Underestimated diversity in high elevations of a global biodiversity hotspot: two new endemic species of Aethionema (Brassicaceae) from the alpine zone of Iran

Although the mountains in South-West Asia are a global biodiversity hotspot, our understanding of their biodiversity, especially in the commonly remote alpine and subnival zones, is still limited. This is well exemplified here by Aethionema umbellatum (Brassicaceae), a species considered to have a wide yet disjoint distribution in the Zagros and Yazd-Kerman mountains of western and central Iran. Morphological and molecular phylogenetic data (based on plastid trnL-trnF and nuclear ITS sequences) show that A. umbellatum is restricted to a single mountain range in southwestern Iran (Dena Mts., southern Zagros), whereas populations from central Iran (Yazd-Kerman and central Zagros) and from western Iran (central Zagros) belong to species new to science, A. alpinum and A. zagricum, respectively. Both new species are phylogenetically and morphologically close to A. umbellatum, with which they share unilocular fruits and one-seeded locules. However, they are easily distinguishable by leaf shape, petal size, and fruit characters. This study confirms that the alpine flora of the Irano-Anatolian region is still poorly known. As the proportion of rare and local endemic species in alpine habitats is high, these habitats are of prime interest for conservation efforts.

Pulvinatusia (Brassicaceae), a new cushion genus from China and its systematic position

The new genus and species Pulvinatusiaxuegulaensis (Brassicaceae) are described and illustrated. The species is a cushion plant collected from Xuegu La, Xizang, China. Its vegetative parts are most similar to those of Arenariabryophylla (Caryophyllaceae) co-occurring in the same region, while its leaves and fruits closely resemble those of Xerodrabapatagonica (Brassicaceae) from Patagonian Argentina and Chile. Family-level phylogenetic analyses based on both nuclear ITS and plastome revealed that it is a member of the tribe Crucihimalayeae, but the infra-/intergeneric relationships within the tribe are yet to be resolved.

Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species

Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make-up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo- and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.

Al-Shehbaz I, Yue J, Sun H. Sisymbriumlinifolium and Sisymbriopsisschugnana (Brassicaceae), two new records from Xinjiang, China

Sisymbriumlinifolium and Sisymbriopsisschugnana, previously confined to western North America and Tajikistan, respectively, were discovered in Xinjiang during a recent field trip to this autonomous region of China. The identity of these two species was subsequently confirmed by extensive morphological and molecular studies. The biogeographical significance of these new floristic records is briefly addressed.

New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data

As currently delimitated, the species-rich mustard tribe Euclidieae DC. (Brassicaceae) comprises 28 genera and 152 species distributed primarily in Asia. To date, no tribe-wide comprehensive phylogenetic analysis has been conducted. In this study, sequence data from the nuclear ribosomal internal transcribed spacer (nrITS) region of 82 species in all 28 genera of Euclidieae were used to test its monophyly and infer inter- and intra-generic relationships within. Phylogenetic analyses revealed that Rhammatophyllum and Sisymbriopsis are embedded within Solms-laubachia s.l., and Solms-laubachia lanuginosa (Eurycarpus lanuginosus) fell outside the tribe. Therefore, Solms-laubachia s.l. as currently recognized is not monophyletic and its generic delimitation needed further study. Besides, our results suggest that the genera Lepidostemon, Neotorularia, and Tetracme are polyphyletic.

Fruit fracture biomechanics and the release of Lepidium didymum pericarp-imposed mechanical dormancy by fungi

The biomechanical and ecophysiological properties of plant seed/fruit structures are fundamental to survival in distinct environments. Dispersal of fruits with hard pericarps (fruit coats) encasing seeds has evolved many times independently within taxa that have seed dispersal as their default strategy. The mechanisms by which the constraint of a hard pericarp determines germination timing in response to the environment are currently unknown. Here, we show that the hard pericarp of Lepidium didymum controls germination solely by a biomechanical mechanism. Mechanical dormancy is conferred by preventing full phase-II water uptake of the encased non-dormant seed. The lignified endocarp has biomechanically and morphologically distinct regions that serve as predetermined breaking zones. This pericarp-imposed mechanical dormancy is released by the activity of common fungi, which weaken these zones by degrading non-lignified pericarp cells. We propose that the hard pericarp with this biomechanical mechanism contributed to the global distribution of this species in distinct environments.

