Amplified fragment length polymorphism (AFLP) reveals introgression in weedy Onopordum thistles: hybridization and invasion

Intraspecific Variations in Functional and Molecular Traits of Near-Endemic Onopordum alexandrinum Boiss. in Natural and Anthropogenic Habitats along the Western Mediterranean Coast of Egypt: Implications for Conservation

Onopordum alexandrinum is a near-endemic to Egypt and neighboring countries. Its habitats are designated as priority sites for conservation in the south and east Mediterranean regions. We hypothesize that variation in morphological, reproductive, and molecular traits could provide a survival strategy that allows the species to occupy landscapes including anthropogenic habitats (barley and abandoned fields) and natural habitats (sand dunes and desert plateau) with different soil resources along the western Mediterranean coast of Egypt. The results indicated that plant functional traits associated with high rates of resource acquisition and growth (e.g., high values of vegetative height and specific leaf area, and low values of leaf dry matter content) occurred in populations located in abandoned fields with high soil resources. The genetic diversity analyses indicated similarity in genetic diversity of the present populations of O. alexandrinum in barley and abandoned fields with those of sand dunes. However, the genetic structures of these populations were different from those of natural desert plateau, which suggests reduced rates of gene flow. In this framework, it is essential to monitor and reduce the anthropogenic activity which will not only support the conservation of genetic diversity within populations but will also help ensure the resilience of O. alexandrinum in the face of environmental and climatic changes.

Big thistle eats the little thistle: does unidirectional introgressive hybridization endanger the conservation of Onopordum hinojense?

Hybridization is known to have a creative role in plant evolution. However, it can also have negative effects on parental species. Onopordum is a large genus whose species frequently hybridize. In the Southwest Iberian Peninsula, the rare O. hinojense co-occurs with the widely distributed O. nervosum, and hybrids between these two taxa have been described as O. × onubense. In this study we determine the extinction risk in a hybrid zone, both for hybrids and parentals, using analyses of morphological and cytogenetic traits as well as genetic markers and demographic models. To investigate the introgression process we used amplified fragment length polymorphism (AFLP) markers, Bayesian analyses and genome scan methods. Morphology, genome size and molecular markers confirmed homoploid hybridization and also indicated unidirectional backcrossing of F₁ hybrids with O. nervosum, which is likely to swamp O. hinojense, the parental with lower pollen size and a very low fruit set (8%). Genome scan methods revealed several loci significantly deviating from neutrality. Finally, our demographic modeling indicated that the higher fitness of O. nervosum threats the survival of O. hinojense by demographic swamping. Our study provides strong new evidence for a scenario of rapid extinction by unidirectional introgression and demographic swamping. The multifaceted approach used here sheds new light on the role of introgression in plant extinctions.

AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations

BACKGROUND

In spite of a large diversity of approaches to investigate loci under selection from a population genetic perspective, very few programs have been specifically designed to date to test selection in hybrids using dominant markers. In addition, simulators of dominant markers are very scarce and they do not usually take into account hybridization.

RESULTS

Here, we present a new, multifunctional, R package for dominant genetic markers, AFLPsim. This package can simulate dominant markers in hybridizing populations and implements genome scan methods for detecting outlier dominant loci in hybrids. In addition, it includes tools for further manipulating the results, plotting them and other tasks. We describe and tabulate the major functions implemented in AFLPsim. In addition, we provide some demonstration of its use and we perform a comparative study with other software. Finally, we conclude by briefly describing the input and output formats.

CONCLUSIONS

The R package AFLPsim application provides several useful tools in the context of hybridization studies. It can simulate dominant markers in hybridizing populations and predict their demographic evolution. In addition, we implement a new genome scan method for detecting outlier dominant loci in hybrids, which shows a rather high sensitivity and is very conservative in comparison with Gagnaire et al.'s, Bayescan and introgress. The application is downloadable at http://cran.r-project.org/web/packages/AFLPsim/.

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.)

