Molecular evidence for polyploid origins in Saxifraga (Saxifragaceae): the narrow arctic endemic S. svalbardensis and its widespread allies

Homoploid hybrids are common but evolutionary dead ends, whereas polyploidy is not linked to hybridization in a group of Pyrenean saxifrages

Hybridization and polyploidy are major forces in plant evolution. Homoploid hybridization can generate new species via hybrid speciation, or modify extant evolutionary lineages through introgression. Polyploidy enables instantaneous reproductive isolation from the parental lineage(s) and is often coupled with evolutionary innovations, especially when linked to hybridization. While allopolyploidy is a well-known and common mechanism of plant speciation, the evolutionary role of autopolyploidy might have been underestimated. Here, we studied the saxifrages of Saxifraga subsection Saxifraga in the Pyrenees, which easily hybridise and include polyploid populations of uncertain origin, as a model to unravel evolutionary consequences and origin of hybridization and polyploidy. Additionally, we investigate the phylogenetic relationship between the two subspecies of the endemic S. pubescens to ascertain whether they should rather be treated as different species. For these purposes, we combined ploidy-informed restriction associated DNA analyses, plastid DNA sequences and morphological data on a comprehensive population sample of seven species. Our results unravel multiple homoploid hybridization events at the diploid level between different species pairs, but with limited evolutionary impact. The ploidy-informed analyses reveal that all tetraploid populations detected in the present study belong to the widespread alpine species S. moschata. Although of autopolyploid origin, they are to some extent morphologically differentiated and underwent a different evolutionary pathway than their diploid parent. However, the high plastid DNA diversity and the internal structure within eastern and western population groups suggest multiple origins of the polyploids. Finally, our phylogenetic analyses show that S. pubescens and S. iratiana are clearly not sister lineages, and should consequently be considered as independent species.

The Role of Hybridisation in the Making of the Species-Rich Arctic-Alpine Genus Saxifraga (Saxifragaceae)

Evolutionary processes fuelling rapid species diversification are not yet fully understood, although their major contribution to overall patterns of plant biodiversity is well established. Hybridisation is among the least understood of these processes, despite its multifaceted role in speciation processes being widely accepted. Species of the large arctic-alpine genus Saxifraga are notorious for their ability to hybridise; however, the overall role of hybridisation and polyploidisation for the diversification of this genus remains unknown. Here, we provide a comprehensive genus-wide review of hybridisation accounts and ploidy levels. We find that the sections of Saxifraga vary greatly in their propensity to hybridise. The majority of natural hybridisation accounts are from recent localised events (n = 71). Hybridisation hotspots were located in the Pyrenees and the European Alps, thus contrasting with the overall distribution of species richness in the genus. Hybrids or hybrid populations are often short-lived in Saxifraga due to a multitude of reproductive barriers, most commonly low F1 hybrid fertility. However, these barriers are not always fully effective, allowing for backcrossing and the formation of hybrid swarms. In addition, we find that the incidence of polyploidy varies widely across different sections of Saxifraga, with species-rich sections Porphyrion and Saxifraga showing divergent polyploidy proportions. Overall, we show that hybridisation and polyploidisation played differential roles in the diversification of this large genus. Nevertheless, a significant proportion of species are yet to be scrutinised, particularly among the Asian Saxifraga species, illustrating the need for systematic further study to fully unravel the role of hybridisation during the evolution of Saxifraga.

A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology and hybrid sterility

BACKGROUND AND AIMS

Polyploidy has played a major role in the origin of new plant species, probably because of the expansion of polyploid populations in the species' ecological niche, and because reproductive isolation can be established between a new polyploid population and its diploid progenitor species. It is well established that most polyploid species are polyphyletic, with multiple independent origins, and that polyploid genomes may undergo rapid change after their duplication and hybridization associated with their origin. We considered whether multiple independent origins and rapid genomic change might lead to reproductive isolation between polyploid populations of the same ploidy but with potentially different evolutionary histories.

