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Alien invasive species are problematic both economically and ecologically, particularly on islands. As such, understanding how they interact with their environment is necessary to inform invasive species management. Here, we ask the following questions: What are the main functional traits that correlate with invasion success of alien plants on Robben Island? How does phylogenetic structure shape biotic interactions on the island? Using multiple approaches to explore these questions, we found that alien invasive species flower later during the year and for longer period, although flowering phenology was sensitive to alternative starting date. Additionally, we observed that alien invasive species are mostly abiotically pollinated and are generally hermaphroditic whilst their native counterparts rely on biotic pollinators, flower earlier, and are generally dioecious, suggesting that alien invasive and native species use different ecological niches. Furthermore, we found a facilitative interaction between an alien invasive legume and other invasive plants as predicted by the invasional meltdown hypothesis, but this does not influence the phylogenetic structure of plant communities. Finally, phylogenetically diverse set of native species are less receptive to alien invasive species. Collectively, our findings reveal how biotic interactions and phylogenetic relatedness structure alien invasive – native co-existence. [ABSTRACT FROM AUTHOR]

Aizoaceae is the largest succulent plant family in the world, including in excess of 1800 species. Despite its richness, a large proportion of its taxa are listed as data deficient and as such, has been identified as the top priority for taxonomic research in South Africa. Limitations to accurate taxonomic identification of taxa in the family may be partly attributed to the degree of technical knowledge required to identify taxa in the Aizoaceae. DNA barcoding may provide an alternative method of identification; however, the suitability of commonly used gene regions has not been tested in the family. Here, we analyse variable and parsimony informative characters (PIC), as well as the barcoding gap, in commonly used plastid regions (atpB-rbcL, matK, psbA-trnH, psbJ-petA, rpl16, rps16, trnD-trnT, trnL-trnF, trnQ-rps16, and trnS-trnG) and the nuclear region ITS (for Aizooideae only) across two subfamilies and two expanded clades within the Aizoaceae. The relative percentage of PIC was much greater in subfamilies Aizooideae and Mesembryanthemoideae than in Ruschioideae. Although nrITS had the highest percentage of PIC, barcoding gap analyses identified neither ITS nor any chloroplast region as suitable for barcoding of the family. From the results, it is evident that novel barcoding regions need to be explored within the Aizoaceae. [ABSTRACT FROM AUTHOR]

Senegalia is a genus of the legume family (Leguminosae: Mimosoideae) that has a pantropical distribution with centers of diversity in Brazil, Mexico and southern Africa. The genus is characterized by plants having bipinnate leaves, presence of petiolar nectaries, prickles on the branches, and pollen grains arranged in polyads with 16 grains. Morphology is an important tool for identification of Senegalia species, but it is not sufficient to resolve all taxonomic issues and elucidate the evolutionary history of this genus. Prior molecular analyses of Mimosoideae have lacked breadth of samplingwithin Senegalia, leavingmany relationships uncertain, particularly the relationship among Brazilian species and other members of the genus. The aim of this study was to identify Senegalia s. s. lineages that contain Brazilian species, and to investigate the relationship of these species with non-Brazilian Senegalia species. We present the first comprehensively sampled phylogeny of American and African Senegalia, however Asian species are not sampled.We sequenced four plastid and one nuclear DNA (ITS) regions for 125 samples of 59 Senegalia and one Parasenegalia species. Both Bayesian andmaximum likelihood analyses were performed.Neither the American or African species form monophyletic lineages. The lack of monophyly of these groups suggests a more complicated evolutionary history of the genus than previously considered, including probable transatlantic dispersal events. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discuss various reports within the special issue on topics including the DNA barcoding, detection of invasive species, and species interactions in food webs.

Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils. [ABSTRACT FROM AUTHOR]

Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications. [ABSTRACT FROM AUTHOR]

Game parks are the last preserve of many large mammals, and in savanna ecosystems, management of surface waters poses a conservation challenge. In arid and semi-arid regions, water can be a scarce resource during dry seasons and drought. Artificial waterholes are common in parks and reserves across Africa, but can alter mammal community composition by favoring drought intolerant species, with consequences for disease dynamics, and population viability of drought-tolerant species. Analysis of waterborne environmental DNA (eDNA) is increasingly used to inform conservation of rare and invasive species, and conduct large-scale biodiversity assessments. To explore the reliability of eDNA as an indicator of mammal waterhole use in savannas, we compare eDNA metabarcoding and camera traps for documenting artificial waterhole use in the Kruger National Park, South Africa, a global hotspot for mammal diversity. We show that eDNA metabarcoding can recover the majority of mammal species detected by camera traps, including a number of endangered species, but DNA signatures of mammal visitation are temporally limited, with best performance when tracking water-dependent large bodied mammals visiting within two days of sampling. Our results highlight limitation of eDNA based monitoring in these systems, including the lack of long-term eDNA persistence in small and highly utilized waterholes, and variability in detection rates among species. However, we demonstrate that eDNA-based approaches can be used to track mammals of conservation concern, and reflect patterns of recent waterhole use and co-occurrence across water-dependent species, both of which are crucial for making evidence-based decisions regarding water management and provisioning. [ABSTRACT FROM AUTHOR]