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

Evolution of the polyploid north-west Iberian Leucanthemum pluriflorum clan (Compositae, Anthemideae) based on plastid DNA sequence variation and AFLP fingerprinting

BACKGROUND AND AIMS

The genus Leucanthemum is a species-rich polyploid complex from southern and central Europe, comprising 41 species with ploidy ranging from 2x to 22x. The present contribution aims at reconstructing the evolutionary history of a geographically isolated species group (the L. pluriflorum clan) from the north-west Iberian Peninsula comprising the diploid L. pluriflorum, the tetraploids L. ircutianum subsp. pseudosylvaticum and L. × corunnense (a putative hybrid taxon based on crossing between L. pluriflorum and L. merinoi), and the hexaploids L. sylvaticum and L. merinoi.

METHODS

Chromosome number variation (determined flow cytometrically) and sequence variation were analysed for two intergenic spacer regions on the plastid genome (psbA-trnH and trnC-petN) for individuals from 54 populations in combination with amplified fragment length polymorphism (AFLP) fingerprinting of 246 representative individuals from these populations.

KEY RESULTS

Plastid sequence data revealed that all surveyed members of the L. pluriflorum clan possess plastid haplotypes that are closely related to each other and distinctly separated from other Leucanthemum species. AFLP fingerprinting resulted in allopolyploid fragment patterns for most of the polyploid populations, except for the tetraploid L. × corunnense and a further tetraploid population in northern Galicia, which cluster with the diploids rather than with the other polyploids. In silico modelling of (auto)tetraploid AFLP genotypes further corroborates the allopolyploid nature of L. ircutianum subsp. pseudosylvaticum, L. sylvaticum and L. merinoi.

CONCLUSIONS

The present study provides evidence for recognizing one diploid (L. pluriflorum), one autotetraploid (L. corunnense), one allotetraploid (L. pseudosylvaticum) and one allohexaploid (L. sylvaticum with the two geographically and ecologically differentiated subspecies subsp. sylvaticum and subsp. merinoi) in the L. pluriflorum clan. It also has implications for the understanding of biogeographical patterns in the Iberian Peninsula.

What does population structure analysis reveal about the Pterostylis longifolia complex (Orchidaceae)?

Morphologically similar groups of species are common and pose significant challenges for taxonomists. Differences in approaches to classifying unique species can result in some species being overlooked, whereas others are wrongly conserved. The genetic diversity and population structure of the Pterostylis longifolia complex (Orchidaceae) in Tasmania was investigated to determine if four species, and potential hybrids, could be distinguished through genomic AFLP and chloroplast restriction-fragment-length polymorphism (RFLP) markers. Analysis of molecular variance (AMOVA) results indicated that little genetic variation was present among taxa, whereas PCoA analyses revealed genetic variation at a regional scale irrespective of taxa. Population genetic structure analyses identified three clusters that correspond to regional genetic and single taxon-specific phenotypic variation. The results from this study suggest that "longifolia" species have persisted throughout the last glacial maximum in Tasmania and that the complex may be best treated as a single taxon with several morphotypes. These results could have serious evolutionary and conservation implications as taxonomic changes could result in the instatement of a single, widespread taxon in which rarer morphotypes are not protected.

Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis

Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.

Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria)

In spite of the ecological and economic importance of temperate bamboos, relatively little is known about their population biology or evolutionary history. Recently, hybridization has emerged as a potential source of diversity in this group, as well as an underlying cause of taxonomic problems. As part of a broader phylogenetic study of the temperate bamboos, we report the results of an analysis of the North American Arundinaria gigantea species complex, including estimates of genetic variation and molecular evidence of natural hybridization among A. gigantea, A. tecta, and A. appalachiana. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species plus individuals with intermediate or unusual morphological characteristics (putative hybrids). Molecular results support the recognition of three species previously defined on the basis of morphology, anatomy, and ecology, with most of the molecular variance accounted for by among-species variation. Molecular evidence also demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. The role of hybridization in the phylogenetic history of Arundinaria is discussed along with implications for the evolution and taxonomy of the temperate woody bamboos.

