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R_JAGS code for estimation and analysis of species-area-relationship (SAR) parameters from NEON (National Ecological Observatory Network) data on plant surveys

Invasive species science is heavily geared toward the invasive agent. However, management to protect native species also requires a proactive approach focused on understanding the features affecting community vulnerability to invasion impacts. Vulnerability is likely the result of factors acting across spatial scales, from local to regional, and it is the combined effects of these factors that will determine the magnitude of vulnerability. We introduce an analytical framework that quantifies the scale-dependent impact of biological invasions from the shape of the native species-area-relationship (SAR). We leverage newly available, biogeographically extensive vegetation data from the US National Ecological Observatory Network to assess plant community vulnerability to invasion impact as a function of factors acting across scales. We analyzed more than 1000 SARs widely distributed across the USA along environmental gradients and under different levels of invasion. Results show that a decrease in native richness is consistently associated with invasive species cover, but it is only at relatively high levels of invasion that native richness is compromised. After accounting for variation in baseline ecosystem diversity, net primary productivity, and human modification, ecoregions that are colder and wetter seem to be most vulnerable to losses of native plant species at the local level, while warmer and wetter areas seem most susceptible at the landscape level. We also document how the combined effects of cross-scale factors result in a heterogenous spatial pattern of vulnerability. This pattern cannot be predicted by analyses at any single scale, underscoring the importance of accounting for factors acting across scales. Simultaneously assessing differences in vulnerability between distinct plant communities at local, landscape and regional scales provided outputs that can be used to inform policy and management aimed at reducing vulnerability to the impact of plant invasions.

Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats

Species and their interactions are more dynamic over time and space in fragmented habitats than in continuous habitats. In fragmented habitats, the low nestedness of mutualistic networks may be related to the position change of stable (high persistence over time/space) species and interactions in the networks. Previous studies have shown that stable species and interactions tend to be in the core position of mutualistic networks. However, in fragmented habitats, it remains unknown whether stable species or interactions still tend to be in the core position. To address this gap, here we evaluated the correlation between the position of proximity to the network core and the temporal/spatial stability of species and interactions, using the observation of 42 plant-pollinator networks conducted in a fragmented island landscape over 3 years. We showed that temporally/spatially stable species and interactions deviated from the network core to varying degrees. Temporally stable plants were most likely to deviate from the network core, followed by pollinators and interactions, while only spatially stable pollinators tend to deviate from the network core. When unstable species (present in few time/space points, typically specialists) and interactions occupy the network core, they cannot interact with most species in the network as generalists do, resulting in the decrease of network nestedness. Therefore, from the perspective of position and stability, stable species and interactions deviate from the network core in fragmented habitats, which is an important reason for the decrease of nestedness in mutualistic networks. Our study suggests that protecting plants that occupy the core in large plant-pollinator networks is essential for maintaining the network persistence in fragmented habitats.

Fig. 4. A–J in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 4. A–J. Habitus of males of Ebenacobius Haran gen. nov. in lateral view (part 1). A. E. curvisetis Haran gen. et sp. nov. B. E. thoracicus Haran gen. et sp. nov. C. E. rectirostris Haran gen. et sp. nov. D. E. xhosa Haran gen. et sp. nov. E. E. duplicatus Haran gen. et sp. nov. F. E. san Haran gen. et sp. nov. G. E. grobbelaarae Haran gen. et sp. nov. H. E. kuscheli Haran gen. et sp. nov. I. E. costalis (Fåhraeus, 1844) gen. et comb. nov. J. E. mulanjensis Haran gen. et sp. nov. A–J = not to scale.

Fig. 8 in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 8. Best-fit ML tree of Ebenacobius Haran gen. nov. and Afrotropical Derelomini resulting from the partitioned analyses of the concatenated molecular dataset (the scale bar represents the estimated number of nucleotide substitutions per site). Support values (*) at nodes indicate SH-aLRT ≥ 80% and uBV ≥ 95% values, in that order.

Fig. 7 in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 7. Habitus in natura, host plants and habitats of Ebenacobius Haran gen. nov. A. Habitus of adult of E. rectirostris Haran gen. et sp. nov. B. Inflorescence of Euclea natalensis A.DC. (Ebenaceae), host of E. rectirostris. C. Biotope of E. rectirostris in the Mpumalanga Province of South Africa. D. Habitus of adult of E. san Haran gen. et sp. nov. E. Inflorescence of Euclea racemosa L. (Ebenaceae), host of E. san. F. Biotope of E. san in the Western Cape Province of South Africa.

