Plant Phylogeny Research Articles

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

BackgroundThe chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation.ResultsAnalysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes.ConclusionThis study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

The Evolutionary Ecology of Plant Chemical Defenses: From Molecules to Communities

Classic theory relates herbivore pressure to the ecology and evolution of plant defenses. Here, we summarize current trends in the study of plant–herbivore interactions and how they shape the evolution of plant chemical defenses, host choice, and community composition and diversity. Inter- and intraspecific variation in defense investment is driven by resource availability. The evolution of defenses at deeper nodes of plant phylogeny is conserved, yet defenses are highly labile at the tips. On an ecological timescale, while greater specialization of tropical herbivores enhances local diversity by reducing the performance of plants with similar defenses, in temperate ecosystems with more generalist herbivores, rare defense profiles are at a disadvantage. On an evolutionary timescale, host choice by herbivores is largely determined by plant defenses rather than host phylogeny, leading to evolutionary tracking by herbivores rather than cocladogenesis. The interplay between plants and herbivores shapes both the origin and maintenance of diversity.

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Neophytes may promote hybridization and adaptations to a changing planet.

Human activities erode geographic barriers, facilitating hybridization among previously isolated taxa. However, limited empirical research exists on the consequences of introduced species (neophytes) for hybridization and subsequent evolutionary outcomes. To address this knowledge gap, we employed a macroecological approach. First, we examined the spatial and phylogenetic overlap between neophytes and hybrids by integrating the Plants of the World Online database with the Global Naturalized Alien Flora database. Second, leveraging the largest dated plant phylogeny available, we compared diversification rates between genera containing hybrids and neophytes versus those without. Third, focusing on the extensively studied hybrid flora of Britain, we studied the spatial distributions of hybrids in relation to neophyte and native parents, assessing potential adaptations to anthropogenic disturbances and impacts on native species. Overall, our findings highlight positive ties between contemporary biodiversity redistribution and hybridization. Spatially (across countries) and phylogenetically (across genera), neophyte incidence was positively associated with hybrid incidence. Genera comprising both hybrids and neophytes displayed significantly higher diversification rates. Neophyte hybrids primarily occupied areas with a higher human footprint, with limited evidence of hybrids threatening native species throughout their range in more natural habitats. These results challenge the notion that species naturalizations and hybridizations exclusively yield negative outcomes for biodiversity. While it is conceivable that anthropogenic hybridization may facilitate recombination of genetic variation and contribute to conserving genetic diversity in disturbed environments, further research is needed to fully understand these processes.

A symbiotic footprint in the plant root microbiome

BackgroundA major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure.ResultsWe grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts.ConclusionOur results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome – which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.

Plant phylogeny determines host selection and acceptance of the oligophagous leaf beetle Cassida rubiginosa.

Predicting the host range of biocontrol agents is important for the safe and effective implementation of biocontrol of weeds. In this study, we examined the phylogenetic pattern of host selection and acceptance by the biocontrol beetle, Cassida rubiginosa. The beetle was released in New Zealand for control of Cirsium arvense, its primary host plant, but has potential to attack many Cardueae (thistles and knapweeds) species. We conducted a series of no-choice and choice experiments and modelled the responses of Cassida rubiginosa in relation to phylogenetic distance from Cirsium arvense. The olfactory recognition (single odour) and preference (two odours) of the beetle showed a significant phylogenetic relationship. These relationships showed a high degree of correlation with 66.9% of the variation in olfactory recognition and 82.8% of the variation in olfactory preference explained by phylogeny. Where the beetle could contact plants, under no-choice conditions there was no phylogenetic pattern to host plant acceptance. However, under choice conditions, phylogenetic distance was a strong predictor of feeding and oviposition preference. These relationships showed a high degree of correlation, with 63.4% of the variation in feeding preference, and 89.0% of the variation in oviposition preference, explained by phylogeny. As far as we are aware, this is the first demonstration of an herbivorous insect that exhibits a phylogenetic pattern to olfactory host plant selection. Host plant utilisation by Cassida rubiginosa in New Zealand will be mostly restricted to Cirsium and Carduus species, with minimal potential for impact on other Cardueae weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Expansion processes of two emblematic Luehdorfia butterflies across the Japanese archipelago