Hybridization and invasion: one of North America's most devastating invasive plants shows evidence for a history of interspecific hybridization

Hybridization has been hypothesized to influence invasion through the generation of novel phenotypes and/or increased levels of genetic variance. Based on morphology, hybrids between diffuse knapweed and spotted knapweed, two invasive plants in North America, are present in the invaded range. Some individuals within most diffuse knapweed sites in North America exhibit intermediate diffuse × spotted floral morphology. We examined hybridization at the molecular level, using amplified fragment length polymorphisms. Approximately a quarter of the assayed North American diffuse knapweed individuals exhibited evidence of introgression from spotted knapweed. However, plants with intermediate morphology did not show evidence of mixed ancestry more often than the plants with typical diffuse knapweed morphology. The high proportion of hybrid individuals in North American diffuse knapweed sites found here, combined with evidence from recent studies, suggests that diffuse knapweed was likely introduced with admixed individuals, and the hybrids are not newly created postintroduction. A century of backcrossing with diffuse knapweed has likely decoupled the relationship between morphology and admixture at the molecular level. In contrast to the scenario encountered in North America, in the native range where diploid diffuse and spotted knapweed overlap, hybrid swarms are common. In such sites, the floral phenotype aligns more closely with the genotype.

AFLP analyses on genetic diversity and structure ofEupatorium adenophorumpopulations in China

Eupatorium adenophorum(crofton weed) is one of the most widespread invasive species in China. Its genetic diversity and population structure in China were analysed by amplified fragment length polymorphism (AFLP). Three primer pairs were selected for the analysis and 490 bands were produced from 62E. adenophorumpopulations selected from five major geographic areas. A total of 328 of the bands showed polymorphism [percentage of polymorphic bands (PPB)=59.4%]. Diversity levels of populations were relatively high (mean expected heterozygosity=0.154, mean Shannon index=0.241). At the regional level, the AMOVA indicated that about 70.25% of variation in the data set was from genotypic variations within populations, whereas 8.04% of the variation was due to regional differences, and the remaining 21.71% to differences among populations within the provincial regions. Cluster analysis based on the unweighted pair-group method using the method of arithmetic averages (UPGMA) grouped the majority ofE. adenophorumpopulations into four main clusters, which correspond to their geographic regions. It is concluded thatE. adenophorumspread mainly by wind or water and its genetic diversity level in newly invaded areas was lower than that in formerly colonized areas.

Taxonomy and conservation: A case study from Chamaedorea alternans

BACKGROUND AND AIMS

The establishment of justified recommendations in conservation biology requires robust taxonomic treatments for the group(s) being considered. Controversial or poorly developed taxonomies can have a negative impact on conservation assessments. One example of a taxonomically difficult and controversial species complex that is important in conservation involves two species of Mexican palms, Chamaedorea tepejilote and C. alternans. The goal of this study was to investigate whether C. alternans and C. tepejilote are genetically distinct within the Los Tuxtlas region of Veracruz.

METHODS

Individuals corresponding to the morphology of C. alternans and C. tepejilote were collected from sympatric and allopatric regions within the Los Tuxtlas Biological Station. Eighty-eight samples were genotyped using amplified fragment length polymorphism (AFLP) markers. Cluster and ordination analyses were used to investigate patterns of differentiation.

KEY RESULTS

UPGMA and PCO analyses of AFLP profiles recovered two divergent clusters corresponding to morphologically defined C. tepejilote and C. alternans. No intermediate genotypes were observed and five of the 45 loci were fixed for either the presence or absence between the species. The patterns of divergence observed do not identify a role for sympatric speciation.

CONCLUSIONS

The observed patterns of differentiation support the recognition of C. alternans as distinct from C. tepejilote. A suite of vegetative and reproductive morphological features can be used to help distinguish these taxa in the field, but they can be difficult to differentiate from preserved material. Previous treatments of the variation found within the complex (C. alternans and C. tepejilote) as intraspecific variance is unjustified. Given that the Los Tuxtlas region has suffered from historical and ongoing deforestation and that Chamaedorea includes numerous endangered taxa, retaining conservation status for C. alternans serves to help safeguard individuals of the species as well as a region and larger taxonomic group all under considerable threat from human activities.

