Plant interactions can lead to emergent relationships between plant community diversity, productivity and vulnerability to invasion.

Understanding what makes a community vulnerable to invasion is integral to the successful management of invasive species. Our understanding of how characteristics of resident plant interactions, such as the network architecture of interactions, can affect the invasibility of plant communities is limited. Using a simulation model, we tested how successfully a new plant invader established in communities with different network architectures of species interactions. We also investigated whether species interaction networks lead to relationships between invasibility and other community properties also affected by species interaction networks, such as diversity, species dominance, compositional stability and the productivity of the resident community. We found that higher invasibility strongly related with a lower productivity of the resident community. Plant interaction networks influenced diversity and invasibility in ways that led to complex but clear relationships between the two. Heterospecific interactions that increased diversity tended to decrease invasibility. Negative conspecific interactions always increased diversity and invasibility, but increased invasibility more when they increased diversity less. This study provides new theoretical insights into the effects of plant interaction networks on community invasibility and relationships between diversity and invasibility. Combined with increasing empirical evidence, these insights could have useful implications for the management of invasive plant species.

Thliphthisasapphus (Rubiaceae, Rubieae), a new species from Lefkada (Ionian Islands, Greece) and its ecological position.

The new species, Thliphthisasapphussp. nov. (Rubiaceae, Rubieae), a narrow endemic of the white cliffs of Lefkátas on the southwest coast of Lefkada (Greece) is described and illustrated and an IUCN assessment is presented. Vegetation relevés were performed at the single known locality, limestone cliffs facing the sea and revealed a new association, the Thliphthisasapphus-Lomelosietumdallaportae. The chromosome number of Thliphthisasapphus was determined as 2n = 4x = 44, being the single tetraploid species in the genus to date. The species also differs markedly morphologically from its morphologically closest relatives, two Greek steno-endemic oreophytes, Th.baenitzii and Th.muscosa by the following characters: densely setose mericarps and corolla, tetraploidy and by its distribution. An identification key for the Greek species of Thliphthisa is provided. Th.sapphus constitutes the westernmost outpost of a group of Greek steno-endemics, highlighting the importance of coastal habitats and their protection as refugia for poorly competitive chamaephytes.

What Is Wrong with Frankenia nodiflora Lam. (Frankeniaceae)? New Insights into the South African Sea-Heaths.

The taxonomic identity and phylogenetic relationships of several southern African perennial taxa related to Frankenia repens are discussed. In particular, F. nodiflora Lam., a misunderstood species described from the Cape region and synonymised to F. pulverulenta, is restored for plants endemic to salt-pans and riverbeds in the coastal lowlands across the Cape Flats (Western Cape province, South Africa). Further, a revision of morphologically close plants, usually identified as F. pulverulenta or F. repens, also occurring in similar saline ecosystems of the inland western South Africa revealed the existence of two distinct new entities not matching any described taxa of the genus. Molecular analyses of nuclear ribosomal (ITS1-5.8S-ITS2 region) DNA sequence data together with morphological divergence allow recognition of those taxa at species rank, within an independent lineage close to F. repens. In consequence, two new sea-heath species are described in the so-called "F. repens group": F. nummularia from the Nama-Karoo Biome (Western Cape and Northern Cape provinces), and F. anneliseae from the Succulent Karoo Biome (Northern Cape province). Full morphological description and type designation are reported for each accepted species as well as data on ecology, habitat, distribution, and taxonomic relationships to other close relatives are given. Further, an identification key is presented to facilitate recognition of the southern African taxa of Frankenia.

Spergularia hanoverensis (Caryophyllaceae): Validation and Recircumscription of a Misinterpreted Species from South Africa.

