (REMAP) markers, which are multilocus PCR-based methods detecting retrotransposon integration events in the genome. IRAP and REMAP allowed the screening of insertional polymorphisms in populations of S. anglica. The populations are composed mainly of one major multilocus genotype, identical to the first-generation hybrid S. x townsendii. Few new integration sites were encountered in the young allopolyploid genome. We also found strict additivity of the parental subgenomes in the allopolyploid. Both these findings indicate that the genome of S. anglica has not undergone extensive changes since its formation. This contrasts with previous results from the literature, which report rapid structural changes in experimentally resynthesized allopolyploids.     

Origin and genetic diversity of Spartina anglica (Poaceae) using nuclear DNA markers

Spartina alterniflora, introduced into the UK in the 1800s, was the seed parent in an interspecific hybridization with S. maritima. The sterile F1 hybrid S. ×townsendii gave rise to the fertile allopolyploid S. anglica by chromosomal doubling. Previous chromosome, isozyme, and cpDNA surveys did not reveal notable genetic variation within either the parental or the hybrid species. We used nuclear DNA markers (random amplified polymorphic DNA ([RAPD]) and inter-simple sequence repeats (ISSR) to further explore the origin, diversity, and parentage of S. anglica. We found DNA fragments in S. ×townsendii were the aggregate of diagnostic DNA fragments from S. maritima and S. alterniflora, thus confirming its hybrid origin. The S. ×townsendii genotype was identical to most of the S. anglica individuals analyzed, establishing the genetic concordance of these two taxa. We found widespread genetic variation within S. anglica. This could indicate that S. anglica arose several times, from different S. maritima sires. Alternatively, alleles could have been lost through recombination and/or through loss of entire chromosomes in S. anglica. Finally, all but one S. anglica individual had a S. alterniflora component that was indistinguishable from a S. alterniflora plant extant in Marchwood, UK, leaving open the possibility that this plant is the actual seed parent of S. anglica.     

Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)

To study the consequences of hybridization and genome duplication on polyploid genome evolution and adaptation, we used independently formed hybrids (Spartina x townsendii and Spartina x neyrautii) that originated from natural crosses between Spartina alterniflora, an American introduced species, and the European native Spartina maritima. The hybrid from England, S. x townsendii, gave rise to the invasive allopolyploid, salt-marsh species, Spartina anglica. Recent studies indicated that allopolyploid speciation may be associated with rapid genetic and epigenetic changes. To assess this in Spartina, we performed AFLP (amplified fragment length polymorphism) and MSAP (methylation sensitive amplification polymorphism) on young hybrids and the allopolyploid. By comparing the subgenomes in the hybrids and the allopolyploid to the parental species, we inferred structural changes that arose repeatedly in the two independently formed hybrids. Surprisingly, 30% of the parental methylation patterns are altered in the hybrids and the allopolyploid. This high level of epigenetic regulation might explain the morphological plasticity of Spartina anglica and its larger ecological amplitude. Hybridization rather than genome doubling seems to have triggered most of the methylation changes observed in Spartina anglica.     

Spartina anglica C. E. Hubbard: a natural model system for analysing early evolutionary changes that affect allopolyploid genomes

Spartina anglica arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced East American Spartina alterniflora and following genome duplication of the hybrid ( S.  ×  townsendii ). This system allows investigations of the early evolutionary changes that accompany stabilization of a new allopolyploid species in natural populations. Various molecular data indicate that S. anglica has resulted from a unique parental genotype. This young species contains two distinctly divergent homoeologous genomes that have not undergone extensive change since their reunion. No burst of retroelements has been encountered in the F₁ hybrid or in the allopolyploid, suggesting a 'structural genomic stasis' rather than 'rapid genomic changes'. However, modifications of the methylation patterns in the genomes of S.  ×  townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 475–484.     

Molecular evidence for the maternal parentage in the hybrid origin of Spartina anglica C.E. Hubbard

Spartina anglica is a textbook example of a natural amphiploid, which originated from hybridization between S. alterniflora and S. maritima . Which of these species was the maternal parent has remained a mystery. Inheritance of chloroplast DNA in most angiosperms is strictly maternal and can thus be used to test the parentage of hybrid taxa. The DNA sequence of the chloroplast leucine tRNA gene intron was used to show that the introduced North American S. alterniflora is the female parent of the F ₁ hybrid S. x townsendii and the amphiploid S. anglica . A possible scenario for their origin is given.     

