EpiList 1.0: a global checklist of vascular epiphytes

Epiphytes make up roughly 10% of all vascular plant species globally and play important functional roles, especially in tropical forests. However, to date, there is no comprehensive list of vascular epiphyte species. Here, we present EpiList 1.0, the first global list of vascular epiphytes based on standardized definitions and taxonomy. We include obligate epiphytes, facultative epiphytes, and hemiepiphytes, as the latter share the vulnerable epiphytic stage as juveniles. Based on 978 references, the checklist includes >31,000 species of 79 plant families. Species names were standardized against World Flora Online for seed plants and against the World Ferns database for lycophytes and ferns. In cases of species missing from these databases, we used other databases (mostly World Checklist of Selected Plant Families). For all species, author names and IDs for World Flora Online entries are provided to facilitate the alignment with other plant databases, and to avoid ambiguities. EpiList 1.0 will be a rich source for synthetic studies in ecology, biogeography, and evolutionary biology as it offers, for the first time, a species-level overview over all currently known vascular epiphytes. At the same time, the list represents work in progress: species descriptions of epiphytic taxa are ongoing and published life form information in floristic inventories and trait and distribution databases is often incomplete and sometimes even wrong. Since the epiphytic growth blends into soil-rooted growth and vice versa, the inclusion or exclusion of particular species in the current list will sometimes be contentious. Thus, initiating a well-founded discussion was one of the motivations for compiling this database; our list represents 31,311 hypotheses on the life form of plant species, and we welcome feedback on possible omission or erroneous inclusions. We release these data into the public domain under a Creative Commons Zero license waiver. When you use the data in your publication, we request that you cite this data paper. If EpiList 1.0 is a major part of the data analyzed in your study, you may consider inviting the EpiList 1.0 core team as collaborators.

Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size

Maintaining high rates of photosynthesis in leaves requires efficient movement of CO2 from the atmosphere to the mesophyll cells inside the leaf where CO2 is converted into sugar. CO2 diffusion inside the leaf depends directly on the structure of the mesophyll cells and their surrounding airspace, which have been difficult to characterize because of their inherently three-dimensional organization. Yet faster CO2 diffusion inside the leaf was probably critical in elevating rates of photosynthesis that occurred among angiosperm lineages. Here we characterize the three-dimensional surface area of the leaf mesophyll across vascular plants. We show that genome size determines the sizes and packing densities of cells in all leaf tissues and that smaller cells enable more mesophyll surface area to be packed into the leaf volume, facilitating higher CO2 diffusion. Measurements and modelling revealed that the spongy mesophyll layer better facilitates gaseous phase diffusion while the palisade mesophyll layer better facilitates liquid-phase diffusion. Our results demonstrate that genome downsizing among the angiosperms was critical to restructuring the entire pathway of CO2 diffusion into and through the leaf, maintaining high rates of CO2 supply to the leaf mesophyll despite declining atmospheric CO2 levels during the Cretaceous.

Vascular plants dataset of the herbarium (HSS) of Agrarian Research Institute Finca "La Orden-Valdesequera" (CICYTEX), Extremadura, Spain

The HSS herbarium database includes 69,397 records of vascular plant taxa, representing 91.1% of the herbarium's specimens as for December, 2019, which are available through the Global Biodiversity Information Facility (GBIF) website (accessible at https://doi.org/10.15468/siye1z). The database represents 4,343 species and 787 infraspecific taxa (530 subspecies, 130 varieties and 127 notho-species or hybrids) of 196 families and 1,164 genera, and 105 type sheets. So far, 97.7% of the databased records are georeferenced (geographic coordinates or MRGS coordinates) and the geographic area with the largest number of specimens is the southwest quadrant of the Iberian Peninsula (Spain and Portugal).

Distribution of alien plant species of the Middle Volga Region (South-East of the European part of Russia): a dataset

BACKGROUND

The dataset presented in the current study contains information regarding alien vascular plant species found in the Middle Volga Region (South-East of the European part of Russia). The dataset overall includes 413 species belonging to 247 genera and 67 families. The described dataset is based on the data published during floristic studies from 1851 to 2019. The dataset does not include alien vascular plant species that have presently disappeared from the territory of the region. It contains a total of 7,782 records of occurrences, extracted from the Salix system of information and analytics, developed in the Institute of Ecology of the Volga River Basin of the Russian Academy of Sciences.

