Institute of Botany of the Slovak Academy of Sciences

Abstract. Much confusion exists in the English‐language literature on plant invasions concerning the terms ‘naturalized’ and ‘invasive’ and their associated concepts. Several authors have used these terms in proposing schemes for conceptualizing the sequence of events from introduction to invasion, but often imprecisely, erroneously or in contradictory ways. This greatly complicates the formulation of robust generalizations in invasion ecology. Based on an extensive and critical survey of the literature we defined a minimum set of key terms related to a graphic scheme which conceptualizes the naturalization/invasion process. Introduction means that the plant (or its propagule) has been transported by humans across a major geographical barrier. Naturalization starts when abiotic and biotic barriers to survival are surmounted and when various barriers to regular reproduction are overcome. Invasion further requires that introduced plants produce reproductive offspring in areas distant from sites of introduction (approximate scales: > 100 m over < 50 years for taxa spreading by seeds and other propagules; > 6 m/3 years for taxa spreading by roots, rhizomes, stolons or creeping stems). Taxa that can cope with the abiotic environment and biota in the general area may invade disturbed, seminatural communities. Invasion of successionally mature, undisturbed communities usually requires that the alien taxon overcomes a different category of barriers. We propose that the term ‘invasive’ should be used without any inference to environmental or economic impact. Terms like ‘pests’ and ‘weeds’ are suitable labels for the 50–80% of invaders that have harmful effects. About 10% of invasive plants that change the character, condition, form, or nature of ecosystems over substantial areas may be termed ‘transformers’.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Abstract Aims Vegetation classification consistent with the Braun‐Blanquet approach is widely used in Europe for applied vegetation science, conservation planning and land management. During the long history of syntaxonomy, many concepts and names of vegetation units have been proposed, but there has been no single classification system integrating these units. Here we (1) present a comprehensive, hierarchical, syntaxonomic system of alliances, orders and classes of Braun‐Blanquet syntaxonomy for vascular plant, bryophyte and lichen, and algal communities of Europe; (2) briefly characterize in ecological and geographic terms accepted syntaxonomic concepts; (3) link available synonyms to these accepted concepts; and (4) provide a list of diagnostic species for all classes. Location European mainland, Greenland, Arctic archipelagos (including Iceland, Svalbard, Novaya Zemlya), Canary Islands, Madeira, Azores, Caucasus, Cyprus. Methods We evaluated approximately 10 000 bibliographic sources to create a comprehensive list of previously proposed syntaxonomic units. These units were evaluated by experts for their floristic and ecological distinctness, clarity of geographic distribution and compliance with the nomenclature code. Accepted units were compiled into three systems of classes, orders and alliances (EuroVegChecklist, EVC ) for communities dominated by vascular plants ( EVC 1), bryophytes and lichens ( EVC 2) and algae ( EVC 3). Results EVC 1 includes 109 classes, 300 orders and 1108 alliances; EVC 2 includes 27 classes, 53 orders and 137 alliances, and EVC 3 includes 13 classes, 24 orders and 53 alliances. In total 13 448 taxa were assigned as indicator species to classes of EVC 1, 2087 to classes of EVC 2 and 368 to classes of EVC 3. Accepted syntaxonomic concepts are summarized in a series of appendices, and detailed information on each is accessible through the software tool EuroVegBrowser. Conclusions This paper features the first comprehensive and critical account of European syntaxa and synthesizes more than 100 yr of classification effort by European phytosociologists. It aims to document and stabilize the concepts and nomenclature of syntaxa for practical uses, such as calibration of habitat classification used by the European Union, standardization of terminology for environmental assessment, management and conservation of nature areas, landscape planning and education. The presented classification systems provide a baseline for future development and revision of European syntaxonomy.