The evolution of Spartina anglica C.E. Hubbard (Gramineae): origin and genetic variability

An extensive survey of isozyme phenotypes in British populations of the amphidiploid salt marsh grass Spartina anglica and its putative parents has confirmed that the species arose by chromosome doubling in S. × townsendii , a sterile hybrid between S. maritima and S. alterniflora. Isozyme phenotypes and seed protein profiles indicate that S. anglica is almost totally lacking in genetic variation. Isozyme evidence also indicates that the parental species are characterized by low levels of genetic variation. The lack of variation in S. anglica is proposed as being due to a narrow genetic base resulting from a single origin, or a multiple origin from uniform parents; the fact that many populations are derived from very small founder populations; and because preferential pairing between identical homologous chromosomes prevents recombination between the divergent component genomes of the species. The low levels of isozyme variation that occur appear to be due to chromosome loss.
The consequences for the future evolution of S. anglica , given its lack of genetic variation, are discussed.     

The evolution of Spartina anglica G. E. Hubbard (Gramineae): genetic variation and status of the parental species in Britain

The perennial salt marsh grass Spartina anglica is one of the classic examples of allopolyploid speciation. It originated on the south coast of England at the end of the nineteenth century following chromosome doubling in S. × townsmdii , a hybrid between the native British S. marilima and a species introduced from the United States, S. alterniflora. The nature of the origin of S. anglica is beyond doubt; however, it is not known whether it had a single or multiple origin. In order to address this problem we undertook a survey of the genetic variation in the parental species of S. anglica using isozyme electrophoresis. The results show that S. alterniflora has no detectable variation and that S. maritima has extremely low levels of variation. These results, unfortunately, prevent the question of a single or multiple origin from being answered. Possible reasons for the low levels of variation and its influence on the future of the species are discussed. Another problem concerning the parental species is the rapid decline of S. maritima in Britain. It is often assumed that the major factor in this regression is the invasion of its habitats by S. anglica. We have examined the status of S. marilima throughout its range in Britain and have found that S. anglica rarely co-occurs with S. maritima. We propose that the decline of S. maritima is largely due to the physical erosion of its habitats and that this erosion may produce suitable habitats for colonization by S. anglica.     

Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae)

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing species. Twelve Spartina species have been sequenced for two nuclear DNA regions (ITS of ribosomal DNA, and part of the Waxy gene) and one chloroplast DNA spacer (trnT-trnL). Separate and conditional combined phylogenetic analyses using Cynodon dactylon as the outgroup have been conducted. Spartina is composed of two lineages. The first clade includes all hexaploid species: the Euro-African S. maritima (2n = 60), the East-American S. alterniflora (2n = 62) and the West-American S. foliosa (2n = 60). Spartina alterniflora appears as a closely related sister species to S. foliosa. Although belonging to the same lineage, Spartina maritima appears consistently more genetically differentiated from S. alterniflora than S. foliosa. The tetraploid species S. argentinensis (2n = 40) is placed at the base of this first clade according to the Waxy data, but its position is not well resolved by the other sequences. The second well-supported main lineage within genus Spartina includes the other tetraploid American species. Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora, suggesting a possible reticulate evolution for this species. The results agree with hybridization patterns occurring in Spartina: introgression involving closely related species (S. alterniflora and S. foliosa) on one hand, and alloploid speciation involving more differentiated species (S. alterniflora and S. maritima) on the other hand.     

Hybridization between invasive Spartina densiflora (Poaceae) and native S. foliosa in San Francisco Bay, California, USA

Rapid evolution in contemporary time can result when related species, brought together through human-aided introduction, hybridize. The significant evolutionary consequences of post-introduction hybridization range from allopolyploid speciation to extinction of species through genetic amalgamation. Both processes are known to occur in the perennial cordgrass genus, Spartina. Here we report the existence of a third recent Spartina hybridization, discovered in 2002, between introduced S. densiflora and native S. foliosa in San Francisco Bay, California, USA. We used nuclear and chloroplast DNA analysis and nuclear DNA content with chromosome counts to examine plants of morphology intermediate between S. densiflora and S. foliosa in a restored marsh in Marin County, California. We found 32 F(1) diploid hybrids and two triploid plants, all having S. densiflora and S. foliosa as parents; there is also evidence of a genetic contribution of S. alterniflora in some hybrids. None of these hybrids set germinable seed. In 2007 we found a hybrid over 30 miles away in a marsh where both parental species occurred, suggesting hybridization may not be a localized phenomenon. The presence of diploid and triploid hybrids is important because they indicate that several avenues existed that may have given rise to a new allopolyploid species. However, such an event is now unlikely because all hybrids are targets of eradication efforts.     