The name "Spergularia hanoverensis Simon" has been misapplied to an endemic taxon confined to inland semidesert ecosystems in central-western South Africa. It is commonly accepted as a small annual species occurring in saline habitats in a wide elevation range, but its identity still remains obscure. In the context of taxonomic and phylogenetic research on the African species of Spergularia, we found that the name was never validly published. After revision of herbarium material housed in South African herbaria, a voucher collected from Hanover was found at PRE bearing some labels handwritten by E. Simon that suggest it might be an intended type for the name. Additional herbarium material and wild populations from the Karoo region were identified that matched the samples in that voucher, and taxonomic research was conducted to clarify their identity. Among other characters, those Karoo plants show a woody dense compact habit, woody perennial at base; stems prostrate to ascendent; leaves entirely glabrous, somewhat glaucous; large white-hyaline conspicuous stipules; inflorescence glanduliferous, many-flowered subdichasial cyme, with minute bracts; flowers small, with white petals approximately equalling sepals in length, stamens 7-8, and styles free from base; capsule small, with seeds dimorphic, unwinged to broadly winged, with testa always densely tuberculate. Molecular analyses of plastid (trnL-trnF region) and nuclear ribosomal (5.8S-ITS2 region) DNA sequence data support morphological differentiation of the Karoo plants, for which the name S. hanoverensis is here effectively published. A full morphological description and data on ecology, habitat, distribution, and taxonomic and phylogenetic relationships of S. hanoverensis are compared to other members of the "South African group", namely S. glandulosa, S. namaquensis, and S. quartzicola, from which the new species considerably differs. The adaptative significance of dimorphic seeds of S. hanoverensis is briefly commented on in the context of the species habitat preference. An identification key is presented for the South African related taxa.

Metabarcoding of soil environmental DNA to estimate plant diversity globally.

Introduction: Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods: We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results: Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion: eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Global diversity and distribution of nitrogen-fixing bacteria in the soil.

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.

Corrigendum: Evolution of tandem repeats is mirroring post-polyploid cladogenesis in Heliophila (Brassicaceae).

[This corrects the article DOI: 10.3389/fpls.2020.607893.].

Plant clonality in a soil-impoverished open ecosystem: insights from southwest Australian shrublands.

BACKGROUND AND AIMS: Clonality is a key life-history strategy promoting on-spot persistence, space occupancy, resprouting after disturbance, and resource storage, sharing and foraging. These functions provided by clonality can be advantageous under different environmental conditions, including resource-paucity and fire-proneness, which define most mediterranean-type open ecosystems, such as southwest Australian shrublands. Studying clonality-environment links in underexplored mediterranean shrublands could therefore deepen our understanding of the role played by this essential strategy in open ecosystems globally. METHODS: We created a new dataset including 463 species, six traits related to clonal growth organs (CGOs; lignotubers, herbaceous and woody rhizomes, stolons, tubers, stem fragments), and edaphic predictors of soil water availability, nitrogen (N) and phosphorus (P) from 138 plots. Within two shrubland communities, we explored multivariate clonal patterns and how the diversity of CGOs, and abundance-weighted and unweighted proportions .of clonality in plots changed along with the edaphic gradients. KEY RESULTS: We found clonality in 65 % of species; the most frequent were those with lignotubers (28 %) and herbaceous rhizomes (26 %). In multivariate space, plots clustered into two groups, one distinguished by sandy plots and plants with CGOs, the other by clayey plots and non-clonal species. CGO diversity did not vary along the edaphic gradients (only marginally with water availability). The abundance-weighted proportion of clonal species increased with N and decreased with P and water availability, yet these results were CGO-specific. We revealed almost no relationships for unweighted clonality. CONCLUSIONS: Clonality is more widespread in shrublands than previously thought, and distinct plant communities are distinguished by specific suites (or lack) of CGOs. We show that weighting belowground traits by aboveground abundance affects the results, with implications for trait-based ecologists using abundance-weighting. We suggest unweighted approaches for belowground organs in open ecosystems until belowground abundance is quantifiable.

Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities.

Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense "packing" in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions. Current empirical support, however, is mixed. We tested these expectations using published data on arbuscular mycorrhizal (AM) fungal community composition worldwide. We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance. However, contrary to expectations, dominance was pronounced in communities where more specialists were present and, conversely, richness was higher in communities with more generalists. Thus, resource competition and niche packing appear to be of limited importance in AM fungal community assembly; rather, patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes.

Global taxonomic and phylogenetic assembly of AM fungi.

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.

Plant functional traits are correlated with species persistence in the herb layer of old-growth beech forests.