AbstractAimAdaptation to local environments has been considered a driving force of ecological speciation. Previous phylogenetic studies at higher taxonomic levels have strongly suggested that herbivore diversification occurs through local adaptation to host plants. However, whether similar mechanisms contribute to within‐species diversification remains poorly understood. We reconstructed species expansion processes using the phylogenetic relationships between two Luehdorfia butterflies and their host plants and tested the local adaptation hypothesis during species diversification.LocationJapanese archipelago.TaxaLuehdorfia japonica and L. puziloi.MethodsWe analysed mitochondrial DNA and single‐nucleotide polymorphisms to trace the expansion processes of two species in the Japanese archipelago. We analysed data collected during trans‐host plant feeding experiments to test for local host plant adaptation in L. japonica.ResultsLuehdorfia japonica differentiated 17.0 million years ago (MYA) from a group of four Luehdorfia species in East Asia, and L. puziloi differentiated 13.3 MYA from the remaining three species. We observed several genetic groups in both species, reflecting geographical differences among populations. Some host plants had detrimental effects on the pupation rates of L. japonica, demonstrating the presence of genetic barriers between populations of this species.Main ConclusionsAlthough these two sibling species were influenced by the geological formation of the Japanese archipelago, their present population structures differ greatly: L. japonica expanded its distribution and adapted to local host plants along at least four expansion routes independent of host plant phylogeny, and L. puziloi exhibited a more isolated population structure and was less strongly influenced by gene flow among populations. These results suggest that both isolation by distance and isolation by adaptation have been important drivers resulting in the present‐day population structure of L. japonica. Unidirectional gene flow through local adaptation to the host plant may have played a role in initial speciation.

Palynotaxonomical study of honeybees (Apis mellifera var. adansonii) forage and/or preference plants in South-Western Nigeria

The disputed issues of higher plant taxonomy and phylogeny are greatly impacted by pollen morphology because pollen grains have clear distinctive characteristics that are typically labeled. Palynotaxonomical study of Honeybees preference plants in South-Western Nigeria were conducted between the months of May, 2019 and June 2021 using fresh polleniferous materials which were extracted through acetolysis methods. Results showed that ninety-two (92) plant species belonging to thirty-six (36) plant families of apicultural importance most visited by honeybees (Apis mellifera var. adansonii) were documented. At x100 magnification, thorough morphological studies were performed, and the results showed that pollen grains from plant species in the family Asteraceae were spinolous and spherical in shape; those from the Fabaceae sub-families Caesalpinoideae, Mimosoideae, and Papilionoideae, on the other hand, had a great deal of morphological diversity with variations in symmetry, position and distribution. Those of the families Malvaceae was echinate and Myrtaceae were colporate; syncolpate and prolate respectively. However, the variations above were generally reduced within species in the same genera. Tricolpate aperture type was observed in the genus Euphorbia; giving reason for their classification in the same genera. The genus Combretum was all heterocolpate, circular in shape and heteroporate. Sculpturing was psilate or scabrate and pollen shape class were sub-prolate, oblate-spheroidal or prolate spheroidal. Similar form and symmetry observed in all the species studied were reason for their classification into the same family. The study revealed that the flowering period for most of these honeybees’ forage plants were between the months of October to March. Identification, propagation, cultivation, conservation, and sustainable exploitation of these honeybee (Apis mellifera var. adansonii) forage and preference plants would be beneficial in potentially increasing the efficiency of apiculture and commercial cultivation in South-Western Nigeria.

Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)

BackgroundThe Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade.ResultsThese 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599–31,486 bp) separated by a large single-copy region (LSC: 82,048–94,046 bp) and a small single-copy region (SSC: 16,343–17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL–accD, ycf4–cemA, petA–psbJ, ycf1–ndhF, ndhF–rpl32 and ycf1, and it was found that ndhF–rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes.ConclusionThe Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF–rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber.

Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China.

Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long-term selection pressures.