Hybrid origin and differentiation of two tetraploid Achillea species in East Asia: molecular, morphological and ecogeographical evidence

Achillea (Asteraceae-Anthemideae) offers classical models for speciation by hybridization and polyploidy. Here, we test the suspected allotetraploid origin of two species, Achillea alpina and Achillea wilsoniana between phylogenetically distinct lineages in East Asia. A total of 421 AFLP bands from 169 individuals and 19 populations of five 2x- and two 4x-species were obtained. The data set was analysed with a newly developed model that accounts for polyploidy and assumes lack of recombination between the parental chromosome sets (i.e. disomic inheritance). A. alpina and A. wilsoniana then appear to be allotetraploids between Achillea acuminata-2x (sect. Ptarmica) and Achillea asiatica-2x (sect. Achillea). The two 4x-species share 44% and 48% of their AFLP bands with A. acuminata-2x, and 39% and 38% with A. asiatica-2x, respectively. Eight plastid haplotypes (A-H) were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses. A. alpina-4x and A. wilsoniana-4x share haplotype F only with A. asiatica-2x. This is consistent with the hybrid origin(s) involving the latter as the maternal ancestor. This result corroborates our previous DNA sequence data, where A. alpina-4x and A. wilsoniana-4x are also placed close to A. asiatica-2x. Morphology, ecology, and amplified fragment length polymorphism (AFLP) profiles of the two 2x-species are distinct, whereas the two 4x-species, grouped as A. alpina aggregate, form a nearly continuous link between them. Considering all evidence, this 4x-aggregate is regarded as the product of a hybridization between genetically distant 2x-ancestors limited to China and adjacent areas: one A. acuminata-like, and the other A. asiatica-like. The allopolyploid A. alpina agg. exhibits considerable morphological variation and ecological flexibility, and has expanded throughout eastern Asia and to northern North America, far beyond the ranges of their presumed 2x-ancestors.

The role of hybridization, polyploidization and glaciation in the origin and evolution of the apomictic Ranunculus cassubicus complex

The Ranunculus cassubicus complex, comprising diploids and polyploids, is a good model for studying the role of hybridization and polyploidy in the origin of apomixis. Results from amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses performed on 448 individuals were combined with evidence from morphology, isozymes, karyology and distribution. Our results indicated a unique hybrid origin for the apomictic hexaploid R. carpaticola from north-western Slovakia, involving two sexual parents: autotetraploid R. cassubicifolius from the northern pre-Alps, and diploid R. carpaticola from central Slovakia. The hybrids were intermediate to the parents, but unique alleles have resulted from genomic reorganisation in the allopolyploids, which might also have triggered apomixis. Their distribution patterns and estimated ages suggest that hybridization may be correlated with the last glacial period. Hybridization seems to be the major origination for apomicts in the R. cassubicus complex. Polyploidy creates novel sexual genotypes and acts as a springboard for the production of new hybrids, but it only results in a combination with hybridization in apomixis. In turn, asexuality has permitted the perpetuation and establishment of ecologically divergent hybrid genotypes.

Reciprocal hybridization at different times between Senecio flavus and Senecio glaucus gave rise to two polyploid species in north Africa and south-west Asia

The analysis of hybrid plant taxa using molecular methods has considerably extended understanding of possible pathways of hybrid evolution. Here, we investigated the origin of the tetraploid Senecio mohavensis ssp. breviflorus and the hexaploid Senecio hoggariensis by sequencing of nuclear and chloroplast DNA, and by analysis of the distribution of taxon-specific amplified fragment length polymorphism (AFLP) fragments. Both taxa originated from hybridization between the diploid Senecio flavus and Senecio glaucus. Whereas S. glaucus was the female parent in the origin of S. mohavensis ssp. breviflorus, S. flavus was the female parent in the origin of S. hoggariensis. The distribution of AFLP fragments suggests that S. hoggariensis is an allohexaploid species with two diploid genomes of S. glaucus and one diploid genome of S. flavus. The high frequency of S. flavus-specific fragments in S. mohavensis ssp. breviflorus is explained either as the result of introgression between a primary hybrid and S. flavus or as the result of intergenomic recombination in a primary hybrid. These two alternative processes cannot easily be distinguished.