Abstract The results of recent researches in electro-physiology have familiarised us with the view that any physiological process accompanied by chemical changes involves an associated electrical change. Haacke and Klein have shown that electrical currents in plants are essentially a manifestation of vital phenomena, and that differences in electric potential are connected both with respiration and carbon assimilation. Waller's investigations have also shown that the excitation of living vegetable protoplasm gives electrical response no less than that of animal protoplasm. He has demonstrated that leaves in a condition of active metabolism give an instant electrical response to the influence of sunlight, which was modified under conditions affecting protoplasmic activity. Apparently almost immediately upon the perception of the stimulus of light, electrical energy begins to be absorbed in the process of photosynthesis. Waller approaches very suggestively the existence of two opposing forces in the presence of analytic and synthetic processes, and recognises that the function of assimilation and respiration might be mutually antagonistic as regards visible electric effects. His conception that "the product of dissociation …. gives current from the focus of dissociation, whereas a product of association, during its formation, gives rise to a current in the opposite direction," is of great interest. The line of enquiry now followed lies in the direction only of dissociation, and is a study of electrical effects accompanying fermentation or putrefaction under the influence of micro-organisms such as Saccharomyces or bacteria. The special physiological character of fungi or bacteria demands the disintegration of organic compounds as a necessary source of energy, and where there has been absorption of energy in a synthetic process one must look for its liberation when the change is of an analytic nature. The evolution of caloric energy during fermentation or putrefaction is commonly recognised, and that electrical energy is also liberated during these processes is a conception of considerable interest. In this preliminary communication some experiments are described which were undertaken to determine whether any E. M. F. is developed when organic compounds are broken down through the fermentative activity of yeast and other organisms. Cultures of Saccharomyces cerevisiæ and certain species of bacteria were grown in nutrient media, and the chemical action of their vital processes was utilised to develop electrical energy in a manner parallel to the production of E. M. F. by means of the ordinary galvanic cell.

Summary Pathways describe the processes that result in the introduction of alien species from one location to another. A framework is proposed to facilitate the comparative analysis of invasion pathways by a wide range of taxa in both terrestrial and aquatic ecosystems. Comparisons with a range of data helped identify existing gaps in current knowledge of pathways and highlight the limitations of existing legislation to manage introductions of alien species. The scheme aims for universality but uses the European Union as a case study for the regulatory perspectives. Alien species may arrive and enter a new region through three broad mechanisms: importation of a commodity, arrival of a transport vector, and/or natural spread from a neighbouring region where the species is itself alien. These three mechanisms result in six principal pathways: release, escape, contaminant, stowaway, corridor and unaided. Alien species transported as commodities may be introduced as a deliberate release or as an escape from captivity. Many species are not intentionally transported but arrive as a contaminant of a commodity, for example pathogens and pests. Stowaways are directly associated with human transport but arrive independently of a specific commodity, for example organisms transported in ballast water, cargo and airfreight. The corridor pathway highlights the role transport infrastructures play in the introduction of alien species. The unaided pathway describes situations where natural spread results in alien species arriving into a new region from a donor region where it is also alien. Vertebrate pathways tend to be characterized as deliberate releases, invertebrates as contaminants and plants as escapes. Pathogenic micro‐organisms and fungi are generally introduced as contaminants of their hosts. The corridor and unaided pathways are often ignored in pathway assessments but warrant further detailed consideration. Synthesis and applications. Intentional releases and escapes should be straightforward to monitor and regulate but, in practice, developing legislation has proved difficult. New introductions continue to occur through contaminant, stowaway, corridor and unaided pathways. These pathways represent special challenges for management and legislation. The present framework should enable these trends to be monitored more clearly and hopefully lead to the development of appropriate regulations or codes of practice to stem the number of future introductions.

Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co-occur randomly but are restricted in their co-occurrence by interspecific competition. This concept can be redefined in a more general framework where the co-occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta-analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co-occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta-analyses suggest that non-random co-occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general conclusions about the non-random aspect of assembly in plant communities.