This paper explores which traits are correlated with fine-scale (0.25 m2) species persistence patterns in the herb layer of old-growth forests. Four old-growth beech forests representing different climatic contexts (presence or absence of summer drought period) were selected along a north-south gradient in Italy. Eight surveys were conducted in each of the sites during the period spanning 1999-2011. We found that fine-scale species persistence was correlated with different sets of plant functional traits, depending on local ecological context. Seed mass was found to be as important for the fine-scale species persistence in the northern sites, while clonal and bud-bank traits were markedly correlated with the southern sites characterised by summer drought. Leaf traits appeared to correlate with species persistence in the drier and wetter sites. However, we found that different attributes, i.e. helomorphic vs scleromorphic leaves, were correlated to species persistence in the northernmost and southernmost sites, respectively. These differences appear to be dependent on local trait adaptation rather than plant phylogenetic history. Our findings suggest that the persistent species in the old-growth forests might adopt an acquisitive resource-use strategy (i.e. helomorphic leaves with high SLA) with higher seed mass in sites without summer drought, while under water-stressed conditions persistent species have a conservative resource-use strategy (i.e. scleromorphic leaves with low SLA) with an increased importance of clonal and resprouting ability.

Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes.

BACKGROUND AND AIMS: The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. METHODS: Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. KEY RESULTS: Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). CONCLUSIONS: Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.

Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae).

The unigeneric tribe Heliophileae encompassing more than 100 Heliophila species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity hotspots (Cape Floristic Region and Succulent Karoo). The monospecific Chamira (C. circaeoides), the only crucifer species with persistent cotyledons, is traditionally retrieved as the closest relative of Heliophileae. Our transcriptome analysis revealed a whole-genome duplication (WGD) ∼26.15-29.20 million years ago, presumably preceding the Chamira/Heliophila split. The WGD was then followed by genome-wide diploidization, species radiations, and cladogenesis in Heliophila. The expanded phylogeny based on nuclear ribosomal DNA internal transcribed spacer (ITS) uncovered four major infrageneric clades (A-D) in Heliophila and corroborated the sister relationship between Chamira and Heliophila. Herein, we analyzed how the diploidization process impacted the evolution of repetitive sequences through low-coverage whole-genome sequencing of 15 Heliophila species, representing the four clades, and Chamira. Despite the firmly established infrageneric cladogenesis and different ecological life histories (four perennials vs. 11 annual species), repeatome analysis showed overall comparable evolution of genome sizes (288-484 Mb) and repeat content (25.04-38.90%) across Heliophila species and clades. Among Heliophila species, long terminal repeat (LTR) retrotransposons were the predominant components of the analyzed genomes (11.51-22.42%), whereas tandem repeats had lower abundances (1.03-12.10%). In Chamira, the tandem repeat content (17.92%, 16 diverse tandem repeats) equals the abundance of LTR retrotransposons (16.69%). Among the 108 tandem repeats identified in Heliophila, only 16 repeats were found to be shared among two or more species; no tandem repeats were shared by Chamira and Heliophila genomes. Six "relic" tandem repeats were shared between any two different Heliophila clades by a common descent. Four and six clade-specific repeats shared among clade A and C species, respectively, support the monophyly of these two clades. Three repeats shared by all clade A species corroborate the recent diversification of this clade revealed by plastome-based molecular dating. Phylogenetic analysis based on repeat sequence similarities separated the Heliophila species to three clades [A, C, and (B+D)], mirroring the post-polyploid cladogenesis in Heliophila inferred from rDNA ITS and plastome sequences.

Biome: evolution of a crucial ecological and biogeographical concept.

A biome is a key community ecological and biogeographical concept and, as such, has profited from the overall progress of community ecology, punctuated by two major innovations: shifting the focus from pure pattern description to understanding functionality, and changing the approach from observational to explanatory and, most importantly, from descriptive to predictive. The functional focus enabled development of mechanistic and function-focused predictive and retrodictive modelling; it also shaped the current understanding of the concept of a biome as a dynamic biological entity having many aspects, with deep roots in the evolutionary past, and which is undergoing change. The evolution of the biome concept was punctuated by three synthetic steps: the first synthesis formulated a solid body of theory explaining the ecological and biogeographical meaning of zonality and collated our knowledge on drivers of vegetation patterns at large spatial scales; the second translated this knowledge into effective mechanistic modelling tools, developing further the link between ecosystem functionality and biogeography; and the third (still in progress) is seeking common ground between large-scale ecological and biogeographic phenomena, using macroecology and macroevolutionary research tools.