METHODS

We tested our hypothesis by assessing differences in DNA content and morphology, the evolution of reproductive isolation, and the phylogenetic placement of two broadly sympatric hexaploid lineages of the wind-pollinated annual plant Mercurialis annua hitherto regarded as populations of the same species.

KEY RESULTS

The two hexaploid lineages of M. annua have slightly divergent DNA content, and distinct inflorescence morphology. They also fall into largely different clades of a chloroplast phylogeny and are reproductively isolated from one another.

CONCLUSIONS

The distinct evolutionary histories of the two hexaploid lineages of M. annua have contributed to the remarkable reproductive diversity of the species complex. It seems likely that reproductive interference between them will eventually lead to the displacement of one lineage by the other via pollen swamping. Thus, whereas polyploidization can contribute to speciation, diversification might also be compromised by reproductive interference.

Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)

BACKGROUND

The Carpathians and the Alps are the largest mountain ranges of the European Alpine System and important centres of endemism. Among the distinctive endemic species of this area is Saxifraga wahlenbergii, a Western Carpathians member of the speciose genus Saxifraga. It was frequently considered a taxonomically isolated Tertiary palaeopolyploid and palaeoendemic, for which the closest relatives could not yet be traced. A recently described narrow endemic of the Eastern Alps, S. styriaca, was hypothesized to be closely related to S. wahlenbergii based on shared presence of peculiar glandular hairs. To elucidate the origin and phylogenetic relationships of both species we studied nuclear and plastid DNA markers based on multiple accessions and analysed the data in a wide taxonomic context. We applied Sanger sequencing, followed by targeted next-generation sequencing (NGS) for a refined analysis of nrITS variants to detect signatures of ancient hybridization. The ITS data were used to estimate divergence times of different lineages using a relaxed molecular clock.

RESULTS

We demonstrate divergent evolutionary histories for the two mountain endemics. For S. wahlenbergii we revealed a complicated hybrid origin. Its maternal parent belongs to a Western Eurasian lineage of high mountain taxa grouped in subsect. Androsaceae and is most likely the widespread S. androsacea. The putative second parent was most likely S. adscendens, which belongs to the distantly related subsect. Tridactylites. While Sanger sequencing of nrITS only showed S. adscendens-related variants in S. wahlenbergii, our NGS screening revealed presence of sequences from both lineages with clear predominance of the paternal over the maternal lineage.

CONCLUSIONS

Saxifraga styriaca was unambiguously assigned to subsect. Androsaceae and is not the sister taxon of S. wahlenbergii. Accordingly, the similarity of the glandular hairs observed in both taxa rests on parallelism and both species do not constitute an example of a close evolutionary link between the floras of the Western Carpathians and Eastern Alps. With the origin of its paternal, S. adscendens-like ITS DNA estimated to ca. 4.7 Ma, S. wahlenbergii is not a relict of the mid-Tertiary climate optimum. Its hybrid origin is much younger and most likely took place in the Pleistocene.

Is meiosis a fundamental cause of inviability among sexual and asexual plants and animals?

Differences in viability between asexually and sexually generated offspring strongly influence the selective advantage and therefore the prevalence of sexual reproduction (sex). However, no general principle predicts when sexual offspring will be more viable than asexual offspring. We hypothesize that when any kind of reproduction is based on a more complex cellular process, it will encompass more potential failure points, and therefore lower offspring viability. Asexual reproduction (asex) can be simpler than sex, when offspring are generated using only mitosis. However, when asex includes meiosis and meiotic restitution, gamete production is more complex than in sex. We test our hypothesis by comparing the viability of asexual and closely related sexual offspring across a wide range of plants and animals, and demonstrate that meiotic asex does result in lower viability than sex; without meiosis, asex is mechanistically simple and provides higher viability than sex. This phylogenetically robust pattern is supported in 42 of 44 comparisons drawn from diverse plants and animals, and is not explained by the other variables included in our model. Other mechanisms may impact viability, such as effects of reproductive mode on heterozygosity and subsequent viability, but we propose the complexity of cellular processes of reproduction, particularly meiosis, as a fundamental cause of early developmental failure and mortality. Meiosis, the leading cause of inviability in humans, emerges as a likely explanation of offspring inviability among diverse eukaryotes.