NEW INFORMATION

A total of 7,782 records were published on the occurrence of alien vascular plants in the Middle Volga Region. Each entry includes information regarding the place of occurrence of the alien plant species, the year of occurrence, the person who recorded the alien plant and who identified it, status of the species (introduced or invasive), link to the herbarium, which contains the specimen and the literary source. If it were impossible to establish the names of the persons who collected the samples and (or) their identification in the identifiedBy and recordedBy fields, the names of the authors of the publication given in the associatedReferences field were entered. The presented dataset supplements the information on the distribution of alien plant species in the whole European part of Russia and specifies the places of their findings in the Middle Volga Region.

Machine learning predicts large scale declines in native plant phylogenetic diversity

Though substantial effort has gone into predicting how global climate change will impact biodiversity patterns, the scarcity of taxon-specific information has hampered the efficacy of these endeavors. Further, most studies analyzing spatiotemporal patterns of biodiversity focus narrowly on species richness. We apply machine learning approaches to a comprehensive vascular plant database for the United States and generate predictive models of regional plant taxonomic and phylogenetic diversity in response to a wide range of environmental variables. We demonstrate differences in predicted patterns and potential drivers of native vs nonnative biodiversity. In particular, native phylogenetic diversity is likely to decrease over the next half century despite increases in species richness. We also identify that patterns of taxonomic diversity can be incongruent with those of phylogenetic diversity. The combination of macro-environmental factors that determine diversity likely varies at continental scales; thus, as climate change alters the combinations of these factors across the landscape, the collective effect on regional diversity will also vary. Our study represents one of the most comprehensive examinations of plant diversity patterns to date and demonstrates that our ability to predict future diversity may benefit tremendously from the application of machine learning.

Spatial Phylogenetics, Biogeographical Patterns and Conservation Implications of the Endemic Flora of Crete (Aegean, Greece) under Climate Change Scenarios

Human-induced biodiversity loss has been accelerating since the industrial revolution. The climate change impacts will severely alter the biodiversity and biogeographical patterns at all scales, leading to biotic homogenization. Due to underfunding, a climate smart, conservation-prioritization scheme is needed to optimize species protection. Spatial phylogenetics enable the identification of endemism centers and provide valuable insights regarding the eco-evolutionary and conservation value, as well as the biogeographical origin of a given area. Many studies exist regarding the conservation prioritization of mainland areas, yet none has assessed how climate change might alter the biodiversity and biogeographical patterns of an island biodiversity hotspot. Thus, we conducted a phylogenetically informed, conservation prioritization study dealing with the effects of climate change on Crete’s plant diversity and biogeographical patterns. Using several macroecological analyses, we identified the current and future endemism centers and assessed the impact of climate change on the biogeographical patterns in Crete. The highlands of Cretan mountains have served as both diversity cradles and museums, due to their stable climate and high topographical heterogeneity, providing important ecosystem services. Historical processes seem to have driven diversification and endemic species distribution in Crete. Due to the changing climate and the subsequent biotic homogenization, Crete’s unique bioregionalization, which strongly reminiscent the spatial configuration of the Pliocene/Pleistocene Cretan paleo-islands, will drastically change. The emergence of the ‘Anthropocene’ era calls for the prioritization of biodiversity-rich areas, serving as mixed-endemism centers, with high overlaps among protected areas and climatic refugia.