Cryptic gene pools in the Hypericum perforatum-H. maculatum complex: diploid persistence versus trapped polyploid melting

BACKGROUND AND AIMS

In Central Europe Hypericum perforatum and Hypericum maculatum show significant hybridization and introgression as a consequence of Pleistocene range fluctuations, and their gene pools are merging on higher ploidy levels. This paper discusses whether polyploid hybrid gene pools are trapped in the ecological climatic niche space of their diploid ancestors, and tests the idea of geographical parthenogenesis.

METHODS

DNA sequence information of nuclear ribosomal DNA and plastid loci, ploidy level estimates and ecological niche modelling are used to characterize the various diploid and polyploid gene pools and unravel spatio-temporal patterns of gene flow among them.

KEY RESULTS

On the diploid level, the three gene pools are clearly distinct between and within species of H. perforatum (two gene pools) and H. maculatum, and their divergence dates back to the first half of the Pleistocene. All polyploids in Central Europe show high levels of past and contemporary gene flow between all three gene pools. The correlation of genetic and geographical distances breaks down if the latter is larger than 250 km, indicating recent and ongoing gene flow. The two species are ecologically differentiated, but in particular hybrids among all three gene pools do not show significant niche differences compared to their parental gene pools, except for some combinations with H. maculatum.

CONCLUSIONS

Inter- and intraspecific gene flow between inter- and intra-species gene pools is limited on the diploid level, and the geographical distribution of the diploids largely reflects Pleistocene evolutionary history. Secondary contact promoted hybridization and introgression on the polyploid level, enabling offspring to escape the diploid gene pools. However, the hybrid polyploids do not show significant niche differences compared to their diploid progenitors. It is concluded that the observed absence of niche divergence has precluded further differentiation and geographical partitioning of new polyploid lineages being effectively separated from the parental lines. The predominantly apomictic reproducing polyploids are trapped in the polyploid gene pool and the ecological climatic niche space of their diploid ancestors.

Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues

Variation in life history contributes to reproductive success in different environments. Divergence of annual and perennial angiosperm species is an extreme example that has occurred frequently. Perennials survive for several years and restrict the duration of reproduction by cycling between vegetative growth and flowering, whereas annuals live for 1 year and flower once. We used the tribe Arabideae (Brassicaceae) to study the divergence of seasonal flowering behaviour among annual and perennial species. In perennial Brassicaceae, orthologues of FLOWERING LOCUS C (FLC), a floral inhibitor in Arabidopsis thaliana, are repressed by winter cold and reactivated in spring conferring seasonal flowering patterns, whereas in annuals, they are stably repressed by cold. We isolated FLC orthologues from three annual and two perennial Arabis species and found that the duplicated structure of the A. alpina locus is not required for perenniality. The expression patterns of the genes differed between annuals and perennials, as observed among Arabidopsis species, suggesting a broad relevance of these patterns within the Brassicaceae. Also analysis of plants derived from an interspecies cross of A. alpina and annual A. montbretiana demonstrated that cis-regulatory changes in FLC orthologues contribute to their different transcriptional patterns. Sequence comparisons of FLC orthologues from annuals and perennials in the tribes Arabideae and Camelineae identified two regulatory regions in the first intron whose sequence variation correlates with divergence of the annual and perennial expression patterns. Thus, we propose that related cis-acting changes in FLC orthologues occur independently in different tribes of the Brassicaceae during life history evolution.

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae (Brassicaceae) and description of a new tribe, Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae (Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trnL-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers (ITS, ETS) and four chloroplast markers (trnL-F, trnH-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.