High mountain origin, phylogenetics, evolution, and niche conservatism of arctic lineages in the hemiparasitic genus Pedicularis (Orobanchaceae)

The origin of the arctic flora covering the northernmost treeless areas is still poorly understood. Arctic plants may have evolved in situ or immigrated from the adjacent ecosystems. Frequently arctic species have disjunctive distributions between the Arctic and high mountain systems of the temperate zone. This pattern may result from long distance dispersal or from glacial plant migrations and extinctions of intermediate populations. The hemiparasitic genus Pedicularis is represented in the Arctic by c. 28 taxa and ranks among the six most species-rich vascular plant genera of this region. In this study, we test the hypothesis that these lineages evolved from predecessors occurring in northern temperate mountain ranges, many of which are current centers of diversity for the genus. We generated a nuclear ribosomal and chloroplast DNA phylogeny including almost all of the arctic taxa and nearly half of the genus as a whole. The arctic taxa of Pedicularis evolved 12-14 times independently and are mostly nested in lineages that otherwise occur in the high mountains of Eurasia and North America. It appears that only three arctic lineages arose from the present-day center of diversity of the genus, in the Hengduan Mountains and Himalayas. Two lineages are probably of lowland origin. Arctic taxa of Pedicularis show considerable niche conservatism with respect to soil moisture and grow predominantly in moist to wet soils. The studied characteristics of ecology, morphology, and chromosome numbers of arctic Pedicularis show a heterogeneous pattern of evolution. The directions of morphological changes among the arctic lineages show opposing trends. Arctic taxa are chiefly diploid, the few tetraploid chromosome numbers of the genus were recorded only for arctic taxa. Five arctic Pedicularis are annuals or biennials, life forms otherwise rare in the Arctic. Other genera of the Orobanchaceae consist also of an elevated number of short-lived species, thus hemiparasitism may favor this life form in the Arctic.

DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species

Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.

On the evolutionary and biogeographic history of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.)

Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting the North Pacific Rim.

Intraspecific diversity in Sinningia speciosa (Gesneriaceae: Sinningieae), and possible origins of the cultivated florist's gloxinia

BACKGROUND AND AIMS

The florist's gloxinia is a familiar houseplant in the Gesneriaceae, the botanical family that includes the African violet (Saintpaulia) and other ornamental species. The gloxinia's wild progenitor is Sinningia speciosa (Lodd.) Hiern, a Brazilian endemic. Although it has been cultivated for almost 200 years, little is known about the genetic diversity in S. speciosa, how the wild populations relate to one another or even where the cultivated forms originated. Using available wild collections, preliminary phenetic and phylogenetic investigations were conducted to elucidate the interspecific relationships within S. speciosa and to infer the origins of the cultivars.

METHODOLOGY

Amplified fragment length polymorphism (AFLP) analysis was applied to 24 accessions of S. speciosa (17 wild collections, seven cultivars) and one accession each of Sinningia guttata and Sinningia macrophylla. A maximum likelihood (ML) tree was also calculated from an alignment of the nuclear ribosomal internal transcribed spacer sequence from the same 26 accessions.

PRINCIPAL RESULTS

Dice/UPGMA and principal coordinates analysis of the AFLP data partitioned S. speciosa into several distinct clusters, one of which included S. macrophylla. All cultivated 'gloxinias' grouped together in a major cluster with plants from Rio de Janeiro. The AFLP results were compared with a phylogenetic analysis of the ribosomal spacer region, which was informative in S. speciosa. The ML tree generally supported the AFLP results, although several clades lacked strong statistical support.