Evidence of hybridization between Lythrum salicaria (purple loosestrife) and L. alatum (winged loosestrife) in North America

BACKGROUND AND AIMS

Although Lythrum salicaria (purple loosestrife) was introduced to North America from Europe in the early 1800s, it did not become invasive until the 1930s. Whether hybridization with L. alatum (winged loosestrife) could have played a role in its ultimate spread was tested.

METHODS

Six diagnostic morphological traits (flower number per axil, leaf placement, calyx pubescence, style type, plant height and leaf shape) were surveyed in 30 populations of Lythrum across eastern North America. Patterns of AFLP variation were also evaluated using five primer pairs in a 'global screen' of the same North American populations of L. salicaria and L. alatum described above, in L. salicaria from 11 European populations located in Germany, England, Ireland, Austria and Finland, and in six L. salicaria cultivars.

KEY RESULTS

All of the North American L. salicaria populations had individuals with alternate leaf placement and 1-2 flowers per leaf axil, which have not been described in Eurasian L. salicaria but predominate in North American L. alatum. In addition, two L. salicaria populations were intermediate in height and leaf ratio between the typical L. salicaria and L. alatum populations in their native fields and when grown in a common greenhouse. In screens of variation patterns using 279 AFLPs, only two fragments were found that clearly supported introgression from L. alatum to L. salicaria.

CONCLUSIONS

The evidence indicates that L. salicaria may have hybridized with L. alatum, but if so, only a small fraction of L. alatum genes have been retained in the genome of L. salicaria. This is unlikely to have led to a dramatic adaptive shift unless the introgression of a few key genes into L. salicaria stimulated a genomic reorganization. It is more likely that crossing among genotypes of L. salicaria from multiple introductions provided the necessary variability for new adaptations to arise.

AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidization in the evolution of Achillea (Asteraceae-Anthemideae)

Achillea, a temperate genus of herbaceous allogamous perennials, is a model for evolutionary radiation through hybridization and polyploidization. AFLP analyses were performed on 300 individuals of 66 populations and 27 taxa/cytotypes, mainly from the polyploid A. millefolium aggregate and its suspected hybrid links with other clades of the genus. The mosaic genetic structure of hybrids and polyploids is revealed by specific AFLP bands shared with their assumed parents. In E Asia, A. alpina-4x and A. wilsoniana-4x are allotetraploids between A. acuminata-2x (sect. Ptarmica) and A. asiatica-2x (sect. Achillea-A. millefolium agg.). A. virescens-4x is a hybrid species linking A. nobilis agg. and A. millefolium agg. in S Europe. The hybrid swarm A. clypeolata-2x yen A. collina-4x recently formed in Bulgaria shows no AFLP bands additive to its parents; by contrast, other more ancient allopolyploids exhibit genetic innovations. Relationships within A. millefolium agg. are complex. Five 2x-taxa, mostly well separated and regressive, are limited to Eurasia; seven 4x- and 6x-taxa are intimately linked by hybridization, are expansive, and through A. asiatica-2x/4x have formed the N American polyploids. All these results from AFLPs correspond well to other evidence, and indicate a long history of reticulate evolution in Achillea.

Cytoplasmic and nuclear markers reveal contrasting patterns of spatial genetic structure in a natural Ipomopsis hybrid zone

Spatial variation in natural selection may play an important role in determining the genetic structure of hybridizing populations. Previous studies have found that F1 hybrids between naturally hybridizing Ipomopsis aggregata and Ipomopsis tenuituba in central Colorado differ in fitness depending on both genotype and environment: hybrids had higher survival when I. aggregata was the maternal parent, except in the centre of the hybrid zone where both hybrid types had high survival. Here, we developed both maternally (cpDNA PCR-RFLP) and biparentally inherited (nuclear AFLP) species-diagnostic markers to characterize the spatial genetic structure of the natural Ipomopsis hybrid zone, and tested the prediction that the majority of natural hybrids have I. aggregata cytoplasm, except in areas near the centre of the hybrid zone. Analyses of 352 individuals from across the hybrid zone indicate that cytoplasmic gene flow is bidirectional, but contrary to expectation, most plants in the hybrid zone have I. tenuituba cytoplasm. This cytotype distribution is consistent with a hybrid zone in historical transition, with I. aggregata nuclear genes advancing into the contact zone. Further, nuclear data show a much more gradual cline than cpDNA markers that is consistent with morphological patterns across the hybrid populations. A mixture of environment- and pollinator-mediated selection may contribute to the current genetic structure of this hybrid system.

