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Figure 2 from: Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC (2020) Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PhytoKeys 165: 1-25. https://doi.org/10.3897/phytokeys.165.54819

Figure 2 Representative species of canga in new dataset, SFXaAxonopus longispicus (Döll) Kuhlm bDicypellium aff. caryophyllaceum (Mart.) Nees cInga heterophylla Willd dIpomoea decora Meisn eMatelea microphylla Morillo fMimosa dasilvae A.S.L. Silva & Secco gNepsera aquatica (Aubl.) Naudin hOuratea cearensis (Tiegh.) Sastre & Offroy iPachyptera incarnata (Aubl.) Francisco & L.G. Lohmann jPassifora picturata Ker Gawl. kPhyllanthus minutulus Mull.Arg. lRodriguezia lanceolata Ruiz & Pav.

Figure 1 from: Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC (2020) Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PhytoKeys 165: 1-25. https://doi.org/10.3897/phytokeys.165.54819

Figure 1 a Geographic location of the present study site at SFX and the other study areas from Carajás complex b aerial view of an island of canga vegetation surrounding by the rainforest (Photo: Leonardo Vianna) cSerra de Campos of São Félix do Xingu (SFX) phytophysiognomy with shrubby and grassy vegetation.

opencc-zeroNov 2020View details →

Supplementary material 1 from: Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC (2020) Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PhytoKeys 165: 1-25. https://doi.org/10.3897/phytokeys.165.54819

Investigating plant beta diversity of canga outcrops

Figure 4 from: Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC (2020) Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PhytoKeys 165: 1-25. https://doi.org/10.3897/phytokeys.165.54819

Figure 4 a Species richness plotted against area of Carajás. Pearson correlation coefficients: r = 0.806094, P = 0.001548 b the number of species shared between site pairs does not change significantly with geographical distance between regions. r = -0.16; P = 0.08 c the number of shared endemic species between site pairs declines with geographical distance between regions. r= -0.45872; P = 1.37e-07.

Figure 3 from: Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC (2020) Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PhytoKeys 165: 1-25. https://doi.org/10.3897/phytokeys.165.54819

Figure 3 UPGMA (a) and NMDS (b) multivariate analysis clustering areas from FCC and SFX (see Table 2 for area codes). UPGMA cophenetic coefficient: 0.902. b. NMDS stress: 0.1859.

opencc-zeroDec 2020View details →

Using multiple seedlots in restoration planting enhances genetic diversity compared to natural regeneration in fragmented tropical forests

<p>Catastrophic degradation of forests is ongoing worldwide and leads to severe forest fragmentation. Restoration plantings are often necessary to restore fragmented forests, complementing the limited natural regeneration. High genetic diversity is critical for the long-term viability of restored forests. However, there is limited knowledge of whether planted populations capture a genetic variation comparable to natural populations. We measured the efficiency of two forest restoration strategies using the common tropical oak <em>Quercus bambusifolia</em>. The multi-seedlot planting was established over ten years by collecting seeds from several locations in fragmented secondary forests of Hong Kong, while the single seedlot planting was established in just one year with seeds from a single natural location. We analysed the genetic diversity and genetic structure from both plantings and compared them with natural populations. The multi-seedlot planting exhibited a higher rate of genetic recovery, greater genetic diversity (He = 0.69), and higher effective population size (Ne_p = 86.5) compared to natural populations (He = 0.66, Ne_p = 64.3, on average) and the single seedlot planting (He = 0.50, Ne_p = 30.8). The multi-seedlot planting erased the effect of seed shadows which was detected in natural populations while the single seedlot planting strengthened the effect. We conclude that capturing high levels of genetic diversity in the collection of propagules is a standard requirement to ensure the long-term viability of forest restoration. Propagule collection over multiple years is required when only a few parental trees are available to avoid founder effects.</p>

opencc-zeroDec 2014View details →

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

opencc-zeroJun 2019View details →

Data from: Plant diversity increases N removal in constructed wetlands when multiple rather than single N processes are considered