Taxonomic Confirmation of Rare Fruits in West Kalimantan Using rbcL and matK Sequences

Phylogenetic analysis for plants can be very helpful in determining species identification or taxonomic status morphologically. rbcL and matK are widely used as genetic markers in constructing seed plant phylogenies. Different identification and new collection during the re-inventory from the previous study were found in two and four types of rare fruits in Sibohe Forest, West Kalimantan. The six types include pisang karok (Musa sp.) and Kandis (Garcinia sp.), as well as nubik (Artocarpus sp.), tehengan (Artocarpus sp.), smallest arok (Ficus sp.), and amok (Alpinia sp.). This study aimed to analyze the phenetic relationship of six rare fruits from Kalimantan based on rbcL and matK genes. DNA samples were obtained from dried body parts of the previous study and amplified by PCR using both forward and reverse primers for rbcL and matK genes. Amplification was observed on electrophoresis gel for rbcL gene of nubik, tehengan, smallest arok, amok, and pisang karok, while only pisang karok in matK gene. However, matK gene sequence was also obtained for amok even though the band was not seen on the gel. Phylogenetic analysis using the two genes confirmed the morphological identification reported in the previous study; however, using matK as a single gene for taxonomic confirmation must be reconsidered. The information of rbcL and matK sequences of six rare fruits from West Kalimantan could be the first information for building the DNA barcodes of the rare fruits in West Kalimantan.

Deep reticulation: the long legacy of hybridization in vascular plant evolution.

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.

Nitrogen use strategy drives interspecific differences in plant photosynthetic CO2 acclimation.

Rising atmospheric CO2 concentration triggers an emergent phenomenon called plant photosynthetic acclimation to elevated CO2 (PAC). PAC is often characterized by a reduction in leaf photosynthetic capacity (Asat ), which varies dramatically along the continuum of plant phylogeny. However, it remains unclear whether the mechanisms responsible for PAC are also different across plant phylogeny, especially between gymnosperms and angiosperms. Here, by compiling a dataset of 73 species, we found that although leaf Asat increased significantly from gymnosperms to angiosperms, there was no phylogenetic signal in the PAC magnitude along the phylogenetic continuum. Physio-morphologically, leaf nitrogen concentration (Nm ), photosynthetic nitrogen-use efficiency (PNUE), and leaf mass per area (LMA) dominated PAC for 36, 29, and 8 species, respectively. However, there was no apparent difference in PAC mechanisms across major evolutionary clades, with 75% of gymnosperms and 92% of angiosperms regulated by the combination of Nm and PNUE. There was a trade-off between Nm and PNUE in driving PAC across species, and PNUE dominated the long-term changes and inter-specific differences in Asat under elevated CO2 . These findings indicate that nitrogen-use strategy drives the acclimation of leaf photosynthetic capacity to elevated CO2 across terrestrial plant species.

Pinellia genus: A systematic review of active ingredients, pharmacological effects and action mechanism, toxicological evaluation, and multi-omics application

The dried tuber of Pinellia ternata (Thunb.) Breit, Pinelliae Rhizoma (PR, also named ‘Banxia’ in Chinese), is widely used in traditional medicine. This review aims to provide detail summary of active ingredients, pharmacological effects, toxic ingredients, detoxification strategies, and omic researches, etc. Pharmacological ingredients from PR are mainly classified into six categories: alkaloids, amino acids, polysaccharides, phenylpropanoids, essential oils, and glucocerebrosides. Diversity of chemical composition determines the broad-spectrum efficacy and gives a foundation for the comprehensive utilization of P. ternata germplasm resources. The pharmacological compounds are involved in inhibition of cancer cells by targeting various pathways, including activation of immune system, inhibition of proliferation and cycle, induction of apoptosis, and inhibition of angiogenesis. The pharmacological components of PR act on nervous system by targeting neurotransmitters, activating immune system, decreasing apoptosis, and increasing redox system. Lectins, one major class of the toxic ingredients extracted from raw PR, possess significant toxic effects on human cells. Inflammatory factors, cytochrome P450 proteins (CYP) family enzymes, mammalian target of rapamycin (mTOR) signaling factors, transforming growth factor-β (TGF-β) signaling factors, and nervous system, are considered to be the target sites of lectins. Recently, omic analysis is widely applied in Pinellia genus studies. Plastome genome-based molecular markers are deeply used for identifying and resolving phylogeny of Pinellia genus plants. Various omic works revealed and functional identified a series of environmental stress responsive factors and active component biosynthesis-related genes. Our review summarizes the recent progress in active and toxic ingredient evaluation, pharmacological effects, detoxification strategies, and functional gene identification and accelerates efficient utilization of this traditional herb.