Cryptic species in an endangered pondweed community (Potamogeton, Potamogetonaceae) revealed by AFLP markers

Cryptic species are morphologically indistinguishable, yet reproductively isolated. Morphological boundaries between species can also be obscured by hybridization and clonality. Determining the roles of reproductive isolation, hybridization, and clonality in morphologically indistinguishable taxa is essential to determining appropriate species-level taxonomic rankings for conservation purposes. The taxonomic status of the endangered Little Aguja pondweed of west Texas, Potamogeton clystocarpus, is uncertain due to a lack of fixed morphological differences between it and two sympatric congeners. Morphology, amplified fragment length polymorphisms (AFLPs), and sequences of the internal transcribed spacer (ITS) region and trnL-F intron and spacer were used to determine the degree of genetic distinctiveness, hybridization and clonality for this rare species. AFLPs indicate that P. clystocarpus is a genetically distinct lineage compared to P. pusillus and P. foliosus. No hybrids involving P. clystocarpus were detected, but two putative hybrids involving P. pusillus and P. foliosus were identified. Clonal growth was only detected in P. pusillus. A combination of morphological and molecular markers was successful in determining the genetic distinctiveness of an endangered cryptic species, Potamogeton clystocarpus. Further sampling in this and adjacent drainages is necessary to assess the degree of endemism of P. clystocarpus and confidently rule out hybridization and clonality in this taxon.

The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri

An amplified fragment length polymorphism (AFLP) assay was performed on individuals representing discrete haplotypes from two genetically distinct mtDNA lineages of the bamboo viper, Trimeresurus stejnegeri (Schmidt), within Taiwan. AFLP (525 polymorphic markers from five primer pairs) and mtDNA genetic distances were highly correlated and an analysis of molecular variance, and a Bayesian approach similarly partitioned estimates of genetic similarity according to the mtDNA phylogeographical pattern. These results are discussed in relation to biogeographical hypotheses, comparative rates of mtDNA molecular evolution, and in the identification of evolutionary significant units of Taiwanese T. stejnegeri. In spite of the high degree of congruence between the genetic datasets, the AFLP phylogenetic analysis did not support the mtDNA tree, suggesting that no contemporary barriers to gene flow exist between individuals from the two mtDNA lineages.

Genetic introgression as a potential to widen a species' niche: insights from alpine Carex curvula

Understanding what causes the decreasing abundance of species at the margins of their distributions along environmental gradients has drawn considerable interest, especially because of the recent need to predict shifts in species distribution patterns in response to climatic changes. Here, we address the ecological range limit problem by focusing on the sedge, Carex curvula, a dominant plant of high-elevation grasslands in Europe, for which two ecologically differentiated but crosscompatible taxa have been described in the Alps. Our study heuristically combines an extensive phytoecological survey of alpine plant communities to set the niche attributes of each taxon and a population genetic study to assess the multilocus genotypes of 177 individuals sampled in typical and marginal habitats. We found that ecological variation strongly correlates with genetic differentiation. Our data strongly suggest that ecologically marginal populations of each taxon are mainly composed of individuals with genotypes resulting from introgressive hybridization. Conversely, no hybrids were found in typical habitats, even though the two taxa were close enough to crossbreed. Thus, our results indicate that genotype integrity is maintained in optimal habitats, whereas introgressed individuals are favored in marginal habitats. We conclude that gene flow between closely related taxa might be an important, although underestimated, mechanism shaping species distribution along gradients.