A. The protected flora of long-established cemeteries in Hungary: Using historical maps in biodiversity conservation

The role of anthropogenically influenced habitats in conserving elements of the original wildlife has increased worldwide simultaneously with the disappearance of natural sites. Burial places are able to conserve original elements of the wildlife, and this fact has been known for at least a century. To this day, little is known about long-time changes and the effect of long-time management methods in cemeteries on the flora they harbor. The utility of historical maps in research focused on natural values, as well as in answering questions related to conservation was recently demonstrated, but the use of digitized historical maps in biodiversity research of the Carpathian Basin is very limited. In the present paper, we aimed to predict the conservation potential of long-established and newly established cemeteries of Hungarian settlements with various population sizes based on the digitized maps of the 2nd Military Survey of the Austrian Empire (1819-1869), by categorizing cemeteries into 3 distinct (anthropogenic habitat, cemetery, or natural habitat) types. To build our models, we used records of the protected flora from Hungarian cemeteries, based on data of thematic botanical surveys of 991 cemeteries. Out of the surveyed cemeteries, 553 (56%) harbored protected plants, totaling 306.617 estimated individuals of 92 protected species, belonging to 28 plant families. These species represent 12% of the entire protected flora of Hungary. Hungarian cemeteries play a key role mainly in preserving steppe and dry grassland plant species. Long-established and large cemeteries harbor more protected plant species than small and newly established ones. Human population size of the settlements correlated negatively with the number of protected species and individuals. Moreover, woodland cover and proportion of grassland also significantly positively affected the number of protected plant species in cemeteries.

Dark diversity reveals importance of biotic resources and competition for plant diversity across habitats

Species richness is the most commonly used metric to quantify biodiversity. However, examining dark diversity, the group of missing species which can potentially inhabit a site, can provide a more thorough understanding of the processes influencing observed biodiversity and help evaluate the restoration potential of local habitats. So far, dark diversity has mainly been studied for specific habitats or large-scale landscapes, while less attention has been given to variation across broad environmental gradients or as a result of local conditions and biotic interactions. In this study, we investigate the importance of local environmental conditions in determining dark diversity and observed richness in plant communities across broad environmental gradients. Using the ecospace concept, we investigate how these biodiversity measures relate to abiotic gradients (defined as position), availability of biotic resources (defined as expansion), spatiotemporal extent of habitats (defined as continuity), and species interactions through competition. Position variables were important for both observed diversity and dark diversity, some with quadratic relationships, for example, plant richness showing a unimodal response to soil fertility corresponding to the intermediate productivity hypothesis. Interspecific competition represented by community mean Grime C had a negative effect on plant species richness. Besides position-related variables, organic carbon was the most important variable for dark diversity, indicating that in late-succession habitats such as forests and shrubs, dark diversity is generally low. The importance of highly competitive species indicates that intermediate disturbance, such as grazing, may facilitate higher species richness and lower dark diversity.

Evidence for a possible extinction debt in Swiss wetland specialist plants

Habitat loss leading to smaller patch sizes and decreasing connectivity is a major threat to global biodiversity. While some species vanish immediately after a change in habitat conditions, others show delayed extinction, that is, an extinction debt. In case of an extinction debt, the current species richness is higher than expected under present habitat conditions.We investigated wetlands of the canton of Zürich in the lowlands of Eastern Switzerland where a wetland loss of 90% over the last 150 years occurred. We related current species richness to current and past patch area and connectivity (in 1850, 1900, 1950, and 2000). We compared current with predicted species richness in wetlands with a substantial loss in patch area based on the species-area relationship of wetlands without substantial loss in patch area and studied relationships between the richness of different species groups and current and historical area and connectivity of wetland patches.We found evidence of a possible extinction debt for long-lived wetland specialist vascular plants: in wetlands, which substantially lost patch area, current species richness of long-lived specialist vascular plants was higher than would have been expected based on current patch area. Additionally and besides current wetland area, historical area also explained current species richness of these species in a substantial and significant way. No evidence for an extinction debt in bryophytes was found.The possible unpaid extinction debt in the wetlands of the canton of Zürich is an appeal to nature conservation, which has the possibility to prevent likely future extinctions of species through specific conservation measures. In particular, a further reduction in wetlands must be prevented and restoration measures must be taken to increase the number of wetlands.