Invasive species are detrimental ecologically and economically. Their negative impacts in Africa are extensive and call for a renewed commitment to better understand the correlates of invasion success., Here, we explored several putative drivers of species invasion among woody non-native trees and shrubs in southern Africa, a region of high floristic diversity. We tested for differences in functional traits between plant categories using a combination of phylogenetic independent contrasts and a simulation-based phylogenetic anova., We found that non-native species generally have longer flowering duration compared with native species and are generally hermaphroditic, and their dispersal is mostly abiotically mediated. We also revealed that non-native trees and shrubs that have become invasive are less closely related to native trees and shrubs than their non-invasive non-native counterparts. Non-natives that are more closely related to the native species pool may be more likely to possess traits suited to the new environment in which they find themselves and thus have greater chance of establishment. However, successful invaders are less closely related to the native pool, indicating evidence for competitive release or support for the vacant niche theory., Synthesis. Non-native trees and shrubs in southern Africa are characterized by a suite of traits, including long flowering times, a hermaphroditic sexual system and abiotic dispersal, which may represent important adaptations promoting establishment. We suggest that differences in the evolutionary distances separating the native species pool from invasive and non-invasive species might help resolve Darwin's naturalization conundrum. [ABSTRACT FROM AUTHOR]

The article discusses a study which derived a phylogenetic classification for subfamily Alooideae for the species of Asphodelaceae plant. The assessment of the species involved an examination of monophyletic lineages and recognition of several genera including Aloe, Astroloba, and Gasteria. The research cited various traits in the traditional diagnosis of the Alooideae genera such as floral characters, size, symmetry, shape, phytochemistry, and nectar sugar composition.

There has been much debate on the impact of large herbivores on biodiversity, especially given that large mammals are becoming locally extinct in many places., The use of evolutionary information on community structure has typically been limited to evaluating assembly processes, for example, competition or habitat filtering, whereas a lack of long-term experiments has precluded the test of predictions considering more complex biotic interactions., Reconstructing the complete phylogeny of the trees and shrubs of the Kruger National Park from DNA data, we tested for phylogenetic signal in antiherbivory traits and compared the phylogenetic structure of communities under various degrees of herbivore pressure using experimental plots spanning several decades., We show that all antiherbivory traits examined demonstrated weak but significant phylogenetic signal, and that exclusion of large herbivores results in impoverished species diversity in restructured communities. Surprisingly, we also show that reduction in species diversity coupled with community reorganization does not necessarily result in a decrease in phylogenetic diversity, and that community responses to herbivore exclusion depend on initial structure., Synthesis. Extinction of large mammal herbivores will have cascading effects on plant diversity; however, impacts on plant community structure are contingent on initial conditions. This research has implications for best practice when managing large herbivores and natural habitats. [ABSTRACT FROM AUTHOR]

This article presents a study regarding the systematic position of the genus Cadia and the phylogeny of the tribe Podalyrieae. Cadia is an anomalous genus in Papilionoideae that consists of seven species and tribe Podalyrieae is a group of papilionoid legumes that are largely endemic to the Cape Floristic Region of South Africa.

Analysis of plastid rbcL DNA sequence data of the pantropical family Phyllanthaceae (Malpighiales) and related biovulate lineages of Euphorbiaceae sensu lato is presented. Sampling for this study includes representatives of ali 10 tribes and 51 of the 60 genera attributed to Euphorbiaceae-Phyllanthoideae. Centroplacus and Putranjivaceae (Phyllanthoideae-Drypeteae) containing a paraphyletic Drypetes are excluded from Phyllanthaceae. Croizatia, previously thought to be a "basal" member of Euphorbiaceae-Oldfieldioideae (Picrodendraceae), falls within Phyllanthaceae. Phyllanthaceae with the mentioned adjustments form a monophyletic group consisting of two sister clades that mostly correspond to the distribution of tanniniferous leaf epidermal cells and inflorescence structure. With the exception of bigeneric Hymenocardieae and monotypic Bischofleae, none of the current Phyllanthoideae (Phyllanthaceae) tribal circumscriptions are supported by rbcL. Antidesma, Bischofia, Hymenocardia, Martretia, and Uapaca, all of which have previously been placed in monogeneric families, are confirmed as members of Phyllanthaceae. Savia is polyphyletic, and Cleistanthus appears paraphyletic. Paraphyly of Phyllanthus is also indicated, but this pattern lacks bootstrap support. Morphological characters are discussed and mapped for inflorescence structure, tanniniferous epidermal cells, breeding system, and fruit and embryo type. A table summarizes the main characters of six euphorbiaceous lineages. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discusses various reports within the issue on topics including biodiversity, DNA barcoding and molecular wildlife forensics.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions 1,2 . To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores 3 . The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms 4,5 ., (© 2024. The Author(s).)

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m 3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition., (© 2024. The Author(s).)

Background: Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades., Results: Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation., Conclusions: We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants., (© 2021. The Author(s).)

Ideas on hominin evolution have long invoked the emergence from forests into open habitats as generating selection for traits such as bipedalism and dietary shifts. Though controversial, the savanna hypothesis continues to motivate research into the palaeo-environments of Africa. Reconstruction of these ancient environments has depended heavily on carbon isotopic analysis of fossil bones and palaeosols. The sparsity of the fossil record, however, imposes a limit to the strength of inference that can be drawn from such data. Time-calibrated phylogenies offer an additional tool for dating the spread of savanna habitat. Here, using the evolutionary ages of African savanna trees, we suggest an initial tropical or subtropical expansion of savanna between 10 and 15 Ma, which then extended to higher latitudes, reaching southern Africa ca. 3 Ma. Our phylogenetic estimates of the origin and latitudinal spread of savannas broadly correspond with isotopic age estimates and encompass the entire hominin fossil record. Our results are consistent with the savanna hypothesis of early hominin evolution and reignite the debate on the drivers of savanna expansion. Our analysis demonstrates the utility of phylogenetic proxies for dating major ecological transitions in geological time, especially in regions where fossils are rare or absent or occur in discontinuous sediments.

Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.

Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'., (© 2016 The Authors.)

DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a "DNA barcoding gap" is present between intra- and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.