Chloroplast DNA diversity of Hieracium Pilosella (Asteraceae) introduced to New Zealand: reticulation, hybridization, and invasion

The European hawkweed Hieracium pilosella is a successful invader and a troublesome weed in New Zealand. The systematics of the genus Hieracium is extremely complex and contentious, probably due to recent speciation, hybridization, polyploidy, and diverse reproductive strategies. In the first chloroplast DNA survey of the group, we sequenced 285 plants (including H. pilosella and 12 other species of subgenus Pilosella) from New Zealand and Europe for 900 bp of trnL-trnF. Eleven haplotypes were identified with much sharing among species. Three haplotypes (A, D, G) were found in seven, three, and four species, respectively, but two species (H. lactucella and H. auricula) had single, private haplotypes. Our cpDNA data for subgenus Pilosella are consistent with the group's having incomplete lineage sorting and/or recent reticulate evolution. Six haplotypes were identified in H. pilosella, four of these unique to this taxon in our sample. In New Zealand, haplotype A was common and occurred in plants of different ploidy (i.e., 4×, 5×, 6×), whereas haplotypes C, B, and M were restricted to 4×, 5×, and 6× plants, respectively. The distribution of haplotype variation suggests that some or all of the H. pilosella seeds accidentally introduced into New Zealand probably came from east Europe rather than the United Kingdom and that a minimum of four lineages were introduced. Within New Zealand, hybridization of H. pilosella with a related taxon (probably H. praealtum) has occurred at least three times, involving both obligate sexual tetraploids and facultative apomictic pentaploids of H. pilosella.

Comparative genetic study confirms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae)

The Wollemi pine, Wollemia nobilis (Araucariaceae), was discovered in 1994 as the only extant member of the genus, previously known only from the fossil record. With fewer than 100 trees known from an inaccessible canyon in southeastern Australia, it is one of the most endangered tree species in the world. We conducted a comparative population genetic survey at allozyme, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) loci in W. nobilis, Araucaria cunninghamii and Agathis robusta - representatives of the two sister genera. No polymorphism was detected at 13 allozyme loci, more than 800 AFLP loci or the 20 SSR loci screened in W. nobilis. In Ag. robusta only one of 12 allozyme loci, five of 800 AFLP loci and none of the 15 SSR loci were variable. For A. cunninghamii, 10 of > 800 AFLP loci and five of 20 SSR loci were variable. Thus low genetic diversity characterizes all three species. While not ruling out the existence of genetic variation, we conclude that genetic diversity is exceptionally low in the Wollemi pine. To our knowledge this is the most extreme case known in plants. We conclude that the combination of small population effects, clonality and below-average genetic variation in the family are probable contributing factors to the low diversity. The exceptionally low genetic diversity of the Wollemi pine, combined with its known susceptibility to exotic fungal pathogens, reinforces current management policies of strict control of access to the pines and secrecy of the pine locations.

Population genetic consequences of extreme variation in sexual and clonal reproduction in an aquatic plant

Most plants combine sexual reproduction with asexual clonal reproduction in varying degrees, yet the genetic consequences of reproductive variation remain poorly understood. The aquatic plant Butomus umbellatus exhibits striking reproductive variation related to ploidy. Diploids produce abundant viable seed whereas triploids are sexually sterile. Diploids also produce hundreds of tiny clonal bulbils, whereas triploids exhibit only limited clonal multiplication through rhizome fragmentation. We investigated whether this marked difference in reproductive strategy influences the diversity of genotypes within populations and their movement between populations by performing two large-scale population surveys (n = 58 populations) and assaying genotypic variation using random amplified polymorphic DNA (RAPDs). Contrary to expectations, sexually fertile populations did not exhibit higher genotypic diversity than sterile populations. For each cytotype, we detected one very common and widespread genotype. This would only occur with a very low probability (< 10-7) under regular sexual recombination. Compatibility analysis also indicated that the pattern of genotypic variation largely conformed to that expected with predominant clonal reproduction. The potential for recombination in diploids is not realized, possibly because seeds are outcompeted by bulbils for safe sites during establishment. We also failed to find evidence for more extensive movement of fertile than sterile genotypes. Aside from the few widespread genotypes, most were restricted to single populations. Genotypes in fertile populations were very strongly differentiated from those in sterile populations, suggesting that new triploids have not arisen during the colonization of North America. The colonization of North America involves two distinct forms of B. umbellatus that, despite striking reproductive differences, exhibit largely clonal population genetic structures.