CONCLUSIONS

Independent analyses of two different data sets show that S. speciosa is a diverse species comprised of several lineages. Genetic distance estimates calculated from the AFLP data were positively correlated with geographic distances between populations, indicating that reproductive isolation could be driving speciation in this taxon. Molecular markers are under development for population genetic studies in S. speciosa, which will make it possible to define evolutionarily significant units for purposes of conservation.

The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

BACKGROUND

The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The Arabidopsis lyrata complex, which is closely related to the model plant Arabidopsis thaliana, is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of Arabidopsis halleri, and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations.

RESULTS

Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the trnL/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the A. lyrata complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that A. kamchatica is the allotetraploid hybrid between A. lyrata and A. halleri, occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other A. lyrata segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid species in Japan, China, and Kamchatka.

CONCLUSIONS

Unglaciated parts of the Eastern Austrian Alps and arctic Eurasia, including Beringia, served as major glacial refugia of the Eurasian A. lyrata lineage, whereas A. halleri and its various subspecies probably survived in refuges in Central Europe and Eastern Asia with a large distribution gap in between. The North American A. lyrata lineage probably survived the glaciation in the southeast of North America. The dramatic climatic changes during glaciation and deglaciation cycles promoted not only secondary contact and formation of the allopolyploid hybrid A. kamchatica, but also provided the environment that allowed this species to fill a large geographic gap separating the two genetically different A. lyrata lineages from Eurasia and North America. With our example focusing on the evolutionary history of the A. lyrata species complex, we add substantial information to a broad evolutionary framework for future investigations within this emerging model system in molecular and evolutionary biology.

Disentangling reticulate evolution in an arctic-alpine polyploid complex

Although polyploidy plays a fundamental role in plant evolution, the elucidation of polyploid origins is fraught with methodological challenges. For example, allopolyploid species may confound phylogenetic reconstruction because commonly used methods are designed to trace divergent, rather than reticulate patterns. Recently developed techniques of phylogenetic network estimation allow for a more effective identification of incongruence among trees. However, incongruence can also be caused by incomplete lineage sorting, paralogy, concerted evolution, and recombination. Thus, initial hypotheses of hybridization need to be examined via additional sources of evidence, including the partitioning of infraspecific genetic polymorphisms, morphological characteristics, chromosome numbers, crossing experiments, and distributional patterns. Primula sect. Aleuritia subsect. Aleuritia (Aleuritia) represents an ideal case study to examine reticulation because specific hypotheses have been derived from morphology, karyology, interfertility, and distribution to explain the observed variation of ploidy levels, ranging from diploidy to 14-ploidy. Sequences from 5 chloroplast and 1 nuclear ribosomal DNA (nrDNA) markers were analyzed to generate the respective phylogenies and consensus networks. Furthermore, extensive cloning of the nrDNA marker allowed for the identification of shared nucleotides at polymorphic sites, investigation of infraspecific genetic polymorphisms via principal coordinate analyses PCoAs, and detection of recombination between putative progenitor sequences. The results suggest that most surveyed polyploids originated via hybridization and that 2 taxonomic species formed recurrently from different progenitors, findings that are congruent with the expectations of speciation via secondary contact. Overall, the study highlights the importance of using multiple experimental and analytical approaches to disentangle complex patterns of reticulation.

Molecular evidence for hybrid origins of the invasive polyploids Carthamus creticus and C. turkestanicus (Cardueae, Asteraceae)

