Global models and predictions of plant diversity based on advanced machine learning techniques.

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is still incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, and neural networks) and conventional statistical methods (generalized linear models and generalized additive models) to test environment-related hypotheses of broad-scale vascular plant diversity gradients and to model and predict species richness and phylogenetic richness worldwide. To this end, we used 830 regional plant inventories including c. 300 000 species and predictors of past and present environmental conditions. Machine learning showed a superior performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness, illustrating the great potential of such techniques for disentangling complex and interacting associations between the environment and plant diversity. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modeling techniques (ensemble predictions) to reveal global patterns and centers of plant diversity at multiple resolutions down to 7774 km2 . Our predictive maps provide accurate estimates of global plant diversity available at grain sizes relevant for conservation and macroecology.

The global loss of floristic uniqueness.

Regional species assemblages have been shaped by colonization, speciation and extinction over millions of years. Humans have altered biogeography by introducing species to new ranges. However, an analysis of how strongly naturalized plant species (i.e. alien plants that have established self-sustaining populations) affect the taxonomic and phylogenetic uniqueness of regional floras globally is still missing. Here, we present such an analysis with data from native and naturalized alien floras in 658 regions around the world. We find strong taxonomic and phylogenetic floristic homogenization overall, and that the natural decline in floristic similarity with increasing geographic distance is weakened by naturalized species. Floristic homogenization increases with climatic similarity, which emphasizes the importance of climate matching in plant naturalization. Moreover, floristic homogenization is greater between regions with current or past administrative relationships, indicating that being part of the same country as well as historical colonial ties facilitate floristic exchange, most likely due to more intensive trade and transport between such regions. Our findings show that naturalization of alien plants threatens taxonomic and phylogenetic uniqueness of regional floras globally. Unless more effective biosecurity measures are implemented, it is likely that with ongoing globalization, even the most distant regions will lose their floristic uniqueness.

Mycorrhizal types influence island biogeography of plants.

Plant colonization of islands may be limited by the availability of symbionts, particularly arbuscular mycorrhizal (AM) fungi, which have limited dispersal ability compared to ectomycorrhizal and ericoid (EEM) as well as orchid mycorrhizal (ORC) fungi. We tested for such differential island colonization within contemporary angiosperm floras worldwide. We found evidence that AM plants experience a stronger mycorrhizal filter than other mycorrhizal or non-mycorrhizal (NM) plant species, with decreased proportions of native AM plant species on islands relative to mainlands. This effect intensified with island isolation, particularly for non-endemic plant species. The proportion of endemic AM plant species increased with island isolation, consistent with diversification filling niches left open by the mycorrhizal filter. We further found evidence of humans overcoming the initial mycorrhizal filter. Naturalized floras showed higher proportions of AM plant species than native floras, a pattern that increased with increasing isolation and land-use intensity. This work provides evidence that mycorrhizal fungal symbionts shape plant colonization of islands and subsequent diversification.

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.

High-resolution characterization of 12 classical and non-classical HLA loci in Southern Brazilians.

The human leukocyte antigen (HLA) are the most polymorphic genes in the human genome. Because of their importance for antigen recognition, HLA molecules play a central role in host defense and graft rejection upon transplantation. The aim of this study was to characterize allelic diversity of the classical HLA genes HLA-A, -B, -C, -DRA, -DRB1, -DQA1, -DQB1, -DPA1, -DPB1, and the non-classical class I genes HLA-E, -F and -G at high-resolution for a population of predominantly European ancestry from Curitiba, Brazil. Genotyping of 108 individuals was performed by next-generation sequencing on the MiSeq platform and also by Sanger sequencing. The genotype distributions of all loci were in accordance with Hardy-Weinberg equilibrium (P > 0.05) and a total of 202 HLA variants at second field resolution were observed for the 12 loci. The strongest linkage disequilibrium (r2 = 1.0, P < 10-5 ) was observed for the following pairs of alleles: HLA-B*42:01:01 ~ HLA-DRB1*03:02:01; HLA-B*14:02:01 ~ HLA-C*08:02:01; B*42:01:01 ~ HLA-C*17:01:01; HLA-DRB1*03:01:01 ~ HLA-DQB1*02:01:01 ~ DRB1*03:01:01 ~ HLA-DQB1*02:01:01; DRB1*13:01:01~ HLA-DQB1*06:03:01 and HLA-DRB1*09:01:02 ~ HLA-DQA1*03:02. This is the first study to characterize all 12 HLA genes at high resolution in a single population. On the basis of the allelic frequencies of worldwide populations and principal component analysis, we confirmed the similarity of the study population to European and other Euro-descendant populations.

Mycorrhizal fungi influence global plant biogeography.