Characterization of Zinc and Cadmium Hyperaccumulation in Three Noccaea (Brassicaceae) Populations from Non-metalliferous Sites in the Eastern Pyrenees

The Southern slope of the Pyrenees is the meridional limit for the distribution of several Noccaea populations. However, the systematic description of these populations and their hyperaccumulation mechanisms are not well established. Morphological and genetic analysis (ITS and 3 chloroplast regions) were used to identify Noccaea populations localized on non-metallicolous soils during a survey in the Catalonian Pyrenees. Cd and Zn concentrations were analyzed in soils and plants both sampled in the field and grown hydroponically. The expression of selected metal transporter genes was assessed by quantitative PCR. The populations were identified as Noccaea brachypetala (Jord.) F.K. Mey by conspicuous morphological traits. Principal component analysis provided a clear separation among N. brachypetala, Noccaea caerulescens J. Presl & C. Presl and Noccaea occitanica (Jord.) F.K. Mey., three Noccaea species reported in the Pyrenees. Contrastingly, ITS and cpDNA analyses were unable to clearly differentiate these taxa. Differences in the expression of the metal transporter genes HMA3, HMA4, and MTP1 between N. caerulescens and N. brachypetala, and those amongst the N. brachypetala populations suggest differences in the strategies for handling enhanced Cd and Zn availability. This is the first report demonstrating Cd and Zn hyperaccumulation by N. brachypetala both in the field and in hydroponics. This comprehensive study based on taxonomic, molecular, and physiological data allows both the correct identification of this species and the characterization of population differences in hyperaccumulation and tolerance of Zn and Cd.

Evidence for the introduction of the Asian red alga Neosiphonia japonica and its introgression with Neosiphonia harveyi (Ceramiales, Rhodophyta) in the Northwest Atlantic

There is currently conflict in the literature on the taxonomic status of the reportedly cosmopolitan species Neosiphonia harveyi, a common red alga along the coast of Atlantic Canada and New England, USA. Neosiphonia harveyi sensu lato was assessed using three molecular markers: COI-5P, ITS and rbcL. All three markers clearly delimited three genetic species groups within N. harveyi sensu lato in this region, which we identified as N. harveyi, N. japonica and Polysiphonia akkeshiensis (here resurrected from synonymy with N. japonica). Although Neosiphonia harveyi is considered by some authors to be introduced to the Atlantic from the western Pacific, it was only confirmed from the North Atlantic suggesting it is native to this area. In contrast, Neosiphonia japonica was collected from only two sites in Rhode Island, USA, as well as from its reported native range in Asia (South Korea), which when combined with data in GenBank indicates that this species was introduced to the Northwest Atlantic. The GenBank data further indicate that N. japonica was also introduced to North Carolina, Spain, Australia and New Zealand. Despite the fact that all three markers clearly delimited N. harveyi and N. japonica as distinct genetic species groups, the ITS sequences for some N. harveyi individuals displayed mixed patterns and additivity indicating introgression of nuclear DNA from N. japonica into N. harveyi in the Northwest Atlantic. Introgression of DNA from an introduced species to a native species (i.e. 'genetic pollution') is one of the possible consequences of species introductions, and we believe this is the first documented evidence for this phenomenon in red algae.

When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid

Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes.

The current status of the elemental defense hypothesis in relation to pathogens

Metal hyperaccumulating plants are able to accumulate exceptionally high concentrations of metals, such as zinc, nickel, or cadmium, in their aerial tissues. These metals reach concentrations that would be toxic to most other plant species. This trait has evolved multiple times independently in the plant kingdom. Recent studies have provided new insight into the ecological and evolutionary significance of this trait, by showing that some metal hyperaccumulating plants can use high concentrations of accumulated metals to defend themselves against attack by pathogenic microorganisms and herbivores. Here, we review the evidence that metal hyperaccumulation acts as a defensive trait in plants, with particular emphasis on plant-pathogen interactions. We discuss the mechanisms by which defense against pathogens might have driven the evolution of metal hyperaccumulation, including the interaction of this trait with other forms of defense. In particular, we consider how physiological adaptations and fitness costs associated with metal hyperaccumulation could have resulted in trade-offs between metal hyperaccumulation and other defenses. Drawing on current understanding of the population ecology of metal hyperaccumulator plants, we consider the conditions that might have been necessary for metal hyperaccumulation to be selected as a defensive trait, and discuss the likelihood that these were fulfilled. Based on these conditions, we propose a possible scenario for the evolution of metal hyperaccumulation, in which selective pressure for resistance to pathogens or herbivores, combined with gene flow from non-metallicolous populations, increases the likelihood that the metal hyperaccumulating trait becomes established in plant populations.

Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples

Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella.

Intertribal hybrid plants produced from crossing Arabidopsis thaliana with apomictic Boechera

Arabidopsis thaliana and Boechera belong to different tribes of the Brassicaceae and last shared a common ancestor 13-35 million years ago. A. thaliana reproduces sexually but some Boechera accessions reproduce by apomixis (asexual reproduction by seed). The two species are reproductively isolated, preventing introgression of the trait(s) controlling apomixis from Boechera into A. thaliana and their molecular characterisation. To identify if "escapers" from such hybridisation barriers exist, we crossed diploid or tetraploid A. thaliana mothers carrying a conditional male sterile mutation with a triploid Boechera apomict. These cross-pollinations generated zygotes and embryos. Most aborted or suffered multiple developmental defects at all stages of growth, but some seed matured and germinated. Seedlings grew slowly but eventually some developed into mature plants that were novel synthetic allopolyploid hybrids. With one exception, intertribal hybrids contained three Boechera plus either one or two A. thaliana genomes (depending on maternal ploidy) and were male and female sterile. The exception was a semi-fertile, sexual partial hybrid with one Boechera plus two A. thaliana genomes. The synthesis of "escapers" that survive rigorous early developmental challenges in crosses between A. thaliana and Boechera demonstrates that the inviability form of postzygotic reproductive isolation separating these distantly related species is not impenetrable. The recovery of a single semi-fertile partial hybrid also demonstrates that hybrid sterility, another form of postzygotic reproductive isolation, can be overcome between these species.

A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae)

74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.

Systematics and evolution of Arctic-Alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean

PREMISE OF THE STUDY

The high mountains in southern Anatolia and the eastern Mediterranean are assumed to play a major role as a primary center of genetic diversity and species richness in Eurasia. We tested this hypothesis by focusing on the widespread perennial arctic-alpine Arabis alpina and its sympatrically distributed closest relatives in the eastern Mediterranean.

METHODS

Plastid (trnL intron, trnL-F intergenic spacer) and nuclear (ITS) DNA sequence analysis was used for phylogenetic reconstruction. Broad-scale plastid haplotype analyses were conducted to infer ancestral biogeographic patterns.

KEY RESULTS

Five Arabis species, identified from the eastern Mediterranean (Turkey mainland and Cyprus), evolved directly and independently from A. alpina, leaving Arabis alpina as a paraphyletic taxon. These species are not affected by hybridization or introgression, and species divergence took place at the diploid level during the Pleistocene.

CONCLUSIONS

Pleistocene climate fluctuations produced local altitudinal range-shifts among mountain glacial survival areas, resulting not only in the accumulation of intraspecific genotype diversity but also in the formation of five local species. We also show that the closest sister group of Arabis alpina consists exclusively of annuals/winter annuals and diverged prior to Pleistocene climatic fluctuations during the colonization of the lowland Mediterranean landscape. These findings highlight that Anatolia is not only a center of species richness but also a center for life-history diversification.

Reticulate evolutionary history of a complex group of grasses: phylogeny of Elymus StStHH allotetraploids based on three nuclear genes

BACKGROUND

Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting.

METHODOLOGY/PRINCIPAL FINDINGS

We sequenced portions of three unlinked nuclear genes-phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I-from 27 individuals, representing 14 Eurasian and North American StStHHElymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus.