Fig. 2. A–I in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 2. A–I. Habitus of males of Ebenacobius Haran gen. nov. in dorsal view (part 1). A. E. curvisetis Haran gen. et sp. nov. B. E. rectirostris Haran gen. et sp. nov. C. E. duplicatus Haran gen. et sp. nov. D. E. grobbelaarae Haran gen. et sp. nov. E. E. costalis (Fåhraeus, 1844) gen. et comb. nov. F. E. thoracicus Haran gen. et sp. nov. G. E. xhosa Haran gen. et sp. nov. H. E. san Haran gen. et sp. nov. I. E. kuscheli Haran gen. et sp. nov. Scale bars = 1 mm.

Fig. 5. A–H in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 5. A–H. Habitus of males of Ebenacobius Haran gen. nov. in lateral view (part 2). A. E. hessei Haran gen. et sp. nov. B. E. incognitus (Hesse, 1929) gen. et comb. nov. C. E. pedi Haran gen. et sp. nov. D. E. oberprieleri Haran gen. et sp. nov. E. E. tsonga Haran gen. et sp. nov. F. E. turneri (Marshall, 1935) gen. et comb. nov. G. E. hippopotamorum Haran gen. et sp. nov. H. E. rhodesianus (Hesse, 1929) gen. et comb. nov. A–H = not to scale.

Fig. 1 in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 1 (see preceding page). A–M. Details of morphology and measurements of Ebenacobius Haran gen. nov. and Derelomus Schoenherr, 1825. A. Ebenacobius rhodesianus (Hesse, 1929) gen. et comb. nov. in dorsal view, with the white arrows showing where the measurements of width (w) and length (L) are made for the prothorax (top) and elytra (bottom). Black arrow showing the narrowing of prothorax near apical margin. B. Head in lateral view of E. rhodesianus with white arrow showing the groove on forehead and the black arrow showing the convexity of the eyes, exceeding the lateral curve of head. C. Head and apex of prothorax in dorsal view of Derelomus chamaeropsis Fabricius, 1798 with the white arrow showing flat forehead, lacking groove and black arrow showing the constriction on the prothorax near apical margin. D. Detail of the top-left part of the right elytron in E. rhodesianus showing the white scales on interstriae and with the well aligned punctures at base of stria 1 highlighted in white. E. Detail of the top-left part of the right elytron in E. costalis (Fåhraeus, 1844) gen. et comb. nov. showing the setae on interstriae and with the misaligned punctures at base of stria 1 highlighted in white. F. Protibia of males of E. rhodesianus, showing the apical acute mucro and the ante-apical brush of setae. G. Head and prothorax of E. rhodesianus in lateral view with the arrows showing where measurements of rostrum and prothorax length are made. H. Right maxilla of E. rhodesianus in dorsal view. I. Penis of E. costalis in dorsal view showing were measurements are made for the body of penis (white arrows: width; top right black arrows: length) and the length of apodemes (bottom right black arrows). J. Stridulatory plate (tergite VII) in male of E. rhodesianus in dorsal view, with the cuticular tubercles used for stridulation highlighted in white. K–M. Female genitalia. K. Ovipositor in E. rhodesianus. L. Sternite VIII, same species. M. Spermatheca, same species. N. Right mandible, same species. O. Labial prementum, same species. A–O: not to scale.

Fig. 6 in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 6 (part 1). A–I. Male genitalia of Ebenacobius Haran gen. nov., penis in dorsal (left) and lateral (right) view.A. E. curvisetis Haran gen. et sp. nov. B. E. rectirostris Haran gen. et sp. nov. C. E. duplicatus Haran gen. et sp. nov. D. E. grobbelaarae Haran gen. et sp. nov. E. E. costalis (Fåhraeus, 1844) gen. et comb. nov. F. E. thoracicus Haran gen. et sp. nov. G. E. xhosa Haran gen. et sp. nov. H. E. san Haran gen. et sp. nov. I. E. kuscheli Haran gen. et sp. nov. A–I = not to scale.