Biodiversity has a close relationship with ecosystem functioning. For most biodiversity–ecosystem functioning studies, biodiversity has been linked to a single indicator variable of ecosystem functioning. However, there are generally multiple ecosystem processes contributing to ecosystem functioning and they differ in their dependence on biodiversity. Thus, the relationship between biodiversity and ecosystem functioning can be stronger when multiple rather than single ecosystem processes are considered. Using both mass-balance and stable-isotope approaches, we explored the effects of plant diversity on nitrogen (N) removal sustained by multiple N-cycling processes in experimental microcosms simulating constructed wetlands, an ecosystem treating wastewater with high N loading. Four species were used to assemble different plant communities, ranging in richness from one to four species. The removal of N, indicated by low levels of total inorganic N concentration (TIN) present in the effluent, was considered as an integrated measure of ecosystem functioning, combining three constituent N-cycling processes: plant uptake, denitrification and substrate adsorption. Our results showed that: (1) species richness had a positive effect on N removal, in particular, the four-species mixture reduced effluent TIN to a lower level than any monoculture, however, polycultures (two-, three- and four-species mixtures) did not outperform the most-efficient monoculture when each of the three constituent N-cycling processes was considered by itself; (2) species identity had significant impacts on single processes. Communities with the species Coix lacryma-jobi showed the greatest capacity for N uptake and communities with Phragmites australis had the highest denitrification rates; (3) isotope fractionation in the rhizosphere of Coix lacryma-jobi was primarily due to microbial denitrification while multistep isotope fractionation was detected for Phragmites australis and Acorus calamus (indicating recycling of N), suggesting that species differed in the way they transformed N; (4) the enhanced N removal at high diversity may be due to mutualistic interactions among species belonging to different functional types. Our findings demonstrated that although plant species richness had negligible effects on individual N-cycling processes, it enhanced the overall ecosystem functioning (N removal) when these processes were considered collectively. Our study thus contributes to improve the treatment efficiency of constructed wetlands through proper vegetation management.

Data from: Root biomass and exudates link plant diversity with soil bacterial and fungal biomass

Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e. though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-to-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-to-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.

opencc-zeroDec 2013View details →

Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes

Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (1) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (2) in dioecious populations, male clones are larger and flower more often than female clones because of sex-differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet- and genet-based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in eastern N. America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations there was no difference in clone size between females and males; ramet- and genet-based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.

opencc-zeroDec 2010View details →

Data from: Resource heterogeneity, soil fertility, and species diversity: effects of clonal species on plant communities

Spatial heterogeneity in soil resources is widely thought to promote plant species coexistence, and this mechanism figures prominently in resource-ratio models of competition. However, most experimental studies have found that nutrient enhancements depress diversity regardless of whether nutrients are uniformly or heterogeneously applied. This mismatch between theory and empirical pattern is potentially due to an interaction between plant size and the scale of resource heterogeneity. Clonal plants that spread vegetatively via rhizomes or stolons can grow large and may integrate across resource patches, thus reducing the positive effect of small-scale resource heterogeneity on plant species richness. Many rhizomatous clonal species respond strongly to increased soil fertility, and they have been hypothesized to drive the descending arm of the hump-shaped productivity-diversity relationship in grasslands. We tested whether clonals reduce species richness in a grassland community by manipulating nutrient heterogeneity, soil fertility, and the presence of rhizomatous clonal species in a 6-year field experiment. We found strong and consistent negative effects of clonals on species richness. These effects were greatest at high fertility and when soil resources were applied at a scale at which rhizomatous clonals could integrate across resource patches. Thus, we find support for the hypothesis that plant size and resource heterogeneity interact to determine species diversity.

Data from: Spatiotemporal scaling of plant species richness and functional diversity in a temperate semi-natural grassland

The accumulation of biodiversity in space and time has been modelled extensively using the species-area relationship and the species-time relationship, respectively. Recently, these models have been combined into time-area curves in order to investigate spatiotemporal scaling of species richness. This study expands on previous research by applying these spatiotemporal models to functional diversity. Understanding spatiotemporal dynamics of ecological traits is important due to their crucial role in ecosystem functioning and mediating species responses to environmental change. We present a new function based on the semi-logarithmic species-area relationship, which was applied with a power function to vegetation survey data from Scottish machair grassland for both species richness and two measures of functional diversity. When taking a whole-study approach using non-linear mixed effects models, the semi-logarithmic function used here shows a positive time-area interaction for species richness, contrasting with the negative interaction of the power law found in previous investigations. Although there was a negative time-area interaction for functional diversity measures at the whole-study scale, parameter estimates were inconsistent at the individual site level. Overall, the results reveal differing spatiotemporal dynamics of species and their traits and suggest that the appropriate scale for space-for-time substitutions depends on the aspect of biodiversity being investigated. The new model developed in this study, and the novel application to functional diversity, opens up future possible research into spatiotemporal dynamics of biodiversity.