CONCLUSIONS/SIGNIFICANCE

Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees-identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.

Colonizing the American continent: Systematics of the genus Arabis in North America (Brassicaceae)

The circumscription of the genus Arabis underwent many and drastic changes within the past. Using DNA sequence information from the nuclear ribosomal RNA and parts of the plastid genome (trnL-trnLF), as well as a critical evaluation of herbarium material from East Asia and North America, we circumscribe the various Arabis taxa of North America. The American and East Asian Arabis species are closely related and, contrary to what was previously believed, they are not closely related to the Eurasian A. hirsuta. Using cpDNA, we found five North American lineages of Arabis with distinct distribution patterns, of which only the purple/red-flowered lineage consists of proven diploids that evolved directly from East Asian progenitors. All other four lineages evolved via ancient hybridization either on the Asian continent prior to migration to North America or showed significant evidence for hybridization and reticulation while diversifying on the American continent. We also provide the first evidence for the systematic circumscription of East Asian Arabis taxa, which together with the North American taxa, form one clade distantly related to European A. ciliata and Eurasian A. hirsuta. The findings also represent the first record of A. pycnocarpa for the floras of China, Japan, and Russian Far East.

A bicontinental origin of polyploid Australian/New Zealand Lepidium species (Brassicaceae)? Evidence from genomic in situ hybridization

BACKGROUND AND AIMS

Incongruence between chloroplast and nuclear DNA phylogenies, and single additive nucleotide positions in internal transcribed spacer (ITS) sequences of polyploid Australian/New Zealand (NZ) Lepidium species have been used to suggest a bicontinental hybrid origin. This pattern was explained by two trans-oceanic dispersals of Lepidium species from California and Africa and subsequent hybridization followed by homogenization of the ribosomal DNA sequence either to the Californian (C-clade) or to the African ITS-type (A-clade) in two different ITS-lineages of Australian/NZ Lepidium polyploids.

METHODS

Genomic in situ hybridization (GISH) was used to unravel the genomic origin of polyploid Australian/NZ Lepidium species. Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) probes was applied to test the purported ITS evolution, and to facilitate chromosome counting in high-numbered polyploids.

KEY RESULTS

In Australian/NZ A-clade Lepidium polyploids, GISH identified African and Australian/NZ C-clade species as putative ancestral genomes. Neither the African nor the Californian genome were detected in Australian/NZ C-clade species and the Californian genome was not detected in Australian/NZ A-clade species. Five of the eight polyploid species (from 7x to 11x) displayed a diploid-like set of rDNA loci. Even the undecaploid species Lepidium muelleriferdinandi (2n = 11x = 88) showed only one pair of each rDNA repeat. In A-clade allopolyploids, in situ rDNA localization combined with GISH corroborated the presence of the African ITS-type.

CONCLUSIONS

The nuclear genomes of African and Australian/NZ C-clade species were detected by GISH in allopolyploid Australian/NZ Lepidium species of the A-clade, supporting their hybrid origin. The presumed hybrid origin of Australian/NZ C-clade taxa could not be confirmed. Hence, it is assumed that Californian ancestral taxa experienced rapid radiation in Australia/NZ into extant C-clade polyploid taxa followed by hybridization with African species. As a result, A-clade allopolyploid Lepidium species share the Californian chloroplast type and the African ITS-type with the C-clade Australian/NZ polyploid and African diploid species, respectively.

Toward a Global Phylogeny of the Brassicaceae

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.

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.