Rare species, functional groups, and evolutionary lineages drive successional trajectories in disturbed forests

Following natural disturbances, additional anthropogenic disturbance may alter community recovery by affecting the occurrences of species, functional groups, and evolutionary lineages. However, our understanding of whether rare, common, or dominant species, functional groups, or evolutionary lineages are most strongly affected by an additional disturbance, particularly across multiple taxa, is limited. Here, we used a generalized diversity concept based on Hill numbers to quantify the community differences of vascular plants, bryophytes, lichens, wood-inhabiting fungi, saproxylic beetles, and birds in a storm-disturbed, experimentally salvage logged forest. Communities of all investigated species groups showed dissimilarities between logged and unlogged plots. Most species groups showed no significant changes in dissimilarities between logged and unlogged plots over the first seven years of succession, indicating a lack of community recovery. In general, the dissimilarities of communities were mainly driven by rare species. Convergence of dissimilarities occurred more often than divergence during the early stages of succession for rare species, indicating a major role in driving decreasing taxonomic dissimilarities between logged and unlogged plots over time. Trends in species dissimilarities only partially match the trends in dissimilarities of functional groups and evolutionary lineages, with little significant changes in successional trajectories. Nevertheless, common and dominant species contributed to a convergence of dissimilarities over time in the case of the functional dissimilarities of wood-inhabiting fungi. Our study shows that salvage logging following disturbances can alter successional trajectories in early stages of forest succession following natural disturbances. However, community changes over time may differ remarkably in different taxonomic groups and are best detected based on taxonomic, rather than functional or phylogenetic dissimilarities.

Assessment of a large number of empirical plant species niche models by elicitation of knowledge from two national experts

Quantitative models play an increasing role in exploring the impact of global change on biodiversity. To win credibility and trust, they need validating. We show how expert knowledge can be used to assess a large number of empirical species niche models constructed for the British vascular plant and bryophyte flora. Key outcomes were (a) scored assessments of each modeled species and niche axis combination, (b) guidance on models needing further development, (c) exploration of the trade-off between presenting more complex model summaries, which could lead to more thorough validation, versus the longer time these take to evaluate, (d) quantification of the internal consistency of expert opinion based on comparison of assessment scores made on a random subset of models evaluated by both experts. Overall, the experts assessed 39% of species and niche axis combinations to be "poor" and 61% to show a degree of reliability split between "moderate" (30%), "good" (25%), and "excellent" (6%). The two experts agreed in only 43% of cases, reaching greater consensus about poorer models and disagreeing most about models rated as better by either expert. This low agreement rate suggests that a greater number of experts is required to produce reliable assessments and to more fully understand the reasons underlying lack of consensus. While area under curve (AUC) statistics showed generally very good ability of the models to predict random hold-out samples of the data, there was no correspondence between these and the scores given by the experts and no apparent correlation between AUC and species prevalence. Crowd-sourcing further assessments by allowing web-based access to model fits is an obvious next step. To this end, we developed an online application for inspecting and evaluating the fit of each niche surface to its training data.

The FLORIVON flora survey in the Netherlands between 1902 and 1950

In 1902, the nationwide citizen science project, known as FLORIVON, for mapping the flora of the Netherlands was launched, resulting in the publication of a complete flora atlas in 1980. Until 2004, the atlas dataset of the fieldwork between 1902 and 1950 had only been partly digitised and observations were aggregated and anonymised. Between 2001 and 2018, the dataset has been entirely digitised from the original field forms, including notes on non-native taxa. This paper presents key characteristics and figures of the dataset and provides an overview of the historical survey project, the digitisation process and subsequent validation of the data. The dataset is currently curated in the National Database Flora and Fauna and published in GBIF.

Vascular plants dataset of the herbarium (COFC) of the University of Cordoba, Spain

This paper describes the herbarium (COFC) dataset of vascular plants of the University of Cordoba (SW Spain). This dataset is made up of two collections, the General collection (61,377 specimens) and the Historical collection (1,614 specimens). This study has focused mainly on the General collection, which contains the largest number of vascular plant specimens, predominantly angiosperms, mainly provincial and regional (Andalusia, Spain), but also with a good representation of other areas of the Iberian Peninsula and neighboring countries. The place of collection is specified in 99.7% of the labels, about 35% being georeferenced, and it is estimated that, currently, about 86% of the material housed in the herbarium has been databased using Elysia v1.0. software. With more than 178 families, 1,178 genera, and 3,750 species, this collection not only has educational importance, but is a valuable research tool that has been useful for the development of important works such as "Flora Vascular de Andalucía Occidental" and the "Flora iberica". The dataset described in this paper is registered with GBIF (accessible at https://doi.org/10.15468/fdzzal).

