The legacy of the extinct Neotropical megafauna on plants and biomes

Large mammal herbivores are important drivers of plant evolution and vegetation patterns, but the extent to which plant trait and ecosystem geography currently reflect the historical distribution of extinct megafauna is unknown. We address this question for South and Central America (Neotropical biogeographic realm) by compiling data on plant defence traits, climate, soil, and fire, as well as on the historical distribution of extinct megafauna and extant mammal herbivores. We show that historical mammal herbivory, especially by extinct megafauna, and soil fertility explain substantial variability in wood density, leaf size, spines and latex. We also identified three distinct regions (‘‘antiherbiomes’’), differing in plant defences, environmental conditions, and megafauna history. These patterns largely matched those observed in African ecosystems, where abundant megafauna still roams, and suggest that some ecoregions experienced savanna-to-forest shifts following megafauna extinctions. Here, we show that extinct megafauna left a significant imprint on current ecosystem biogeography.

Divergent Abiotic Stressors Drive Grassland Community Assembly of Tibet and Mongolia Plateau

Multiple ecological processes simultaneously govern community assembly, but it remains unclear how abiotic stressors regulate the relative importance of these processes among different biogeographic regions. Therefore, we conducted a comprehensive study on the responses of community assembly to varying environmental gradients, using the mean, variance, skewness, and kurtosis of plant height (height), specific leaf area (SLA) and leaf dry matter content (LDMC) distributions on the Tibetan Plateau (TP) and the Mongolian Plateau (MP). Our results showed that the prevalence of trait convergence across all grasslands in both TP and MP seem to be the result of abiotic filtering or weaker competitive exclusion etc. These trait-convergence assembly processes decrease the functional dispersion but increase the evenness of the trait frequency distribution. The mean, variance, skewness, and kurtosis responses of grassland communities to abiotic stress varied between the TP and MP. On average, plant trait distribution was mainly driven by temperature on the TP, and low-temperature stress altered the community assembly rules. In contrast, water availability shaped plant trait frequency distributions on the MP, and drought stress mediated the balance between different assembly processes. Our results provide empirical evidence that divergent abiotic stressors regulate the grassland community assembly on the TP and MP. Together, our study speculates that different aspects of future climate change, such as climate warming and changing precipitation patterns, on community assembly are dependent on regional climatic regimes.

Climatic and soil factors explain the two-dimensional spectrum of global plant trait variation

Plant functional traits can predict community assembly and ecosystem functioning and are thus widely used in global models of vegetation dynamics and land–climate feedbacks. Still, we lack a global understanding of how land and climate affect plant traits. A previous global analysis of six traits observed two main axes of variation: (1) size variation at the organ and plant level and (2) leaf economics balancing leaf persistence against plant growth potential. The orthogonality of these two axes suggests they are differently influenced by environmental drivers. We find that these axes persist in a global dataset of 17 traits across more than 20,000 species. We find a dominant joint effect of climate and soil on trait variation. Additional independent climate effects are also observed across most traits, whereas independent soil effects are almost exclusively observed for economics traits. Variation in size traits correlates well with a latitudinal gradient related to water or energy limitation. In contrast, variation in economics traits is better explained by interactions of climate with soil fertility. These findings have the potential to improve our understanding of biodiversity patterns and our predictions of climate change impacts on biogeochemical cycles.

Geometric and topological approaches to shape variation in Ginkgo leaves

Leaf shape is a key plant trait that varies enormously. The range of applications for data on this trait requires frequent methodological development so that researchers have an up-to-date toolkit with which to quantify leaf shape. We generated a dataset of 468 leaves produced by Ginkgo biloba , and 24 fossil leaves produced by evolutionary relatives of extant Ginkgo . We quantified the shape of each leaf by developing a geometric method based on elastic curves and a topological method based on persistent homology. Our geometric method indicates that shape variation in modern leaves is dominated by leaf size, furrow depth and the angle of the two lobes at the leaf base that is also related to leaf width. Our topological method indicates that shape variation in modern leaves is dominated by leaf size and furrow depth. We have applied both methods to modern and fossil material: the methods are complementary, identifying similar primary patterns of variation, but also revealing different aspects of morphological variation. Our topological approach distinguishes long-shoot leaves from short-shoot leaves, both methods indicate that leaf shape influences or is at least related to leaf area, and both could be applied in palaeoclimatic and evolutionary studies of leaf shape.

PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes

AbstractOver the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major deficiency, as they lack to develop marker sets that target only genes controlling a specific pathway or certain biological process. Herein, we present the PlantPathMarks database (PPMdb) as a comprehensive, web-based, user-friendly, and interactive hub for pathway-based markers in plant genomes. Based on our newly developed pathway gene set mining approach, two novel pathway-based marker systems called pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs) were developed as a novel class of annotation-based markers. In the PPMdb database, 2,690,742 pathway-based markers reflecting 9,894 marker panels were developed across 82 plant genomes. The markers include 691,555 PGTMs and 1,999,187 PMTMs. Across these genomes, 165,378 enzyme-coding genes were mapped against 126 KEGG reference pathway maps. PPMdb is furnished with three interactive visualization tools (Map Browse, JBrowse and Species Comparison) to visualize, map, and compare the developed markers over their KEGG reference pathway maps. All the stored marker panels can be freely downloaded. PPMdb promises to create a radical shift in the paradigm of the area of molecular marker research. The use of PPMdb as a mega-tool represents an impediment for non-bioinformatician plant scientists and breeders. PPMdb is freely available at http://ppmdb.easyomics.org.

Plant Trait Assembly in Species-Rich Forests at Varying Elevations in the Northwest Andes of Colombia

Andean forests are home to a strikingly high diversity of plants, making it difficult to understand the main drivers of species assembly. Trait-based approaches, however, help overcome some challenges associated with high taxonomic complexity, providing insights into the main drivers of species coexistence. Here, we evaluated the roles of climate, soil fertility, and symbiotic root associations on shaping the assembly of six plant functional traits (leaf area, specific leaf area, dry leaf matter content, leaf thickness, leaf toughness, and wood density) along an elevational gradient in the species-rich northwestern Andean forests of Colombia. The two main axes of the correspondence RLQ analysis explained 95.75% of the variability. The first axis was associated with the leaf economic spectrum, while the second axis with the tradeoff between growth and survival. Furthermore, the fourth corner method showed that both regional (climatic variables) and local factors (soil fertility, symbiotic root associations, and light distribution) played a key role in determining plant trait assembly. In summary, our study emphasizes the importance of considering both individual size and local factors to better understand drivers of plant trait assembly along environmental gradients.

AusTraits, a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

Global trade-offs in tree functional traits

Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. When considering trait relationships across the entire plant kingdom, plant trait frameworks typically must omit traits unique to large woody species, thereby limiting our understanding of how these distinct ecological pressures shape trait relationships in trees. Here, by considering 18 functional traits—reflecting leaf economics, wood structure, tree size, reproduction, and below-ground allocation—we quantify the major axes of variation governing trait expression of trees worldwide. We show that trait variation within and across angiosperms and gymnosperms is captured by two independent processes: one reflecting tree size and competition for light, the other reflecting leaf photosynthetic capacity and nutrient economies. By exploring multidimensional relationships across clusters of traits, we further identify a representative set of seven traits which captures the majority of variation in form and function in trees: maximum tree height, stem conduit diameter, specific leaf area, seed mass, bark thickness, root depth, and wood density. Collectively, this work informs future trait-based research into the functional biogeography of trees, and contributes to our fundamental understanding of the ecological and evolutionary controls on forest biodiversity and productivity worldwide.

Development of a Csy4-processed guide RNA delivery system with soybean-infecting virus ALSV for genome editing

Background A key issue for implementation of CRISPR-Cas9 genome editing for plant trait improvement and gene function analysis is to efficiently deliver the components, including guide RNAs (gRNAs) and Cas9, into plants. Plant virus-based gRNA delivery strategy has proven to be an important tool for genome editing. However, its application in soybean which is an important crop has not been reported yet. ALSV (apple latent spherical virus) is highly infectious virus and could be explored for delivering elements for genome editing. Results To develop a ALSV-based gRNA delivery system, the Cas9-based Csy4-processed ALSV Carry (CCAC) system was developed. In this system, we engineered the soybean-infecting ALSV to carry and deliver gRNA(s). The endoribonuclease Csy4 effectively releases gRNAs that function efficiently in Cas9-mediated genome editing. Genome editing of endogenous phytoene desaturase (PDS) loci and exogenous 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) sequence in Nicotiana. benthamiana (N. benthamiana) through CCAC was confirmed using Sanger sequencing. Furthermore, CCAC-induced mutagenesis in two soybean endogenous GW2 paralogs was detected. Conclusions With the aid of the CCAC system, the target-specific gRNA(s) can be easily manipulated and efficiently delivered into soybean plant cells by viral infection. This is the first virus-based gRNA delivery system for soybean for genome editing and can be used for gene function study and trait improvement.