Island biogeography has traditionally focused primarily on abiotic drivers of colonization, extinction and speciation. However, establishment on islands could also be limited by biotic drivers, such as the absence of symbionts. Most plants, for example, form symbioses with mycorrhizal fungi, whose limited dispersal to islands could act as a colonization filter for plants. We tested this hypothesis using global-scale analyses of ~1.4 million plant occurrences, including ~200,000 plant species across ~1,100 regions. We find evidence for a mycorrhizal filter (that is, the filtering out of mycorrhizal plants on islands), with mycorrhizal associations less common among native island plants than native mainland plants. Furthermore, the proportion of native mycorrhizal plants in island floras decreased with isolation, possibly as a consequence of a decline in symbiont establishment. We also show that mycorrhizal plants contribute disproportionately to the classic latitudinal gradient of plant species diversity, with the proportion of mycorrhizal plants being highest near the equator and decreasing towards the poles. Anthropogenic pressure and land use alter these plant biogeographical patterns. Naturalized floras show a greater proportion of mycorrhizal plant species on islands than in mainland regions, as expected from the anthropogenic co-introduction of plants with their symbionts to islands and anthropogenic disturbance of symbionts in mainland regions. We identify the mycorrhizal association as an overlooked driver of global plant biogeographical patterns with implications for contemporary island biogeography and our understanding of plant invasions.

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.

The role of adaptive strategies in plant naturalization.

Determining the factors associated with the naturalization of alien species is a central theme in ecology. Here, we tested the usefulness of a metric for quantifying Grime's seminal concept of adaptive strategies - competitors, stress-tolerators and ruderals (CSR) - to explain plant naturalizations worldwide. Using a global dataset of 3004 vascular plant species, and accounting for phylogenetic relatedness and species' native biomes, we assessed the associations between calculated C-, S- and R-scores and naturalization success for species exhibiting different life forms. Across different plant life forms, C-scores were positively and S-scores negatively associated with both the probability of naturalization and the number of regions where the species has naturalized. R-scores had positive effects on the probability of naturalization. These effects of the scores were, however, weak to absent for tree species. Our findings demonstrate the utility of CSR-score calculation to broadly represent, and potentially explain, the naturalization success of plant species.

Terminology and quantification of environmental heterogeneity in species-richness research.

Spatial environmental heterogeneity (EH) is an important driver of species diversity, and its influence on species richness has been analysed for numerous taxa, in diverse ecological settings, and over a large range of spatial scales. The variety and ambiguity of concepts and terminology, however, have hampered comparisons among studies. Based on a systematic literature survey of 192 studies including 1148 data points, we provide an overview of terms and measures related to EH, and the mechanisms that relate EH to species richness of plants and animals in terrestrial systems. We identify 165 different measures used to quantify EH, referred to by more than 350 measure names. We classify these measures according to their calculation method and subject area, finding that most studies have analysed heterogeneity in land cover, topography, and vegetation, whereas comparatively few studies have focused on climatic or soil EH. Overall, elevation range emerged as the most frequent measure in our dataset. We find that there is no consensus in the literature about terms (such as 'habitat diversity' or 'habitat complexity'), their meanings and associated quantification methods. More than 100 different terms have been used to denote EH, with largely imprecise delimitations. We reveal trends in use of terms and quantification with respect to spatial scales, study taxa, and locations. Finally, we discuss mechanisms involved in EH-richness relationships, differentiating between effects on species coexistence, persistence, and diversification. This review aims at guiding researchers in their selection of heterogeneity measures. At the same time, it shows the need for precise terminology and avoidance of ambiguous synonyms to enhance understanding and foster among-study comparisons and synthesis.

Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales.

Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity-richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity-richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity-richness studies. We provide the first quantitative support for the generality of positive heterogeneity-richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity-richness research.

The evolution and function of vessel and pit characters with respect to cavitation resistance across 10 Prunus species.

Various structure-function relationships regarding drought-induced cavitation resistance of secondary xylem have been postulated. These hypotheses were tested on wood of 10 Prunus species showing a range in P50 (i.e., the pressure corresponding to 50% loss of hydraulic conductivity) from -3.54 to -6.27 MPa. Hydraulically relevant wood characters were quantified using light and electron microscopy. A phylogenetic tree was constructed to investigate evolutionary correlations using a phylogenetically independent contrast (PIC) analysis. Vessel-grouping characters were found to be most informative in explaining interspecific variation in P50, with cavitation-resistant species showing more solitary vessels than less resistant species. Co-evolution between vessel-grouping indices and P50 was reported. P50 was weakly correlated with the shape of the intervessel pit aperture, but not with the total intervessel pit membrane area per vessel. A negative correlation was found between P50 and intervessel pit membrane thickness, but this relationship was not supported by the PIC analysis. Cavitation resistance has co-evolved with vessel grouping within Prunus and was mainly influenced by the spatial distribution of the vessel network.