Drivers of the relative richness of naturalized and invasive plant species on Earth

Biological invasions are a defining feature of the Anthropocene, but the factors that determine the spatially uneven distribution of alien plant species are still poorly understood. Here, we present the first global analysis of the effects of biogeographic factors, the physical environment and socio-economy on the richness of naturalized and invasive alien plants. We used generalized linear mixed-effects models and variation partitioning to disentangle the relative importance of individual factors, and, more broadly, of biogeography, physical environment and socio-economy. As measures of the magnitude of permanent anthropogenic additions to the regional species pool and of species with negative environmental impacts, we calculated the relative richness of naturalized (= RRN) and invasive (= RRI) alien plant species numbers adjusted for the number of native species in 838 terrestrial regions. Socio-economic factors (per-capita gross domestic product (GDP), population density, proportion of agricultural land) were more important in explaining RRI (~50 % of the explained variation) than RRN (~40 %). Warm-temperate and (sub)tropical regions have higher RRN than tropical or cooler regions. We found that socio-economic pressures are more relevant for invasive than for naturalized species richness. The expectation that the southern hemisphere is more invaded than the northern hemisphere was confirmed only for RRN on islands, but not for mainland regions nor for RRI. On average, islands have ~6-fold RRN, and >3-fold RRI compared to mainland regions. Eighty-two islands (=26 % of all islands) harbour more naturalized alien than native plants. Our findings challenge the widely held expectation that socio-economic pressures are more relevant for plant naturalization than for invasive plants. To meet international biodiversity targets and halt the detrimental consequences of plant invasions, it is essential to disrupt the connection between socio-economic development and plant invasions by improving pathway management, early detection and rapid response.

Vascular plant species of the Kingdom of Tonga by vegetation type, species origin, growth form, and dispersal mechanism

The aim of this research is to compile a database of vascular plants found in the Kingdom of Tonga in western Polynesia, a phyto-geographic subregion of the South Pacific. The Tongan islands are spread over ~600,000 km² of the Pacific Ocean between 15-23° S latitude and 173-177° W longitude. The archipelago is comprised of 171 islands with an aggregate land area of about 720 km² . Since there is no comprehensive or updated flora for Tonga, we use 143 published sources to compile a database for 1,020 plant species, of which more than 450 are indigenous to these islands. Tonga is noteworthy for its low proportion of endemics, accounting for <5% of the indigenous species and <2% of the total plant species. Our database documents species presence in Tonga as a whole, and more specifically on 11 Tongan islands or island groups. We have assembled ecological information for each plant species according to growth form, vegetation type, origin (endemic, indigenous, and introduced species), and dispersal mechanisms. We include introduced species in our database because they represent over half of the plant species growing in Tonga. Species origins reflect human alteration of Tongan ecosystems in which endemic and indigenous species represent pre-human vegetation and introduced species indicate plants brought by either Polynesian or European settlers. For example, on Tongatapu, the largest and longest occupied island, more than half the plants are introduced, whereas on the sparsely populated, more remote islands, 70-90% of the species are indigenous. Dispersal mechanisms, which may include more than one mechanism per species, are documented in over 100 publications. Our database provides information on the whole suite of plant dispersal mechanisms over entire communities or island groups in Tonga. Plant species dispersal differs across environmental variables, including island geology, topography, vegetation type, and species origin. The older limestone islands have more bird, water, and human-dispersed plants, while the youngest volcanic islands have the most wind-dispersed species. Our database documents plant species endemism, introductions, vegetation types and dispersal mechanisms that reveal key biogeographic dynamics of the Tongan archipelago in the South Pacific. Please cite this Ecology Data Paper if the data are used in publication, presentation, or teaching activities. There are no copyright restrictions.