The hexaploids Carthamus creticus and C. turkestanicus are noxious weeds with wide but non-overlapping Mediterranean distributions, and C. creticus, together with another polyploid, C. lanatus, have also invaded similar climatic regions in North and South America, South Africa and Australia. Here we infer their origins using sequences of the plastid intergenic spacer trnH-psbA and the intron trnK and three introns of nuclear low-copy genes of the RNA Polymerase family (RPD2 and the duplicated RPC2), as well as RAPD markers (random amplified polymorphic DNA). Phylogenetic analyses of the nuclear introns and additivity analysis of the RAPD markers support the hypotheses that the two hexaploids are allopolyploids sharing a tetraploid progenitor lineage represented by the broadly Mediterranean C. lanatus, combined with different diploid progenitor lineages consistent with the different geographic distributions of the hexaploids. Whereas C. leucocaulos from the south-eastern Greek Islands represents the diploid progenitor lineage of the western C. creticus, the Irano-Turanian C. glaucus represents the diploid progenitor lineage of the eastern C. turkestanicus. The plastid data suggest that the diploid lineages served as the maternal progenitors of the hexaploids.

Genetic enrichment of the arctic clonal plant Saxifraga cernua at its southern periphery via the alpine sexual Saxifraga sibirica

Isolation of populations at the margins of a species range may lead to decreasing genetic diversity via genetic drift and inbreeding. Hybridization between peripheral populations of two species can, however, counteract genetic impoverishment. The mainly clonal, polyploid plant Saxifraga cernua has a wide arctic distribution but also extends southwards into alpine sites. In the Ural Mountains, its peripheral distribution overlaps with that of its sexually reproducing, diploid relative Saxifraga sibirica, and fertile polyploids of more or less intermediate appearance are found in this overlap zone. We used amplified fragment length polymorphism (AFLP) analysis to address the potential impact of interspecific gene flow on genetic diversity in the peripheral populations. A total of 149 plants from 17 populations along a 1650 km south-north gradient were analysed for 253 markers. The results suggest that three Middle Ural populations containing fertile and morphologically more or less intermediate plants have been affected by hybridization. All of these plants formed a strongly supported (100%) group with S. cernua in a neighbour-joining tree, but their AFLP phenotypes assigned either to S. cernua or to artificial (simulated) F(1) hybrids between S. cernua and S. sibirica in multilocus assignment tests. The three populations were highly diverse with virtually every plant representing a distinct AFLP phenotype, providing additional evidence for formation of later-generation hybrids and/or backcrossing to S. cernua. In contrast, other peripheral populations of S. cernua were typically monoclonal, suggesting that hybridization with S. sibirica can increase genetic diversity in S. cernua at its southern periphery.

Patterns of recurrent evolution and geographic parthenogenesis within apomictic polyploid Easter daises (Townsendia hookeri)

Geographic patterns of parthenogenesis and the number of transitions from sexual diploidy to asexual (apomictic) autopolyploidy were examined for 40 populations of the Easter daisy, Townsendia hookeri. Analyses of pollen diameter and stainability characterized 15 sexual diploid and 25 apomictic polyploid populations from throughout the plant's western North American range. Sexual diploids were restricted to two Wisconsin refugia: Colorado/Wyoming, south of the ice sheets, and northern Yukon/Beringia. Chloroplast DNA sequencing uncovered 17 polymorphisms within the ndhF gene and trnK intron, yielding 10 haplotypes. Phylogenetic analyses indicated that five exclusively polyploid haplotypes were derived from four haplotypes that are shared among ploidies, conservatively inferring a minimum of four origins of apomictic polyploidy. Three of these apomictic polyploid origins were derived from southern sexual diploids, while the fourth origin was derived from northern sexual diploids. Analyses of regional diversity were suggestive of a formerly broad distribution for sexual diploids that has become subsequently fragmented, possibly due to the last round of glaciation. As sexual diploids were exclusively found north and south of the glacial maximum, while formerly glaciated areas were exclusively inhabited by asexual polyploids derived from both northern and southern sexual lineages, it is more likely that patterns of glaciation, as opposed to a particular latitudinal trend, played a causal role in the establishment of the observed pattern of geographic parthenogenesis in Easter daisies.