Thesiumnautimontanum, a new species of Thesiaceae (Santalales) from South Africa.

Thesiumnautimontanum M.A. García, Nickrent & Mucina, a new species from the Matroosberg Mt. of Western Cape Province of South Africa, is described and illustrated. This species shows several morphological features unusual for the genus including stem sympodial branching, indeterminate spicate inflorescences subtended by numerous bracts and fleshy, non-trichome tissue lining the inside of the corolla lobes. Molecular phylogenetic analyses using nuclear ribosomal internal transcribed spacer sequences place this taxon as sister to all African, Madagascan and South American Thesium species. Given that only two proximal populations are known, this species is of conservation concern.

Towards an eco-evolutionary understanding of endemism hotspots and refugia.

Background: Refugia are island-like habitats that are linked to long-term environmental stability and, as a result, high endemism. Conservation of refugia and endemism hotspots should be based on a deep ecological and evolutionary understanding of their functioning, which remains limited. Although functional traits can provide such insights, a corresponding, coherent framework is lacking. Proposed Framework: Plant communities in refugia and endemism hotspots should, due to long-term environmental stability, display unique functional characteristics linked to distinct phylogenetic patterns. Therefore, such communities should be characterized by a functional signature that exhibits: (1) distinct values and combinations of traits, (2) higher functional diversity and (3) a prevalence of similar traits belonging to more distantly related lineages inside, compared to outside, of endemism hotspots and refugia. While the limited functional trait data available from refugia and endemism hotspots do not allow these predictions to be tested rigorously, three potential applications of the functional signature in biogeography and conservation planning are highlighted. Firstly, it allows the functional characteristics of endemism hotspots and refugia to be identified. Secondly, the strength of the functional signature can be compared among these entities, and with the surrounding landscape, to provide an estimate of the capacity of endemism hotspots and refugia to buffer environmental changes. Finally, the pattern of the functional signature can reveal ecological and evolutionary processes driving community assembly and functioning, which can assist in predicting the effect of environmental changes (e.g. climate, land-use) on communities in endemism hotspots and refugia. Conclusion: The proposed functional signature concept allows the systematic integration of plant functional traits and phylogeny into the study of endemism hotspots and refugia, but more data on functional traits in these entities are urgently needed. Overcoming this limitation would facilitate rigorous testing of the proposed predictions for the functional signature, advancing the eco-evolutionary understanding of endemism hotspots and refugia.

Impact of ecological redundancy on the performance of machine learning classifiers in vegetation mapping.

Vegetation maps are models of the real vegetation patterns and are considered important tools in conservation and management planning. Maps created through traditional methods can be expensive and time-consuming, thus, new more efficient approaches are needed. The prediction of vegetation patterns using machine learning shows promise, but many factors may impact on its performance. One important factor is the nature of the vegetation-environment relationship assessed and ecological redundancy. We used two datasets with known ecological redundancy levels (strength of the vegetation-environment relationship) to evaluate the performance of four machine learning (ML) classifiers (classification trees, random forests, support vector machines, and nearest neighbor). These models used climatic and soil variables as environmental predictors with pretreatment of the datasets (principal component analysis and feature selection) and involved three spatial scales. We show that the ML classifiers produced more reliable results in regions where the vegetation-environment relationship is stronger as opposed to regions characterized by redundant vegetation patterns. The pretreatment of datasets and reduction in prediction scale had a substantial influence on the predictive performance of the classifiers. The use of ML classifiers to create potential vegetation maps shows promise as a more efficient way of vegetation modeling. The difference in performance between areas with poorly versus well-structured vegetation-environment relationships shows that some level of understanding of the ecology of the target region is required prior to their application. Even in areas with poorly structured vegetation-environment relationships, it is possible to improve classifier performance by either pretreating the dataset or reducing the spatial scale of the predictions.