Evolution in Spartina (Gramineae) IV. The cytology of S. alterniflora Loisel. in North America

A cytological survey of Spartina alterniflora Loisel. populations in Canada and north-eastern U.S.A. establishes the widespread and seemingly exclusive occurrence of the 2 n = 62 chromosome number in that region. The data indicate that the introduced and relict populations of S. alterniflora in Southampton Water, Britain (whence arose S. × townsendii ) are not cyto-logically atypical of the main body of this species in North America, and there is therefore no reason to doubt, on the grounds of aberrant chromosome number, the role of S. alterniflora as a parent of S. × townsendii.
2 n = 62 is anomalous with respect to the basic number of x = 10 generally found in the genus. The present results indicate that 2 n = 62 is widespread in north-eastern North American S. alterniflora , and no other chromosome number has been found in a survey of the region. But the species is wide-ranging and the possibility of 2 n = 60 occurring in other areas, especially in the south of its range, cannot be ruled out. However, the only chromosome number so far confirmed in southern populations is a count of 2 n = 62 from Texas.     

Uniformity of the nuclear and chloroplast genomes of Spartina maritima (Poaceae), a salt-marsh species in decline along the Western European Coast

Spartina maritima is a salt-marsh species from European and African Atlantic coasts. In the northern range of the species (including north-west France), a rapid decline of the populations has been observed during the 20th century. In this paper, the molecular diversity of 10 populations of S. maritima from France has been investigated using nuclear and chloroplast DNA markers: inter-simple sequence polymorphism (ISSR), randomly amplified polymorphic DNA (RAPD), inter-retrotransposon amplified polymorphism (IRAP), and PCR-RFLP of a 5 kb long portion of chloroplast DNA. The results reveal an extremely low level of genetic variation in this species: only one nuclear marker (out of 98) was polymorphic, with the presence of two genotypes randomly distributed among the populations. The lack of genetic diversity is interpreted in light of the almost exclusive vegetative propagation of the species in its northern range, the colonization history of the populations, and the origin of S. maritima (2n = 60) in the hexaploid lineage of the genus and in the context of the management of S. maritima populations.     

Reciprocal hybrid formation of Spartina in San Francisco Bay

Diversity in the tRNALEU1 intron of the chloroplast genome of Spartina was used to study hybridization of native California cordgrass, Spartina foliosa, with S. alterniflora, introduced to San Francisco Bay approximately 25 years ago. We sequenced 544 bases of the tRNALEU1 intron and found three polymorphic sites, a pyrimidine transition at site 126 and transversions at sites 382 and 430. Spartina from outside of San Francisco Bay, where hybridization between these species is impossible, gave cpDNA genotypes of the parental species. S. foliosa had a single chloroplast haplotype, CCT, and this was unique to California cordgrass. S. alterniflora from the native range along the Atlantic coast of North America had three chloroplast haplotypes, CAT, TAA, and TAT. Hybrids were discriminated by random amplified polymorphic DNA (RAPD) phenotypes developed in a previous study. We found one hybrid that contained a cpDNA haplotype unknown in either parental species (TCT). The most significant finding was that hybridization proceeds in both directions, assuming maternal inheritance of cpDNA; 26 of the 36 hybrid Spartina plants from San Francisco Bay contained the S. foliosa haplotype, nine contained haplotypes of the invading S. alterniflora, and one had the cpDNA of unknown origin. Furthermore, cpDNA of both parental species was distributed throughout the broad range of RAPD phenotypes, suggesting ongoing contributions to the hybrid swarm from both. The preponderance of S. foliosa cpDNA has entered the hybrid swarm indirectly, we propose, from F1s that backcross to S. foliosa. Flowering of the native precedes by several weeks that of the invading species, with little overlap between the two. Thus, F1 hybrids would be rare and sired by the last S. foliosa pollen upon the first S. alterniflora stigmas. The native species produces little pollen and this has low viability. An intermediate flowering time of hybrids as well as pollen that is more vigourous and abundant than that of the native species would predispose F1s to high fitness in a vast sea of native ovules. Thus, spread of hybrids to other S. foliosa marshes could be an even greater threat to the native species than introductions of alien S. alterniflora.     