Molecular evidence for multiple polyploidization and lineage recombination in the Chrysanthemum indicum polyploid complex (Asteraceae)

The Chrysanthemum indicum polyploid complex comprises morphologically differentiated diploids, tetraploids and hybrids between C. indicum and C. lavandulifolium. The relationships between species and cytotypes within this complex remain poorly understood. Random amplified polymorphic DNAs (RAPDs), intersimple sequence repeats (ISSRs) and chloroplast SSR markers were used to elucidate the genetic diversity and relationships of the C. indicum polyploid complex. Molecular analysis of three diploid and nine tetraploid populations provided strong evidence for recurrent origins and lineage recombination in the C. indicum polyploid complex. The high similarity in molecular marker profiles and cpDNA haplotypes between the diploids and tetraploids distributed in the Shen-Nong-Jia Mountain area of China suggested an autopolyploid origin of the tetraploids, while the tetraploids from other populations may have originated via allopolyploidization. Lineage recombination was revealed by the extensive sharing of chloroplast haplotypes and genetic markers among the tetraploid populations with different origins. Multiple differentiation and hybridization/polyploidization cycles have led to an evolutionary reticulation in the C. indicum polyploid complex, and resulted in the difficulties in systematic classification.

Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data

Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.

Amplified fragment length polymorphism versus random amplified polymorphic DNA markers: clonal diversity in Saxifraga cernua

Random amplified polymorphic DNA (RAPD) markers are sensitive to changes in reaction conditions and may express polymorphisms of nongenetic origin. Taxa with variable chromosome numbers are particularly challenging cases, as differences in DNA content may also influence marker reproducibility. We addressed these problems by comparing RAPD and amplified fragment length polymorphism (AFLP) analyses of clonal identity and relationships in a chromosomally variable arctic plant, the polyploid Saxifraga cernua, which has been thought to be monoclonal over large geographical distances. Fifty-seven plants from four Greenland populations were analysed using a conservative scoring approach. In total, 26 AFLP and 32 RAPD multilocus phenotypes (putative clones) were identified, of which 21 were identical and each of the remaining five AFLP clones was split into two to three very similar RAPD clones. This minor difference can be explained by sampling error and stochastic variation. The pattern observed in Greenland corroborates our previous results from Svalbard, suggesting that rare sexual events in S. cernua are sufficient to maintain high levels of clonal diversity even at small spatial scales. We conclude that although AFLP analysis is superior in terms of efficiency, RAPDs may still be used as reliable markers in small low-tech laboratories.

History and evolution of the arctic flora: in the footsteps of Eric Hultén

A major contribution to our initial understanding of the origin, history and biogeography of the present-day arctic flora was made by Eric Hultén in his landmark book Outline of the History of Arctic and Boreal Biota during the Quarternary Period, published in 1937. Here we review recent molecular and fossil evidence that has tested some of Hultén's proposals. There is now excellent fossil, molecular and phytogeographical evidence to support Hultén's proposal that Beringia was a major northern refugium for arctic plants throughout the Quaternary. In contrast, most molecular evidence fails to support his proposal that contemporary east and west Atlantic populations of circumarctic and amphi-Atlantic species have been separated throughout the Quaternary. In fact, populations of these species from opposite sides of the Atlantic are normally genetically very similar, thus the North Atlantic does not appear to have been a strong barrier to their dispersal during the Quaternary. Hultén made no detailed proposals on mechanisms of speciation in the Arctic; however, molecular studies have confirmed that many arctic plants are allopolyploid, and some of them most probably originated during the Holocene. Recurrent formation of polyploids from differentiated diploid or more low-ploid populations provides one explanation for the intriguing taxonomic complexity of the arctic flora, also noted by Hultén. In addition, population fragmentation during glacial periods may have lead to the formation of new sibling species at the diploid level. Despite the progress made since Hultén wrote his book, there remain large gaps in our knowledge of the history of the arctic flora, especially about the origins of the founding stocks of this flora which first appeared in the Arctic at the end of the Pliocene (approximately 3 Ma). Comprehensive analyses of the molecular phylogeography of arctic taxa and their relatives together with detailed fossil studies are required to fill these gaps.