Conservation priorities and distribution patterns of vascular plant species along environmental gradients in Aberdare ranges forest

Distribution patterns of biodiversity and the factors influencing them are important in conservation and management strategies of natural resources. With impending threats from increased human population and global climatic changes, there is an urgent need for a comprehensive understanding of these patterns, more so in species-rich tropical montane ecosystems where little is known about plant diversity and distribution. Vascular species richness along elevation and climatic gradients of Aberdare ranges forest were explored. A total of 1337 species in 137 families, 606 genera, 82 subspecies and 80 varieties were recorded. Correlations, simple linear regression and Partial least square regression analysis were used to assess richness and diversity patterns of total plants, herbs, shrubs, climbers, arboreal and endemic species from 2000-4000 m above sea level. Total plant species richness showed a monotonic declining relationship with elevation with richness maxima at 2000-2100 m a.s.l., while endemic species richness had a positive unimodal increase along elevation with peaks at 3600-3700 m a.s.l. Herbs, shrubs, climbers and arboreal had significant negative relationships with altitude, excluding endemism which showed positive relations. In contrast, both air and soil temperatures had positive relationships with taxa richness groups and negative relations with endemic species. Elevation was found to have higher relative influence on plant richness and distribution in Aberdare ranges forest. For effective conservation and management of biodiversity in Aberdare, localized dynamic conservation interventions are recommended in contrast to broad and static strategies. Establishment of conservation zones and migration corridors are necessary to safeguard biodiversity in line with envisaged global climatic vicissitudes.

Thermal niche predictors of alpine plant species

Within the context of species distribution models, scrutiny arises from the choice of meaningful environmental predictors. Thermal conditions are not the sole driver, but are the most widely acknowledged abiotic driver of plant life within alpine ecosystems. We linked long-term measurements of direct, plant-relevant, near-surface temperatures to plant species frequency. Across 47 sites located along environmental gradients within the Scandinavian mountain chain, the thermal preferences of 26 focal species of vascular plants, lichens, and bryophytes were explored. Based on partial least-squares regression, we applied a relative importance analysis to derive inductively the thermal variables that were best related to a species' frequency. To discover potential seasonal variability of thermal controls, analyses were both differentiated according to meteorological season and integrated across the entire year. The pronounced interspecies and temporal variability of thermal constraints revealed the thermal niches were much more nuanced and variable than they have commonly been represented. This finding challenges us to present, interrogate, and interpret data representing these thermal niches, which seems to be required in order to move beyond purely probabilistic and correlative descriptions of species' range limits. Thus, this information will help improve predictions of species distributions in complex arctic-alpine landscapes.

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE

At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high alpine flora in the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.

METHODS

We used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assessed whether maximum elevation explains phylogenetic structure. To evaluate similarities between summits, we quantified phylogenetic turnover, taking into consideration microhabitats (talus vs. meadows).

RESULTS

We found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely not different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: overdispersion degraded as elevation increased. Between summits, we found high phylogenetic turnover driven by greater niche heterogeneity on summits with alpine meadows.

CONCLUSIONS

Our results provide further evidence that stochastic processes may also play an important role in the assembly of vascular plant communities in high alpine habitats at regional scales. However, order-specific patterns suggest that adaptations are still important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important in disentangling the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

An annotated checklist of vascular plants of Cherangani hills, Western Kenya

Cherangani hills, located in Western Kenya, comprises of 12 forest blocks, maintaining great plant diversity. However, little attention to plant diversity studies has been paid to it in the past years. Here, we present a checklist of the vascular plants of this region obtained through intensive field investigations and matching of herbarium specimens. In total, 1296 species, including 17 endemic species are documented, belonging to 130 families and 608 genera. This flora represents 18.50%, 43.83% and 54.17% of the Kenyan species, genera and families, respectively. The habit, habitat and voucher specimens, as well as brief notes on the distribution of each taxon recorded are presented in this checklist. It is the first exhaustive inventory of the terrestrial vascular plants in Cherangani hills which is a significant regional centre for plant diversity.