BACKGROUND: Biological invasions are a major ecological and socio-economic problem in many parts of the world. Despite an explosion of research in recent decades, much remains to be understood about why some species become invasive whereas others do not. Recently, polyploidy (whole genome duplication) has been proposed as an important determinant of invasiveness in plants. Genome duplication has played a major role in plant evolution and can drastically alter a plant's genetic make-up, morphology, physiology and ecology within only one or a few generations. This may allow some polyploids to succeed in strongly fluctuating environments and/or effectively colonize new habitats and, thus, increase their potential to be invasive. SCOPE: We synthesize current knowledge on the importance of polyploidy for the invasion (i.e. spread) of introduced plants. We first aim to elucidate general mechanisms that are involved in the success of polyploid plants and translate this to that of plant invaders. Secondly, we provide an overview of ploidal levels in selected invasive alien plants and explain how ploidy might have contributed to their success. CONCLUSIONS: Polyploidy can be an important factor in species invasion success through a combination of (1) 'pre-adaptation', whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the 'evolution of invasiveness'. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.

The global biogeography of microorganisms remains largely unknown, in contrast to the well-studied diversity patterns of macroorganisms. We used arbuscular mycorrhizal (AM) fungus DNA from 1014 plant-root samples collected worldwide to determine the global distribution of these plant symbionts. We found that AM fungal communities reflected local environmental conditions and the spatial distance between sites. However, despite AM fungi apparently possessing limited dispersal ability, we found 93% of taxa on multiple continents and 34% on all six continents surveyed. This contrasts with the high spatial turnover of other fungal taxa and with the endemism displayed by plants at the global scale. We suggest that the biogeography of AM fungi is driven by unexpectedly efficient dispersal, probably via both abiotic and biotic vectors, including humans.

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.

Forests exchange large amounts of CO 2 with the atmosphere and can influence and be influenced by atmospheric CO 2 . There has been a recent proliferation of literature on the effects of atmospheric CO 2 on forest trees. More than 300 studies of trees on five different continents have been published in the last five years. These include an increasing number of field studies with a long‐term focus and involving CO 2 ×stress or environment interactions. The recent data on long‐term effects of elevated atmospheric CO 2 on trees indicate a potential for a persistent enhancement of tree growth for several years, although the only relevant long‐term datasets currently available are for juvenile trees. The current literature indicates a significantly larger average long‐term biomass increment under elevated CO 2 for conifers (130%) than for deciduous trees (49%) in studies not involving stress components. However, stimulation of photosynthesis by elevated CO 2 in long‐term studies was similar for conifers (62%) and deciduous trees (53%). Recent studies indicate that elevated CO 2 causes a more persistent stimulation of biomass increment and photosynthesis than previously expected. Results of seedling studies, however, might not be applicable to other stages of tree development because of complications of age‐dependent and size‐dependent shifts in physiology and carbon allocation, which are accelerated by elevated CO 2 . In addition, there are many possible avenues to down‐regulation, making the predicted canopy CO 2 exchange and growth of mature trees and forests in a CO 2 ‐rich atmosphere uncertain. Although, physiological down‐regulation of photosynthetic rates has been documented in field situations, it is rarely large enough to offset entirely photosynthetic gains in elevated CO 2 . A persistent growth stimulation of individual mature trees has been demonstrated although this effect is more uncertain in trees in natural stands. Resource interactions can both constrain tree responses to elevated CO 2 and be altered by them. Although drought can reduce gas‐exchange rates and offset the benefits of elevated CO 2 , even in well watered trees, stomatal conductance is remarkably less responsive to elevated CO 2 than in herbaceous species. Stomata of a number of tree species have been demonstrated to be unresponsive to elevated CO 2 . We conclude that positive effects of CO 2 on leaf area can be at least as important in determining canopy transpiration as negative, direct effects of CO 2 on stomatal aperture. With respect to nutrition, elevated CO 2 has the potential to alter tree–soil interactions that might influence future changes in ecosystem productivity. There is continued evidence that in most cases nutrient limitations diminish growth and photosynthetic responses to elevated CO 2 at least to some degree, and that elevated CO 2 can accelerate the appearance of nutrient limitations with increasing time of treatment. In many studies, tree biomass responses to CO 2 are artefacts in the sense that they are merely responses to CO 2 ‐induced changes in internal nutritional status of the tree. There are numerous interactions between CO 2 and factors of the biotic and abiotic environment. The importance of increasing atmospheric CO 2 concentrations for productivity is likely to be overestimated if these are not taken into account. Many interactions, however, are simply additive rather than synergistic or antagonistic. This appears to hold true for many parameters under elevated CO 2 in combination with temperature, elevated O 3 , and other atmospheric pollutants. However, there is currently little evidence that elevated CO 2 will counteract O 3 damage. When the foliage content of C, mineral nutrients and secondary metabolites is altered by elevated CO 2 , tree×insect interactions are modified. In most trees, mycorrhizal interactions might be less important for direct effects of CO 2 than for alleviating general nutrient deficiencies. Since many responses to elevated CO 2 and their interactions with stress show considerable variability among species/genotypes, one principal research need is for comparative studies of a large variety of woody species and ecosystems under realistic conditions. We still need more long‐term experiments on mature trees and stands to address critical scaling issues likely to advance our understanding of responses to elevated CO 2 at different stages of forest development and their interactions with climate and environment. The only tools available at present for coping with the consequences of rising CO 2 are management of resources and selection of genotypes suitable for the future climate and environment. CONTENTS Summary 396 I. Introduction 396 II. Influence of experimental approach 398 III. Growth and development 403 IV. Impact of water relations 405 V. Photosynthesis and respiration 410 VI. Foliar chemical composition 415 VII. Interaction with mineral nutrition 417 VIII. Interactions with temperature 419 IX. Interactions with air pollution, u.v.‐B and salt 420 X. Biotic interactions 422 XI. The Ecosystem 423 XII. Future research needs and unresolved questions 429 Acknowledgements 429 References 430