Molecular evidence for the hybrid origin of species in the soft coral genus Alcyonium (Cnidaria: Anthozoa: Octocorallia)

Several recent studies have suggested that hybridization may play a previously unrecognized and important role in the evolution of corals. Our observations of polymorphic and recombinant sequences in the multicopy ribosomal internal transcribed spacer (ITS) region suggested the possible hybrid origin of two European soft coral species, Alcyonium hibernicum and Bellonella bocagei. To examine this possibility further we cloned and sequenced ITS-1 from multiple individuals and populations of these two species as well as two sympatric congeners, A. coralloides and A. sp. M2. Phylogenetic analyses separated the observed sequence variants into two distinct clades. All A. coralloides sequences belonged to clade A, while A. sp. M2 had only clade B sequences. A majority of A. hibernicum individuals, however, contained both clade A and B sequences that were identical to the predominant sequence variants found in A. coralloides and A. sp. M2, respectively. This pattern of additivity suggests that A. hibernicum originated from a hybrid cross between A. coralloides and A. sp. M2, a hypothesis that is supported by its unusual mode of reproduction (meiotic parthenogenesis). The predominant sequence variant found in B. bocagei was a unique, derived clade B sequence; in addition, however, most individuals of this species also had copies of a sequence identified as a recombinant between clade A and clade B sequence types. The presence of this recombinant sequence in the B. bocagei genome suggests that this species may also be the product of past hybridization events within the clade. Reticulate evolution may explain the failure of several previous studies to resolve the phylogeny of these four species.

Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation

The orchid genus Calopogon R.Br. (Orchidaceae), native to eastern North America and the northern Caribbean, currently contains five species and up to three varieties. Using nuclear internal transcribed spacer (ITS) ribosomal DNA sequences, amplified fragment length polymorphisms (AFLPs), chloroplast DNA restriction fragments, and chromosome counts, we present a phylogenetic and taxonomic study of the genus. Calopogon multiflorus and C. pallidus are consistently sister species, but the relationships of C. barbatus, C. oklahomensis, and C. tuberosus are not as clear. In the ITS analysis C. oklahomensis is sister to C. barbatus, whereas it is sister to C. tuberosus in the plastid restriction fragment analysis. Furthermore, all species were found to have chromosome numbers of 2n = 38 and 40, with the exception of the putatively hybrid-derived C. oklahomensis with 2n = 114 and 120. The hexaploidy of the latter, plus the discrepancy in its position between the ITS and plastid restriction fragment trees, could suggest that it is of hybrid origin. However, the presence of unique morphological and molecular characters might indicate that it is either an ancient hybrid or not of hybrid derivation at all. Finally, using these molecular methods all taxa appear to generally be discrete groups, with the exception of C. tuberosus vars. latifolius and tuberosus, the former of which is best combined with the latter.

Comparative biogeography of the cytotypes of annual Microthlaspi perfoliatum (Brassicaceae) in Europe using isozymes and cpDNA data: refugia, diversity centers, and postglacial colonization

In the last few years, the biogeography of many European plant species has been analyzed using molecular markers, and some consistent patterns of Pleistocenic differentiation and range fluctuations have been established. These studies mostly focused on perennial herbs or woody species, rarely considering annual taxa. This study focused on the annual Microthlaspi perfoliatum, which is distributed all over Europe and comprises three cytotypes. Morphologically, these cytotypes are hard to distinguish, although, based on molecular markers, they should be treated as two different species. Diploid and polyploid cytotypes had a different biogeographical history, with distinct glacial refugia. For the polyploids, a well-known distribution pattern of relict areas was confirmed, with Iberia, Italy, and the Balkans serving as primary Pleistocene refugia. Secondary refuge areas have been detected in southeastern France and neighboring Switzerland, with closer affinity to the Iberian refugium than to any other region based on allozyme and cpDNA haplotype data. For the diploids, two refugia have been characterized, one of which is congruent to the secondary refugium of the polyploids in France and Switzerland. The second refuge of diploid populations is located in unglaciated lowland areas of East Austria and Croatia. Isozyme and cpDNA haplotype data favor a postglacial colonization of diploid populations into Germany from Austrian lowland areas along the Danube River as well as from Switzerland. This scenario is also true for polyploids in Germany, Belgium, and Sweden.

Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae)

Two intergenic spacers, trnT-trnL and trnL-trnF, and the trnL intron of cpDNA were sequenced to study phylogenetic relationships and biogeography of 73 Lepidium taxa. Insertions/deletions of ≥3 bp (base pairs) provided reliable phylogenetic information whereas indels ≤2 bp, probably originating from slipped-strand mispairing, are prone to parallelism in the context of our phylogenetic framework. For the first time, an hypothesis of the genus Lepidium is proposed based on molecular phylogeny, in contrast to previous classification schemes into sections and greges (the latter category represents groups of related species within a given geographic region), which are based mainly on fruit characters. Only a few of the taxa as delimited in the traditional systems represent monophyletic lineages. The proposed phylogeny would suggest three main lineages, corresponding to (1) sections Lepia and Cardaria, (2) grex Monoplocoidea from Australia, and (3) remaining taxa, representing the bulk of Lepidium species with more or less resolved sublineages that sometimes represent geographical correspondence. The fossil data, easily dispersible mucilaginous seeds, widespread autogamous breeding systems, and low levels of sequence divergence between species from different continents or islands suggest a rapid radiation of Lepidium by long-distance dispersal in the Pliocene/Pleistocene. As a consequence of climatic changes in this geological epoch, arid/semiarid areas were established, providing favorable conditions for the radiation of Lepidium by which the genus attained its worldwide distribution.

Evolutionary Changes in Floral Structure within Lepidium L. (Brassicaceae)

The basic floral ground plan is remarkably constant across Brassicaceae. However, within Lepidium (ca. 175 species), deviations from this ground plan are common, with over half of Lepidium species having only two stamens rather than the usual six and a further eighth of the species having only four stamens. Furthermore, petals are reduced in size in a majority of Lepidium species. In order to determine the frequency and direction of changes in floral structure within Lepidium, we have inferred the phylogeny within the genus from sequences of the internal transcribed spacers of the nuclear ribosomal DNA. On the basis of this inferred phylogeny, we conclude that floral structure within Lepidium is relatively fluid. In order to account for the phylogenetic distributions of the different floral ground plans, at least two independent reductions to the two-stamen condition and at least one reversal to flowers with increased organ numbers are likely to have occurred. To account for the frequency of morphological evolution observed within the genus, we propose that some clades within Lepidium may be predisposed to changes in floral structure. In addition, several transoceanic dispersals are needed to explain the geographic distributions of the clades inferred from the phylogeny.

Molecular biogeography and evolution of the Microthlaspi perfoliatum s.l. polyploid complex (Brassicaceae): chloroplast DNA and nuclear ribosomal DNA restriction site variation

The genusThlaspi L. s.l. comprises numerous segregate lineages, which have been recognized as single genera. One of these, Microthlaspi, represents one such segregate. It consists of morphologically similar annual species. The species have different ploidy levels (2x, 4x, 6x) and are usually summarized under the designation Thlaspi perfoliatum agg. The assumed ancestral diploid members of the species complex, Microthlaspi granatense (Boiss. & Reut.) F.K. Meyer, Microthlaspi umbellatum (Steven ex DC.) F.K. Meyer, and Microthlaspi natolicum (Boiss.) F.K. Meyer, are restricted to northwestern Africa, southeastern Spain and Turkey, northern Iran, and Lebanon. Microthlaspi perfoliatum (L.) F.K. Meyer is widely distributed all over Europe and shows three ploidy levels. Diploid M. perfoliatum is restricted to Middle Europe, whereas tetraploid and hexaploid M. perfoliatum are distributed all over Europe. Individual plants from 125 natural populations throughout the geographic range were analysed using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) restriction site analysis. Within Microthlaspi, 31 cpDNA restriction site mutations, six nrDNA restriction site variations, and two length mutations in the IGS region of the nrDNA were found, and a molecular phylogeny of the species complex has been derived. Polymorphisms in molecular data partitioned cytotypes of M. perfoliatum. The geographical distribution patterns apparently reflect ancient speciation processes and postglacial vegetation history.Key words: chloroplast DNA, nuclear ribosomal DNA, Microthlaspi perfoliatum polyploid complex, molecular phylogeny, biogeography.