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

BACKGROUND

Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank.

RESULTS

The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications.

CONCLUSIONS

The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for "planetary-scale" projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.

Ecological restoration of eroded karst utilizing pioneer moss and vascular plant species with selection based on vegetation diversity and underlying soil chemistry

Soil erosion in karst areas not only destroys the natural environment but also accelerates the decline in land productivity together with the associated increase in poverty for local communities. There are no simple or straightforward answers to controlling soil erosion on karst. Such erosion has become a serious problem in China. This study addresses both the diversity of vegetation (mosses, herbs, shrubs and trees) on karst and the underlying soil chemical characteristics, in order to provide a scientific basis by which suitable plant species can be selected for recovery and restoration of karst degraded by soil erosion. Vegetation diversity and soil chemistry were assessed in areas with five different grades of soil erosion in Guiyang Karst Park, Guizhou, China. Mosses are more tolerant than vascular plants of soil erosion and associated environmental degradation of karst and the order of species diversity was: mosses > herbs > shrubs > trees. Mosses were found to play a major role in ecological restoration of microhabitats on karst. Soil microbial biomass carbon was found to be significantly higher in soil under mosses than in bare soil associated with other plant categories. Mosses were more effective in converting unavailable potassium to available potassium. Vascular plants were found to have a positive effect on total nitrogen fixation and the availability of phosphorus in the soil. Increasing soil degradation was associated with lower levels of total Nitrogen in soil underlying mosses than in soil underlying vascular plants. Thus, based on their different but complementary contributions to soil chemistry, mosses and vascular plants in combination can provide the most practical outcome for the repair and restoration of areas of karst affected by soil erosion. The combination of the moss species, Homomallium plagiangium, Cyrto-hypnum pygmaeuman and Brachythecium perminusculum, the herbs Veronica arvensis and Youngia japonica, and the tree Prunus salicina, are recommended as suitable pioneer plant species to cultivate for use in restoration of regions of karstic soil erosion.

The Global Naturalized Alien Flora (GloNAF) database

This dataset provides the Global Naturalized Alien Flora (GloNAF) database, version 1.2. GloNAF represents a data compendium on the occurrence and identity of naturalized alien vascular plant taxa across geographic regions (e.g. countries, states, provinces, districts, islands) around the globe. The dataset includes 13,939 taxa and covers 1,029 regions (including 381 islands). The dataset is based on 210 data sources. For each taxon-by-region combination, we provide information on whether the taxon is considered to be naturalized in the specific region (i.e. has established self-sustaining populations in the wild). Non-native taxa are marked as "alien", when it is not clear whether they are naturalized. To facilitate alignment with other plant databases, we provide for each taxon the name as given in the original data source and the standardized taxon and family names used by The Plant List Version 1.1 (http://www.theplantlist.org/). We provide an ESRI shapefile including polygons for each region and information on whether it is an island or a mainland region, the country and the Taxonomic Databases Working Group (TDWG) regions it is part of (TDWG levels 1-4). We also provide several variables that can be used to filter the data according to quality and completeness of alien taxon lists, which vary among the combinations of regions and data sources. A previous version of the GloNAF dataset (version 1.1) has already been used in several studies on, for example, historical spatial flows of taxa between continents and geographical patterns and determinants of naturalization across different taxonomic groups. We intend the updated and expanded GloNAF version presented here to be a global resource useful for studying plant invasions and changes in biodiversity from regional to global scales. We release these data into the public domain under a Creative Commons Zero license waiver (https://creativecommons.org/share-your-work/public-domain/cc0/). When you use the data in your publication, we request that you cite this data paper. If GloNAF is a major part of the data analyzed in your study, you should consider inviting the GloNAF core team (see Metadata S1: Originators in the Overall project description) as collaborators. If you plan to use the GloNAF dataset, we encourage you to contact the GloNAF core team to check whether there have been recent updates of the dataset, and whether similar analyses are already ongoing.