This article introduces a Special Issue on biodiversity of Palaearctic grasslands and provides a synthesis of the current knowledge on this topic. Four major categories of grasslands can be distinguished in the Palaearctic biogeographic realm: (a) zonal steppes (in areas too dry for forests), (b) arctic-alpine grasslands (in areas too cold for forests), (c) azonal and extrazonal grasslands (where hydrology, soil conditions, relief or natural disturbances within the forest biomes prevent tree growth locally) and (d) secondary grasslands (which replace natural forests in consequence of human land use). We summarize the present knowledge about species richness patterns (mainly of vascular plants) along abiotic and land use gradients. Further, we highlight the usefulness of diversity measures not based on species richness, namely functional diversity, phylogenetic diversity and within-species diversity. The strong differences observed for diversity patterns according to analyzed biodiversity parameter, spatial scale or taxonomic group call for comparative studies and caution when generalizing results. A particular challenge are the extreme plot-scale species richness values found in grasslands of a few European regions. We propose a conceptual model that explains the findings by an interplay of various factors acting at different levels: (i) The largest species pool is expected for habitats under conditions that prevailed over the last few million years, with a slight shift towards intermediate positions, i.e. for the Palaearctic in open, semi-dry, base-rich situations. (ii) The landscape-level species pool is increased by continuity of a grassland patch in space and time and heterogeneity of the surrounding landscape. (iii) The coexistence of regionally available species at a plot scale is due to reduced competitive exclusion according to Intermediate Disturbance Hypothesis, mowing once a year without fertilization being particularly effective. Ecosystem functions and services of Palaearctic grasslands are often positively connected to their biodiversity. At the same time, these communities and their biota are nowadays highly endangered. The semi-natural (High Nature Value) grasslands of Europe are mainly threatened by agricultural intensification or abandonment on low-productive sites in remote areas, while the natural steppes of the Palaearctic have largely been destroyed by conversion into arable land. Finally, we present some promising conservation and management approaches and call for a strong and comprehensive Convention on Grassland Conservation.

A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1, ycf1a and ycf1b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions, and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1b, which was slightly better than the combination of matK and rbcL. For the well-sampled representative plant groups, ycf1b generally performed better than any of the matK, rbcL and trnH-psbA. We concluded that ycf1a or ycf1b is the most variable plastid genome region and can serve as a core barcode of land plants.