Molecular analysis of the Pleistocene history of Saxifraga oppositifolia in the Alps

A recent circumpolar survey of chloroplast DNA (cpDNA) haplotypes identified Pleistocene glacial refugia for the Arctic-Alpine Saxifraga oppositifolia in the Arctic and, potentially, at more southern latitudes. However, evidence for glacial refugia within the ice sheet covering northern Europe during the last glacial period was not detected either with cpDNA or in another study of S. oppositifolia that surveyed random amplified polymorphic DNA (RAPD) variation. If any genotypes survived in such refugia, they must have been swamped by massive postglacial immigration of periglacial genotypes. The present study tested whether it is possible to reconstruct the Pleistocene history of S. oppositifolia in the European Alps using molecular methods. Restriction fragment length polymorphism (RFLP) analysis of cpDNA of S. oppositifolia, partly sampled from potential nunatak areas, detected two common European haplotypes throughout the Alps, while three populations harboured two additional, rare haplotypes. RAPD analysis confirmed the results of former studies on S. oppositifolia; high within, but low among population genetic variation and no particular geographical patterning. Some Alpine populations were not perfectly nested in this common gene pool and contained private RAPD markers, high molecular variance or rare cpDNA haplotypes, indicating that the species could possibly have survived on ice-free mountain tops (nunataks) in some parts of the Alps during the last glaciation. However, the overall lack of a geographical genetic pattern suggests that there was massive immigration of cpDNA and RAPD genotypes by seed and pollen flow during postglacial times. Thus, the glacial history of S. oppositifolia in the Alps appears to resemble closely that suggested previously for the species in northern Europe.

Tribal and subtribal delimitation and phylogeny of the Cardueae (Asteraceae): a combined nuclear and chloroplast DNA analysis

Tribal delimitation of Cardueae is controversial, and the traditional classification in four subtribes (Echinopsidinae, Carlininae, Carduinae, and Centaureinae) has fluctuated widely. Most of the problems are centered in subtribes Echinopsidinae and Carlininae, often segregated with tribal rank. We therefore analyzed DNA sequences of the internal transcribed spaces (ITS) of the nuclear ribosomal DNA genes and the matK gene of the chloroplast DNA of a broad representation of the tribe to examine (1) the phylogeny of the tribe, (2) the position of Echinopsidinae and Carlininae, (3) the circumscription of the subtribes and the position of some conflicting genera, and (4) the delimitation of some generic complexes in the Carduinae. Phylogenetic analysis of ITS and matK sequence variation, both separate and combined, strongly support the monophyly of Cardueae including Carlininae and Echinopsidinae. The combination of both genomes suggest that Xeranthemum and its allies should be included among the Echinopsidinae rather than the Carlininae, which implies that the capitulum of Xeranthemum could be interpreted as a syncephaly. The subtribe Centaureinae forms a well-supported clade, and their sister clades contain the genera Arctium, Cousinia, Jurinea, and Saussurea from the Carduinae. However, some problems persist: Carduinae are a paraphyletic assemblage, and the subtribal placement of Berardia, Cardopatium, Cousiniopsis, and Staehelina remains unresolved. Our results also indicate that present classification in four subtribes is unsatisfactory, but it is still the only practical approach.