The “Plant Phylogeny Posters” (PPP) – Useful Tools for Scientific Research and Education

Wall charts and posters depicting plant structure and evolutionary relationships as phylogenetic trees have been important teaching tools for many decades. With the development of digital technologies, new approaches to the traditional concept have become possible. The article briefly discusses the history, development and significance of the “Plant Phylogeny Posters” project. This project is a joint work of a growing team of more than 200 specialists from more than 50 nations from all around the world. The portfolio currently consists of nearly 600 posters in 54 poster titles and in 45 languages (as of early 2023). All posters are freely available on the Internet and are regularly updated.

Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem.

Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant-epiphyte and plant-endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant-endophyte network, plant-epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.

What drives phylogenetic and trait clustering on islands?

Environmental filtering is an important assembly process that structures plant communities and is commonly inferred from taxonomic, functional trait and phylogenetic patterns. However, while these approaches can be informative, the influence of other co-occurring processes on community diversity, such as competitive exclusion, remains poorly understood. By combing functional traits and a phylogeny of woody plants across anthropogenically created islands, we aim to explore the ways in which environmental filtering and competitive exclusion can simultaneously influence community assembly processes. We expect that communities on smaller islands, where competition for limited space and resources is more intense, should be functionally and phylogenetically less clustered than those on larger islands because this more intense competition should reduce the coexistence of the most closely related or functionally similar species. We used ten functional traits and a phylogeny of 76 woody plant species to assess species diversity and similarity within communities across an island area gradient. We combed functional traits and phylogeny into a functional–phylogenetic distance matrix and calculated the communities’ mean functional-phylogenetic distance (MFPD) and its standardized effect size (SES.MFPD) as measures of ecological similarity. As expected, species were more phylo-functionally similar to one another than expected by chance within islands and this underdispersion grew stronger with island area, indicating that while islands generally contained clustered communities, environmental filtering and competitive exclusion were both likely occurring. By integrating species abundance distributions with community similarity, we found that the most abundant species were phylo-functionally similar to the least abundant species. Species richness increased with island area, as expected, but the additional species found only on larger islands tended to have low abundances, providing opportunities for rare species to persist. With environmental filtering narrowing the number of species that can persist, the loss of phylo-functionally closely related rare species on smaller islands was likely caused by competition or stochastic removals, leading to greater species dissimilarity than on larger islands. On larger islands, the clustered patterns are likely to be the result of a combination of competitive exclusion caused by resource limitation and environmental filtering.

Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases

Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features “signature selections” of ca. 20–30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into “families”, comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked “fossil” introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.

Host plant phylogeny does not fully explain host choice and feeding preferences of Galerucella birmanica, a promising biological control herbivore of Trapa natans

The leaf-beetle Galerucella birmanica is a potential biocontrol herbivore for water chestnut, Trapa natans in North America. During our assessments of effectiveness and safety of G. birmanica in quarantine, we found a narrow fundamental host range with complete development only possible on all T. natans morphospecies present in North America and Brasenia schreberi. Phylogenetic relatedness did not fully explain feeding and oviposition preferences of G. birmanica in no-choice or multiple-choice trials. Instead, feeding and oviposition on non-target plants appears better explained by host-associations of congeneric Galerucella species, underscoring the importance of including additional factors in selecting host-specificity test plant species. To further gauge potential risk to B. schreberi, we used a comparative performance metric proposed by Paynter et al. (2015) and found G. birmanica scored low, further indicating low risk to B. schreberi. Our findings suggest that widespread and safe biocontrol of T. natans in North America appears promising if G. birmanica is granted release approval by regulatory agencies.