Plants would be more vulnerable to water stress and thereafter rewatering or a cycled water environmental change, which occur more frequently under climatic change conditions in terms of the prediction scenarios. Effects of water stress on plants alone have been well-documented in many reports. However, the combined responses to drought and rewatering and its mechanism are relatively scant. As we known, plant growth, photosynthesis and stomatal aperture may be limited under water deficit, which would be regulated by physical and chemical signals. Under severe drought, while peroxidation may be provoked, the relevant antioxidant metabolism would be involved to annihilate the damage of reactive oxygen species. As rewatering, the recoveries of plant growth and photosynthesis would appear immediately through growing new plant parts, re-opening the stomata, and decreasing peroxidation; the recovery extents (reversely: pre-drought limitation) due to rewatering strongly depend on pre-drought intensity, duration and species. Understanding how plants response to episodic drought and watering pulse and the underlying mechanism is remarkably helpful to implement vegetation management practices in climatic changing.

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.

Spatial patterns of biodiversity are inextricably linked to their collection methods, yet no synthesis of bias patterns or their consequences exists. As such, views of organismal distribution and the ecosystems they make up may be incorrect, undermining countless ecological and evolutionary studies. Using 742 million records of 374 900 species, we explore the global patterns and impacts of biases related to taxonomy, accessibility, ecotype and data type across terrestrial and marine systems. Pervasive sampling and observation biases exist across animals, with only 6.74% of the globe sampled, and disproportionately poor tropical sampling. High elevations and deep seas are particularly unknown. Over 50% of records in most groups account for under 2% of species and citizen‐science only exacerbates biases. Additional data will be needed to overcome many of these biases, but we must increasingly value data publication to bridge this gap and better represent species' distributions from more distant and inaccessible areas, and provide the necessary basis for conservation and management.

To fully understand the contemporary genetic structure of plants, both nuclear and plastid markers are needed. Three chloroplast DNA (cpDNA) lineages, which probably diverged before the major Pleistocene glaciations, have been identified in the circumpolar/circumboreal Vaccinium uliginosum. Here we investigate its nuclear DNA variation using nuclear ribosomal internal transcribed spacer (ITS) sequences, DNA ploidy level measurements and amplified fragment length polymorphisms (AFLPs). We also extend the cpDNA dataset. Two ITS lineages, corresponding to diploids and tetraploids, respectively, were identified. However, both main sequence types apparently occurred in most individual plants but showed ploidy-biased homogenization and possibly reflect paralogy predating the origin of V. uliginosum. The ploidy levels were largely consistent with the cpDNA lineages, suggesting that the initial cpDNA divergence followed early polyploidizations. Five main AFLP groups were identified, consistent with recent glacial refugia in Beringia, western Siberia, the southern European mountains and areas south/east of the Scandinavian and Laurentide ice sheets. Except from the southern European mountains, there has been extensive expansion from all refugia, resulting in several contact zones. Surprisingly, the presumably older ploidy and cpDNA patterns were partly inconsistent with the main AFLP groups and more consistent with AFLP subgroups. A likely major driver causing the inconsistencies is recent nuclear gene flow via unreduced pollen from diploids to tetraploids. This may prevent cytoplasmic introgression and result in overlayed patterns formed by processes dominating at different time scales. The data also suggest more recent polyploidizations, as well as several chloroplast capture events, further complicating this scenario. This study highlights the importance of combining different marker systems to unravel intraspecific histories.

Gene duplication plays important roles in organismal evolution, because duplicate genes provide raw materials for the evolution of mechanisms controlling physiological and/or morphological novelties. Gene duplication can occur via several mechanisms, including segmental duplication, tandem duplication and retroposition. Although segmental and tandem duplications have been found to be important for the expansion of a number of multigene families, the contribution of retroposition is not clear. Here we show that plant SKP1 genes have evolved by multiple duplication events from a single ancestral copy in the most recent common ancestor (MRCA) of eudicots and monocots, resulting in 19 ASK (Arabidopsis SKP1-like) and 28 OSK (Oryza SKP1-like) genes. The estimated birth rates are more than ten times the average rate of gene duplication, and are even higher than that of other rapidly duplicating plant genes, such as type I MADS box genes, R genes, and genes encoding receptor-like kinases. Further analyses suggest that a relatively large proportion of the duplication events may be explained by tandem duplication, but few, if any, are likely to be due to segmental duplication. In addition, by mapping the gain/loss of a specific intron on gene phylogenies, and by searching for the features that characterize retrogenes/retrosequences, we show that retroposition is an important mechanism for expansion of the plant SKP1 gene family. Specifically, we propose that two and three ancient retroposition events occurred in lineages leading to Arabidopsis and rice, respectively, followed by repeated tandem duplications and chromosome rearrangements. Our study represents a thorough investigation showing that retroposition can play an important role in the evolution of a plant gene family whose members do not encode mobile elements.