Do quantitative vessel and pit characters account for ion-mediated changes in the hydraulic conductance of angiosperm xylem?

• The hydraulic conductance of angiosperm xylem has been suggested to vary with changes in sap solute concentrations because of intervessel pit properties. • The magnitude of the 'ionic effect' was linked with vessel and pit dimensions in 20 angiosperm species covering 13 families including six Lauraceae species. • A positive correlation was found between ionic effect and vessel grouping parameters, especially the portion of vessel walls in contact with neighbouring vessels. Species with intervessel contact fraction (F(C)) values < 0.1 showed an ionic effect between 2% and 17%, while species with F(C) values > 0.1 exhibited a response between 10% and 32%. The ionic effect increased linearly with the mean fraction of the total vessel wall area occupied by intervessel pits as well as with the intervessel contact length. However, no significant correlation occurred between the ionic effect and total intervessel pit membrane area per vessel, vessel diameter, vessel length, vessel wall area, and intervessel pit membrane thickness. • Quantitative vessel and pit characters are suggested to contribute to interspecific variation of the ionic effect, whereas chemical properties of intervessel pit membranes are likely to play an additional role.

Large-scale purification, dissociation and functional reassembly of the maltose ATP-binding cassette transporter (MalFGK(2)) of Salmonella typhimurium.

The maltose ATP-binding cassette (ABC) transporter of Salmonella typhimurium is composed of a membrane-associated complex (MalFGK(2)) and a periplasmic substrate binding protein. To further elucidate protein-protein interactions between the subunits, we have studied the dissociation and reassembly of the MalFGK(2) complex at the level of purified components in proteoliposomes. First, we optimized the yield in purified complex protein by taking advantage of a newly constructed expression plasmid that carries the malK, malF and malG genes in tandem orientation. Incorporated in proteoliposomes, the complex exhibited maltose binding protein/maltose-dependent ATPase activity with a V(max) of 1.25 micromol P(i)/min/mg and a K(m) of 0.1 mM. ATPase activity was sensitive to vanadate and enzyme IIA(Glc), a component of the enterobacterial glucose transport system. The proteoliposomes displayed maltose transport activity with an initial rate of 61 nmol/min/mg. Treatment of proteoliposomes with 6.6 M urea resulted in the release of medium-exposed MalK subunits concomitant with the complete loss of ATPase activity. By adding increasing amounts of purified MalK to urea-treated proteoliposomes, about 50% of vanadate-sensitive ATPase activity relative to the control could be recovered. Furthermore, the phenotype of MalKQ140K that exhibits ATPase activity in solution but not when associated with MalFG was confirmed by reassembly with MalK-depleted proteoliposomes.

Functional characterization of the maltose ATP-binding-cassette transporter of Salmonella typhimurium by means of monoclonal antibodies directed against the MalK subunit.

The maltose ATP-binding cassette transporter of Salmonella typhimurium is composed of a membrane-associated complex (MalFGK2) and a periplasmic receptor (MalE). In addition to its role in transport, the complex acts as a repressor of maltose-regulated gene expression and is subject to inhibition in the process of inducer exclusion. These activities are thought to be mediated by interactions of the ATPase subunit, MalK, with the transcriptional activator, MalT, and nonphosphorylated enzyme IIA of the glucose phosphotransferase system, respectively. To gain further insight in protein regions that are critical for these functions, we have generated nine MalK-specific monoclonal antibodies. These bind to four nonoverlapping linear epitopes: 60-LFig-63 (5B5), 113-RVNQVAEVLQL-123 (represented by 4H12), 309-GHETQI-314 (2F9) and 352-LFREDGSACR-361 (represented by 4B3). All mAbs recognize their epitopes in soluble MalK and in the MalFGK2 complex with Kd values ranging from 10-6 to 10-8 m. ATP reduced the affinity of the mAbs for soluble MalK, indicating a conformational change that renders the epitopes less accessible. 4H12 and 5B5 inhibit the ATPase activity of MalK and the MalE/maltose-stimulated ATPase activity of proteoliposomes, while their Fab fragments displayed no significant effect. The results suggest a similar solvent-exposed position of helix 3 in the MalK dimer and in the intact complex and might argue against a direct role in the catalytic process. 4B3 and 2F9 exhibit reduced binding to the MalFGK2 complex in the presence of MalT and enzyme IIAGlc, respectively, thereby providing the first direct evidence for the C-terminal domain of MalK being the site of interaction with the regulatory proteins.