Fig. 6 in Ebenacobius Haran, a new southern African genus of flower weevils (Coleoptera: Curculioninae: Derelomini) associated with dicotyledonous plants

Fig. 6 (part 2). J–R. Male genitalia of Ebenacobius Haran gen. nov.. penis in dorsal (left) and lateral (right) view. J. E. mulanjensis Haran gen. et sp. nov. K. E. hessei Haran gen. et sp. nov. L. E. pedi Haran gen. et sp. nov. M. E. tsonga Haran gen. et sp. nov. N. E. hippopotamorum Haran gen. et sp. nov. O. E. incognitus (Hesse, 1929) gen. et comb. nov. P. E. oberprieleri Haran gen. et sp. nov. Q. E. turneri (Marshall, 1935) gen. et comb. nov. R. E. rhodesianus (Hesse, 1929) gen. et comb. nov. J–R = not to scale.

Plant–insect interactions from the mid-Cretaceous at Puy-Puy (Aquitaine Basin, western France) indicates preferential herbivory for angiosperms amid a forest of ferns, gymnosperms, and angiosperms

The nine in-text figures and table below (Appendices S1–S10), and the additional text and excel files attached, provide the raw data, summaries of the raw data, rarefaction analyses, and nonmetric multidimensional scale analyses (NMDS) that support the discussions of the main text. The raw data and their summaries of provide for each plant species or morphotype values important for assessment of their herbivory: percentage of specimens herbivorized, damage type (DT) richness, DT frequency, DT host-plant specificity, herbivorized surface area as a proportion of total surface area, and feeding event occurrences. The rarefaction analyses furnished evaluations of whether the number of samples was sufficient, given the surface area covered by those samples. For comparison, the number of samples was rarified to the number of DTs in those samples. Lastly, two NMDS analyses produced the relationships between the plant orders present in the plant assemblage and their interactive functional feeding groups (FFGs). A separate NMDS analysis shows the association between the three most herbivorized species and their FFGs.

Stable Isotope Mixing Models Demonstrate the Role of an Invasive Plant in Wetland Songbirds Food Webs

We used analysis of natural abundance stable isotopes of 13C and 15N in song sparrow blood, invertebrate food sources, L. latifolium seeds, and other marsh plant seeds to inform Bayesian, concentration-dependent mixing models that predicted average song sparrow diets. Data presented are the csv files and R markdown code for the isotope analysis.

Data from: Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae —primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.

Data: Measuring plant attractiveness to pollinators: methods and considerations

Global pollinator declines have fostered increased public interest in creating pollinator-friendly gardens in human-managed landscapes. Indeed, studies on urban pollinator communities suggest that flower-rich greenspaces can serve as promising sites for conservation. Ornamental flowers, which are readily available at most commercial garden centers, are ubiquitous in these landscapes. These varieties are often non-native and highly bred, and their utility to pollinators is complex. In this study, we used observational data and citizen science to develop a methods framework that will assist stakeholders in the floriculture industry to incorporate metrics of pollinator health into existing breeding and evaluation protocols. The results of this study support how plant attractiveness to pollinators is often dependent on variables such as climate and plant phenology, which should be considered when developing an assessment tool. Furthermore, we found that some cultivars were consistently attractive across all observations while for other cultivars, pollinator visitation was apparently conditional. We determine using multiple statistical tests that 10 min is a sufficient length of time for observation of most plant types to broadly estimate three measures of plant attractiveness: visitor abundance, primary visitors attracted, and cultivar rank attractiveness, without sacrificing efficiency or accuracy. Additionally, we demonstrate that properly trained non-expert observers can collect accurate observational data, and our results suggest that protocols may be designed to maximize consistency across diverse data collectors.

Data from: Global plant ecology of tropical ultramafic ecosystems

This is a compiled geospatial dataset in ESRI polygon shapefile format of ultramafic soils of the neotropics showing the location of ultramafic soils in Guatemala, Cuba, Dominican Republic, Puerto Rico, Costa Rica, Colombia, Argentina, Chile, Venezuela, Ecuador, Brazil, Suriname, French Guiana, and Bolivia. The data are derived from seven geospatial datasets. Original datasets were subset to include only ultramafic areas, datasets were assigned a common projection (WGS84), attribute tables were reconciled to a common set of fields, and the datasets were combined. The dataset includes three components: 1) a geospatial dataset in ESRI polygon shapefile format of ultramafic soils of the neotropics showing the location of ultramafic soils in Guatemala, Cuba, Dominican Republic, Puerto Rico, Costa Rica, Colombia, Argentina, Chile, Venezuela, Ecuador, Brazil, Suriname, French Guiana, and Bolivia. 2) A regional-specific bibliography for all tropical ultramafic regions discussed in the original manuscript (Garnica-Diaz et al. 2022), and 3) an updated list in .csv format of major ultramafic outcrops worldwide including their latitude and longitude coordinates.

Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously, horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial dispersion of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that spatial structure moderated changes in AM fungal composition produced differential feedbacks on plant growth. Our results identify symbiont spatial structure within plant roots as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with cascading effects on plant communities.

Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations

The diversity of plant functional groups in plantations affects soil carbon, but we have limited understanding of the underlying mechanisms for how plant management affects soil carbon dynamics. Here, we conducted a 3-year manipulation experiment of plant functional groups that included understory removal, tree root trenching, and fertilization treatments in 2-year-old and 6-year-old Eucalyptus plantations in the subtropical region. The results showed that soil respiration was significantly suppressed by understory removal (-38%), tree root trenching (-41%), and their interactions (-54%), but that fertilization alone and in interactions had no significant effect. The Chao1 indices for soil bacterial and fungal diversity significantly decreased with understory removal in the 2-year-old plantation and with tree root trenching in the 6-year-old plantation. Soil bacterial and fungal communities were also affected by understory removal and tree root trenching. Soil respiration, physicochemical characteristics, microbial diversity, and community composition were significantly affected by plantation age. Reductions in soil carbon emissions were associated with reductions in plant functional groups and soil microbial groups, while increases in soil respiration were associated with soil physicochemical factors, soil temperature, and plantation age. Our findings highlight that plant managements are of great significance to the soil carbon emission processes in afforested plantations.

Microspines in tropical climbing plants: a small-scale fix for life in an obstacle course

This dataset is associated to the original research article "Microspines in tropical climbing plants: a small-scale fix for life in an obstacle course" published in the Journal of Experimental Botany.  <table> <tbody> <tr> <td>Variable</td> <td>Description</td> <td>Type of variable</td> <td>Units</td> </tr> <tr> <td>sample</td> <td>Sample identifiier</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>sp_code</td> <td>Species identifier</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>sp</td> <td>Species latin name</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>direction</td> <td>Friction test direction</td> <td>Categorical variable</td> <td> </td> </tr> <tr> <td>static_force</td> <td>Force needed to induce motion of the stem segment</td> <td>Continuous variable</td> <td>mN</td> </tr> <tr> <td>sliding_force</td> <td>Force needed to maintain the stem segment in motion</td> <td>Continuous variable</td> <td>mN</td> </tr> <tr> <td>sliding_dist</td> <td>Distance spanned by the stem segment during test</td> <td>Continuous variable</td> <td>mm</td> </tr> <tr> <td>nPeaks</td> <td>Number of force peaks detected during test</td> <td>Discrete variable</td> <td>mN</td> </tr> <tr> <td>peak_frequ</td> <td>Peak frequency during sliding (NPeaks/sliding_dist)</td> <td>Continuous variable</td> <td>peaks.mm-1</td> </tr> <tr> <td>diam</td> <td>Diameter of the tested segment</td> <td>Continuous variable</td> <td>mm</td> </tr> </tbody> </table>

Dataset of Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities

Data used in the article:  Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities Abstract 1- Climate models forecast changes in the amounts and distribution of rain, which may affect ecosystems worldwide, especially in drylands where water is already the limiting factor for plant life. Annual plant communities are common in drylands where they can complete their entire life cycle during the rainy period while avoiding the dry season. Moreover, seed dormancy allows them to disperse over time by remaining in the seed bank for long periods. However, the extent to which these communities will be able to tolerate increasing drought is uncertain. 2- We performed a five-year rainfall reduction treatment under field conditions and determined its effects on annual plant communities in a Mediterranean gypsum ecosystem. We assessed the taxonomic, functional, and phylogenetic diversity of these communities each year for five years. 3-The taxonomic and functional diversity decreased under the rainfall reduction treatment whereas the phylogenetic diversity increased. Moreover, the relative importance of species with drought-resistant functional designs increased in the community assemblages. However, after a rainy season with above average rainfall, all of the diversity values recovered completely even under the rainfall reduction treatment. 4- Our results provide important insights into the responses of these plant communities under a climate change scenario, where they indicate high losses of diversity during drought events but rapid recovery in milder years. Synthesis Our findings highlight the great resilience of annual plant communities in drylands, which may allow them to tolerate increased drought under the present climate change scenario.