米草属引入中国海岸带的利弊分析

1963年以来,中国先后从国外引进3种米草。实践证明,大米草和互花米草是盐渍土壤植物群落形成的先锋植物,适应于中国海岸带自然环境,生长发育正常,具有明显的促淤造陆和保护海岸等生态功能,并具有显著的经济效益.大米草和互花米草在南方海岸繁殖过快是近岸水体富营养化的结果,但并未对环境、动植物种群和人类构成侵害,其在北方海岸未发生异常现象,故应客观地评估米草的功与过。本文从利弊2个方面对中国海岸滩涂引入米草进行了分析。     

The enigmatic invasive Spartina densiflora: a history of hybridizations in a polyploidy context

The aim of this study was to explore the origin of the invasive Spartina densiflora by analysing samples from the native region (South America) and from a recently colonized area (California). A combination of various molecular data (chloroplast and nuclear sequences, molecular fingerprint) and ploidy level estimations was used to answer the question whether the reticulate phylogenetic pattern previously detected in S. densiflora was restricted to California, or alternatively, whether a more ancient hybrid origin preceded formation of this species in its native area. We found that this species is heptaploid in both its native and introduced range. Identification of nuclear homeologous sequences indicate that this species has a reticulate origin in its native range, involving a lineage related to the hexaploid clade formed by S. alterniflora, S.foliosa, and S. maritima, and another lineage related to the sub-Antarctic endemic S. arundinacea that provided the chloroplast genome. The samples from California displayed similar multilocus patterns to the samples from Chile, supporting the hypothesis that this species originated on the southeast American coast (Argentina), from where it eventually spread to the west coast of South America (Chile) first and to the Northern Hemisphere (California) later.     

Hybridization between introduced smooth cordgrass (Spartina alterniflora; Poaceae) and native California cordgrass (S. foliosa) in San Francisco Bay, California, USA

Introduced Spartina alterniflora (smooth cordgrass) is rapidly invading intertidal mudflats in San Francisco Bay, California. At several sites, S. alterniflora co-occurs with native S. foliosa (California cordgrass), a species endemic to California salt marshes. In this study, random amplified polymorphic DNA markers (RAPDs) specific to each Spartina species were identified and used to test for hybridization between the native and introduced Spartina species in the greenhouse and in the field. Greenhouse crosses were made using S. alterniflora as the pollen donor and S. foliosa as the maternal plant, and these crosses produced viable seeds. The hybrid status of the crossed offspring was confirmed with the RAPD markers. Hybrids had low self-fertility but high fertility when back-crossed with S. foliosa pollen. Hybrids were also found established at two field sites in San Francisco Bay; these hybrids appeared vigorous and morphologically intermediate between the parental species. Field observations suggested that hybrids were recruiting more rapidly than the native S. foliosa. Previous work identified competition from introduced S. alterniflora as a threat to native S. foliosa. In this study, we identify introgression and the spread of hybrids as an additional, perhaps even more serious threat to conservation of S. foliosa in San Francisco Bay.     

AN ECOPHYSIOLOGICAL STUDY OF THE SALT SECRETION OF FOUR HALOPHYTES

Plants of Spartina anglica, Limonium vulgare, Armeria maritima and Glaux maritima were collected in the field and grown on different concentrations of NaCl, KCl and CaCl₂. Salt secretion, ion content, water content and transpiration rates were determined. The highest sodium secretion was found in Spartina anglica , a species from the most saline habitat; and a somewhat lower secretion rate in Limonium vulgare. The lowest rates were found in Glaux maritima and Armeria maritima. The sodium secretion efficiency, i.e. the ability to maintain an unchanged internal sodium content, was highest in Spartina anglica. Spartina anglica is the most successful in the removal of excessively absorbed salt, since it secretes 60% of the absorbed sodium. The values for Limonium vulgare, Glaux maritima and Armeria maritima were 33, 20 and 4% respectively. The species studied differ in the preferential sequence of ion secretion as well as in secretion rate and efficiency. This preferential sequence of ion secretion seems to be similar in members of the same taxonomic group (Plumbaginaceae). The comparability of the secretion parameters is discussed with regard to morphological differences between the species.     