This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range. The new family, Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique morphology. The family is sister to Biatriosporaceae and Roussoellaceae. The new genera are Allophaeosphaeria (Phaeosphaeriaceae), Amphibambusa (Amphisphaeriaceae), Brunneomycosphaerella (Capnodiales genera incertae cedis), Chaetocapnodium (Capnodiaceae), Flammeascoma (Anteagloniaceae), Multiseptospora (Pleosporales genera incertae cedis), Neogaeumannomyces (Magnaporthaceae), Palmiascoma (Bambusicolaceae), Paralecia (Squamarinaceae) and Sarimanas (Melanommataceae). The newly described species are the Ascomycota Aliquandostipite manochii, Allophaeosphaeria dactylidis, A. muriformia, Alternaria cesenica, Amphibambusa bambusicola, Amphisphaeria sorbi, Annulohypoxylon thailandicum, Atrotorquata spartii, Brunneomycosphaerella laburni, Byssosphaeria musae, Camarosporium aborescentis, C. aureum, C. frutexensis, Chaetocapnodium siamensis, Chaetothyrium agathis, Colletotrichum sedi, Conicomyces pseudotransvaalensis, Cytospora berberidis, C. sibiraeae, Diaporthe thunbergiicola, Diatrype palmicola, Dictyosporium aquaticum, D. meiosporum, D. thailandicum, Didymella cirsii, Dinemasporium nelloi, Flammeascoma bambusae, Kalmusia italica, K. spartii, Keissleriella sparticola, Lauriomyces synnematicus, Leptosphaeria ebuli, Lophiostoma pseudodictyosporium, L. ravennicum, Lophiotrema eburnoides, Montagnula graminicola, Multiseptospora thailandica, Myrothecium macrosporum, Natantispora unipolaris, Neogaeumannomyces bambusicola, Neosetophoma clematidis, N. italica, Oxydothis atypica, Palmiascoma gregariascomum, Paraconiothyrium nelloi, P. thysanolaenae, Paradictyoarthrinium tectonicola, Paralecia pratorum, Paraphaeosphaeria spartii, Pestalotiopsis digitalis, P. dracontomelon, P. italiana, Phaeoisaria pseudoclematidis, Phragmocapnias philippinensis, Pseudocamarosporium cotinae, Pseudocercospora tamarindi, Pseudotrichia rubriostiolata, P. thailandica, Psiloglonium multiseptatum, Saagaromyces mangrovei, Sarimanas pseudofluviatile, S. shirakamiense, Tothia spartii, Trichomerium siamensis, Wojnowicia dactylidicola, W. dactylidis and W. lonicerae. The Basidiomycota Agaricus flavicentrus, A. hanthanaensis, A. parvibicolor, A. sodalis, Cantharellus luteostipitatus, Lactarius atrobrunneus, L. politus, Phylloporia dependens and Russula cortinarioides are also introduced. Epitypifications or reference specimens are designated for Hapalocystis berkeleyi, Meliola tamarindi, Pallidocercospora acaciigena, Phaeosphaeria musae, Plenodomus agnitus, Psiloglonium colihuae, P. sasicola and Zasmidium musae while notes and/or new sequence data are provided for Annulohypoxylon leptascum, A. nitens, A. stygium, Biscogniauxia marginata, Fasciatispora nypae, Hypoxylon fendleri, H. monticulosum, Leptosphaeria doliolum, Microsphaeropsis olivacea, Neomicrothyrium, Paraleptosphaeria nitschkei, Phoma medicaginis and Saccotheciaceae. A full description of each species is provided with light micrographs (or drawings). Molecular data is provided for 90 taxa and used to generate phylogenetic trees to establish a natural classification for species.