Molecular investigations in populations of Spartina anglica C.E. Hubbard (Poaceae) invading coastal Brittany (France)

Spartina anglica is a classical example of recent alloploid speciation. It arose during the end of the nineteenth century in England by hybridization between the indigenous Spartina maritima and the introduced East-American Spartina alterniflora. Duplication of the hybrid genome (Spartina x townsendii) gave rise to a vigorous allopolyploid involved in natural and artificial invasions on different continents. Spartina anglica was first recorded in France in 1906, and since then, it has spread all along the western French coast. Earlier studies revealed that native British populations display consistent morphological plasticity and lack of isozyme variation. In this paper, we use different molecular markers (randomly amplified polymorphic DNA, intersimple sequence repeats and restriction patterns from nuclear and chloroplast DNA sequences) to analyse the genetic patterns of the French populations of S. anglica. Our results show that French populations are mainly composed of one "major" multilocus genotype. This genotype is identical to the first-generation hybrid S. x townsendii from England. Losses of few markers from this genotype are observed but are restricted to a few populations from Brittany; it is likely that they appeared independently, subsequent to their introduction. In southern Brittany, no hybrids between S. anglica and S. maritima have been found where the two species co-occur. All French populations of S. anglica display the same chloroplast DNA sequences as S. alterniflora, the maternal genome donor. These findings are consistent with a severe genetic bottleneck at the time of the species formation, as a consequence of a unique origin of the species. Both parental nuclear sequences are present in the allopolyploid populations, revealing that for the markers investigated, no extensive changes have occurred in this young species.

Phylogenetic relationships of the silver saxifrages (Saxifraga, sect. Ligulatae haworth): implications for the evolution of substrate specificity, life histories, and biogeography

The silver saxifrages (Saxifraga sect. Ligulatae Haworth; Saxifragaceae) exhibit remarkable variation of substrate specialization, with strictly calcicole to calcifuge species, as well as life histories which range from semelparity to iteroparity. They occur almost exclusively in the European mountain ranges and display high levels of endemism. Sequences from chloroplast and nuclear ribosomal DNA were obtained to resolve phylogenetic relationships among the silver saxifrages and related taxa and to gain insight into the evolution of substrate specificity, life history, and biogeography. The resulting phylogenies suggested that (1) Saxifraga sect. Ligulatae, as traditionally defined, does not constitute a monophyletic group; (2) lime-secreting hydathodes in calcifuge species apparently represent a secondary nonaptation; (3) semelparity evolved independently two or three times in the silver saxifrages and allied sections, possibly in response to climatic changes that occured during the Pleistocene; and (4) narrow endemics, for example S. cochlearis, likely evolved from the fragmentation of the widespread S. paniculata into refugial populations that became isolated during the glacial maxima of the Pleistocene.

Polyploidy: recurrent formation and genome evolution

Polyploidy has played a major role in the evolution of many eukaryotes. Recent studies have dramatically reshaped views of polyploid evolution, demonstrating that most polyploid species examined, both plant and animal, have formed recurrently from different populations of their progenitors. Populations of independent origin can subsequently come into contact and hybridize, generating new genotypes. Because of the frequency of polyploidy in plants, many recognized species are probably polyphyletic. Extensive and rapid genome restructuring can occur after polyploidization. Such changes can be mediated by transposons. Polyploidization could represent a period of transilience, during which genomic changes occur, potentially producing new gene complexes and facilitating rapid evolution.

Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences

A biogeographic study of Saxifraga section Saxifraga was performed based on phylogenetic analyses of ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. ITS sequences from 21 species and 31 populations were examined to identify colonization patterns for the two species of Saxifraga occurring in Macaronesia and for S. globulifera in the west Mediterranean basin. Phylogenetic analysis of the sequence data yield a single most parsimonious tree with many of the major clades well supported by bootstrap and decay values. The ITS tree provided resolution at specific and populational levels that points to two biogeographic patterns within the genus. In contrast to the molecular evidence provided by other authors for a Mediterranean origin of several Macaronesian genera of angiosperms, our results indicate that the Madeiran archipelago was colonized a single time by a species of Saxifraga originating from the Eurosiberian region. On the other hand, the molecular evidence also suggests that populations of S. globulifera from North Africa have been isolated for a long time from populations occurring in the Iberian Peninsula, and that the endemic S. reuteriana has evolved from the Iberian populations of S. globulifera. The Mediterranean Sea has probably been an effective isolating barrier for some plant groups that occur in Europe and North Africa.