Same parental species, but different taxa: molecular evidence for hybrid origins of the rare endemics Saxifraga opdalensis and S. svalbardensis (Saxifragaceae)

Saxifraga opdolensis was described from Oppdal in southern Norway and hypothesized to have originated as the hybrid S. cernua × rivularis or to have been derived from a S . cernua-like progenitor. We tested these alternative hypotheses using uni- and biparentally inherited molecular markers observed in S. opdalensis and its putative parental species at the type locality: PCR-RFLPs (restriction fragment length polymorphisms in amplified fragments of chloroplast DNA; cpDNA), sequences of the cpDNA intron trnL and the spacer tmL-tmF , and RAPDs (random amplified polymorphic DNAs). The data provided unambiguous support for the hybrid hypothesis. The cpDNA analyses distinguished two well-differentiated chloroplast genomes, one in S. opdalensis and S. rivularis , and another in S. cernua . The majority of the RAPD markers showed distinct additivity in S. opdalensis relative to its postulated parental species. Thus, S. opdalensis has probably originated from a hybrid with S. rivularis as the maternal parent and S. cernua as the paternal parent. We also included S. svalbaardnsis in the present study because previous molecular analyses of Svalbard material have shown that this species had probably also originated as a hybrid between S. cernua and S. rivularis . The chloroplast genome of S. svalbaardnsis was identical to that of S. opdalensis , but the two species differed in many RAF'D markers. Although these two endemics probably have been derived from the same hybrid combination, they are morphologically and genetically distinct and should be referred to separate species. Differences between such independently originated hybrid taxa may result from intraspecific variation in their parental taxa. Saxufraga cernua comprises, for example, several highly divergent evolutionary lineages.     

Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group

To better understand genetic events that accompany allopolyploid formation, we studied the rate and time of elimination of eight DNA sequences in F1 hybrids and newly formed allopolyploids of Aegilops and TRITICUM: In total, 35 interspecific and intergeneric F1 hybrids and 22 derived allopolyploids were analyzed and compared with their direct parental plants. The studied sequences exist in all the diploid species of the Triticeae but occur in only one genome, either in one homologous pair (chromosome-specific sequences [CSSs]) or in several pairs of the same genome (genome-specific sequences [GSSs]), in the polyploid wheats. It was found that rapid elimination of CSSs and GSSs is a general phenomenon in newly synthesized allopolyploids. Elimination of GSSs was already initiated in F1 plants and was completed in the second or third allopolyploid generation, whereas elimination of CSSs started in the first allopolyploid generation and was completed in the second or third generation. Sequence elimination started earlier in allopolyploids whose genome constitution was analogous to natural polyploids compared with allopolyploids that do not occur in nature. Elimination is a nonrandom and reproducible event whose direction was determined by the genomic combination of the hybrid or the allopolyploid. It was not affected by the genotype of the parental plants, by their cytoplasm, or by the ploidy level, and it did not result from intergenomic recombination. Allopolyploidy-induced sequence elimination occurred in a sizable fraction of the genome and in sequences that were apparently noncoding. This finding suggests a role in augmenting the differentiation of homoeologous chromosomes at the polyploid level, thereby providing the physical basis for the diploid-like meiotic behavior of newly formed allopolyploids. In our view, this rapid genome adjustment may have contributed to the successful establishment of newly formed allopolyploids as new species.     

Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group

To better understand genetic events that accompany allopolyploid formation, we studied the rate and time of elimination of eight DNA sequences in F1 hybrids and newly formed allopolyploids of Aegilops and Triticum. In total, 35 interspecific and intergeneric F1 hybrids and 22 derived allopolyploids were analyzed and compared with their direct parental plants. The studied sequences exist in all the diploid species of the Triticeae but occur in only one genome, either in one homologous pair (chromosome-specific sequences [CSSs]) or in several pairs of the same genome (genome-specific sequences [GSSs]), in the polyploid wheats. It was found that rapid elimination of CSSs and GSSs is a general phenomenon in newly synthesized allopolyploids. Elimination of GSSs was already initiated in F1 plants and was completed in the second or third allopolyploid generation, whereas elimination of CSSs started in the first allopolyploid generation and was completed in the second or third generation. Sequence elimination started earlier in allopolyploids whose genome constitution was analogous to natural polyploids compared with allopolyploids that do not occur in nature. Elimination is a nonrandom and reproducible event whose direction was determined by the genomic combination of the hybrid or the allopolyploid. It was not affected by the genotype of the parental plants, by their cytoplasm, or by the ploidy level, and it did not result from intergenomic recombination. Allopolyploidy-induced sequence elimination occurred in a sizable fraction of the genome and in sequences that were apparently noncoding. This finding suggests a role in augmenting the differentiation of homoeologous chromosomes at the polyploid level, thereby providing the physical basis for the diploid-like meiotic behavior of newly formed allopolyploids. In our view, this rapid genome adjustment may have contributed to the successful establishment of newly formed allopolyploids as new species.