opencc-zeroDec 2015View details →

Data from: Fire frequency drives habitat selection by a diverse herbivore guild impacting top–down control of plant communities in an African savanna

In areas with diverse herbivore communities such as African savannas, the frequency of disturbance by fire may alter the top–down role of different herbivore species on plant community dynamics. In a seven year experiment in the Kruger National Park, South Africa, we examined the habitat use of nine common herbivore species across annually burned, triennially burned and unburned areas. We also used two types of exclosures (plus open access controls) to examine the impacts of different herbivores on plant community dynamics across fire disturbance regimes. Full exclosures excluded all herbivores > 0.5 kg (e.g. elephant, zebra, impala) while partial exclosures allowed access only to animals with shoulder heights ≤ 0.85 m (e.g. impala, steenbok). Annual burns attracted a diverse suite of herbivores, and exclusion of larger herbivores (e.g. elephant, zebra, wildebeest) increased plant abundance. When smaller species, mainly impala, were also excluded there were declines in plant diversity, likely mediated by a decline in open space available for colonization of uncommon plant species. Unburned areas attracted the least diverse suite of herbivores, dominated by impala. Here, herbivore exclusion, especially of impala, led to strong declines in plant richness and diversity. With no fire disturbance, herbivore exclusion led to competitive exclusion via increases in plant dominance and light limitation. In contrast, on triennial burns, herbivore exclusion had no effect on plant richness or diversity, potentially due to relatively little open space for colonization across exclosure treatments but also little competitive exclusion due to the intermediate fire disturbance. Further, the diverse suite of grazers and browsers on triennial burns may have had a compensating effect of on the diversity of grasses and forbs. Ultimately, our work shows that differential disturbance regimes can result in differential consumer pressure across a landscape and result in heterogeneous patterns in top–down control of community dynamics.

Data from: Selective plant foraging and the top-down suppression of native diversity in a restored prairie

Clarifying what species are being consumed at what times can improve our understanding of how anthropogenic change affects food web dynamics, with implications for community assembly including restoration. This includes human-based changes to plant communities via species introductions, which can interact with consumer feeding preferences to indirectly alter assembly outcomes including reduced restoration success if planted species are preferentially targeted. We used DNA barcoding of plant material in rodent scat, combined with field-based feeding trials, rodent trapping, and rodent exclosures to test for dietary preferences and assembly impacts of native rodents on a restored and regionally rare tallgrass prairie of central North America. We examined whether native rodents preferred non-targeted and mostly non-native oldfield plants that are more locally abundant, thus protecting the rarer native planted species from consumption, or if rodents preferred native plants regardless of abundance. Our results supported the latter outcome. Barcoding revealed that native rodents consumed mostly non-planted oldfield species for ten months of the year (92% of the diet). The exceptions were August–September, when planted prairie species accounted for 87% of plants consumed and coincided with their peak seed production. Cafeteria trials suggested diet seasonality to be explained by food limitation – native prairie seeds were consumed year-round when made available. Non-targeted oldfield species thus appeared to be of sufficient quality to support rodent populations (peaking at 23 individuals ha−1 in summer), but without rescuing rarer prairie species from targeted granivory and resulting in reduced prairie diversity outside of experimental exclosures. Synthesis and applications. Our work illustrates how anthropogenic-based changes to producer communities may affect feeding pathways in grassland food webs, potentially facilitating establishment by non-target species via indirect consumer effects that can be difficult to detect. These findings suggest that rodents may reduce the restoration success of tallgrass prairie in our region, with some planted species likely to suffer future recruitment difficulties due to granivory. Managers may need to consider multiple trophic levels with restoration, not just the commonly planted producer communities but also the consumers and predators associated with them.

Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning

1.Plant-soil feedback (PSF) has been identified as a key driver of local plant diversity and evenness in competitive communities. However, while it has been shown that spatial PSF heterogeneity can alter plant performance and competitive interactions, there is no proof of principle that spatial PSF heterogeneity enhances community diversity. 2.Using a grassland model system we separated two aspects of spatial heterogeneity: the number of species conditioning the soil and spatial distribution of the PSFs. 3.Our data show that PSFs promoted a higher plant evenness when the soil was conditioned by multiple species (mixed-conditioned), then when the soil was conditioned by a single species (mono-conditioned). On mono-conditioned soils, heterospecifics typically outperformed the focal species. In addition, there was a trend for increasing community evenness from uniform, via fine-grained to coarse-grained mixed-conditioned soils, but this was not significant. 4.On mixed-conditioned soils, performance of all competing species was intermediate to the best and the worst mono-conditioned soils, leading to higher community evenness. 5.Our data demonstrate that PSFs play a role in promoting plant evenness. Across mono-conditioned soils, PSF led to altered competitive hierarchies. However, on soils conditioned by multiple species, competitive ability among species was more similar and this led to higher plant evenness. The spatial distribution of the heterogeneity, on the other hand, did not significantly affect plant evenness. Our data therefore show that community evenness was more strongly related to the number of plant species that conditioned the soil than the spatial distribution of the PSF heterogeneity. Future studies need to investigate the importance of PSFs in the field across plant life-stages and multiple generations.

Data from: Does plant diversity increase top–down control of herbivorous insects in tropical forest?

Higher trophic level interactions are key mediators of ecosystem functioning in tropical forests. A rich body of theory has been developed to predict the effects of plant diversity on communities at higher trophic levels and the mechanisms underlying such effects. The 'enemies hypothesis' states that predators exert more effective top–down control of herbivorous insects with increasing plant diversity. Support for this hypothesis has been found in temperate forests and agroecosystems, but remains understudied in tropical forests. We compared incidence of attacks of different natural enemies using artificial caterpillars in a tropical forest landscape and investigated the role of plant community structure (i.e. species richness, composition and density), and the role of forest fragmentation (i.e. patch size, edge distance and canopy openness) on predation intensity. Plant community effects were tested with respect to three vegetation strata: trees, saplings and herbs. Observed predation was substantially due to ants. Predation rates increased with plant species richness for trees and herbs. Density of saplings, herb cover and herb species composition were important factors for predation. No significant patterns were found for fragmentation parameters, suggesting that forest fragmentation has not altered predation intensity. We conclude that in tropical forests, top–down control of herbivorous insects in the understory vegetation is affected by a combination of plant diversity, plant species composition and structural features of the plant community.

opencc-zeroDec 2018View details →

Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens

• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.

Data from: Plant, soil and microbial controls on grassland diversity restoration: a long-term, multi-site mesocosm experiment

The success of grassland biodiversity restoration schemes is determined by many factors; as such their outcomes can be unpredictable. There is a need for improved understanding of the relative importance of belowground factors to restoration success, such as contrasting soil type and management intensities, as well as plant community composition and order of assembly. We carried out an eight-year mesocosm experiment across three locations in the UK to explore the relative and interactive roles of various aboveground and belowground factors in the establishment of target species, to determine general constraints on grassland restoration. Each location had a series of mesocosms with contrasting soil types and management status, which were initially sown with six grasses typical of species-poor grasslands targeted for restoration. Over five years, sets of plant species were added, to test how different vegetation treatments, including early-coloniser species and the hemiparasite Rhinanthus minor, and soil type and management, influenced the establishment of target plant species and community diversity. The addition of early-coloniser species to model grasslands suppressed the establishment of target species, indicating a strong priority effect. Soil type was also an important factor, but effects varied considerably across locations. In the absence of early-coloniser species, low soil nutrient availability improved establishment of target species across locations, although R. minor had no beneficial effect. Synthesis and applications. Our long-term, multi-site study indicates that successful restoration of species rich grassland is dependent primarily on priority effects, especially in the form of early-coloniser species that suppress establishment of slow-growing target species. We also show that priority effects vary with soil conditions, being stronger in clay than sandy soils, and on soils of high nutrient availability. As such, our work emphasises the importance of considering priority effects and local soil conditions in developing management strategies for restoring plant species diversity in grassland.

opencc-zeroDec 2014View details →

Data from: Conserved gene expression programs in developing roots from diverse plants

The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.