Accurate gene diversity estimates from amplified fragment length polymorphism (AFLP) markers

Three procedures for the estimation of null allele frequencies and gene diversity from dominant multilocus data were empirically tested in natural populations of the outcrossing angiosperm Persoonia mollis (Proteaceae). The three procedures were the square root transform of the null homozygote frequency, the Lynch & Milligan procedure, and the Bayesian method. Genotypes for each of 116 polymorphic loci generated by amplified fragment length polymorphism (AFLP) were inferred from segregation patterns in progeny arrays. Therefore, for the plus phenotype (band present), heterozygotes were distinguished from homozygotes. In contrast to previous studies, all three procedures produced very similar mean estimates of heterozygosity, which were in turn accurate estimators of the direct value (HO = 0.28). A second population of P. mollis displayed markedly lower levels of heterozygosity (HO = 0.20) but approximately twice as many polymorphic loci (284). These AFLP results show that biases in estimates of average null allele frequency and heterozygosity are largely eliminated in highly polymorphic dominant marker data sets displaying a J-shaped beta distribution with a high percentage of loci containing more than three null homozygotes and relatively few loci with no null homozygotes. This distribution may be typical of outcrossing angiosperms.

Hybridization as a stimulus for the evolution of invasiveness in plants?

Invasive species are of great interest to evolutionary biologists and ecologists because they represent historical examples of dramatic evolutionary and ecological change. Likewise, they are increasingly important economically and environmentally as pests. Obtaining generalizations about the tiny fraction of immigrant taxa that become successful invaders has been frustrated by two enigmatic phenomena. Many of those species that become successful only do so (i) after an unusually long lag time after initial arrival, and/or (ii) after multiple introductions. We propose an evolutionary mechanism that may account for these observations. Hybridization between species or between disparate source populations may serve as a stimulus for the evolution of invasiveness. We present and review a remarkable number of cases in which hybridization preceded the emergence of successful invasive populations. Progeny with a history of hybridization may enjoy one or more potential genetic benefits relative to their progenitors. The observed lag times and multiple introductions that seem a prerequisite for certain species to evolve invasiveness may be a correlate of the time necessary for previously isolated populations to come into contact and for hybridization to occur. Our examples demonstrate that invasiveness can evolve. Our model does not represent the only evolutionary pathway to invasiveness, but is clearly an underappreciated mechanism worthy of more consideration in explaining the evolution of invasiveness in plants.

Microevolution, low clonal diversity and genetic affinities of parthenogenetic sitobion aphids in new zealand

In sharp contrast to their southeast Asian and European counterparts, Sitobion miscanthi and S. near fragariae aphids in Australia exhibit a complete absence of sexual reproduction. This demands an explanation within the context of the evolution and maintenance of sex and parthenogenesis. Accordingly, we executed a genetic analysis of the two species in neighbouring New Zealand. Microsatellites and single-stranded conformation polymorphism/sequence analysis of the nuclear gene elongation factor 1alpha were used to identify aphid clones and confirm species identification, respectively. Karyotypic variation was also investigated. The New Zealand fauna showed few (nonrecombining) genotypes and appears to have received migrants from both Australia and Asia. Other genotypes have apparently arisen in situ in New Zealand, exhibiting stepwise mutation of microsatellite alleles and also karyotypic change. Thus, these data represent rare evidence of evolution within wild-living parthenogenetic lineages. Karyotypic changes appear to occur at a rate even greater than that of microsatellite evolution. Strong geographical partitioning of genotypes/karyotypes was found, with certain ones predominating over large areas. These data suggest that clonal selection could be important in the distribution and patterning of genetic variation. We present a model to explain the genetic patterns, with particular reference to the absence of sexual reproduction in Sitobion aphids in New Zealand and Australia.