Premise

Pandanus Parkinson (Pandanaceae) is a large genus of paleotropical tree‐like monocots. Previous studies using small DNA regions questioned the monophyly of the seven Pandanus subgenera, but low phylogenetic branch support hindered further investigations. We aimed to (1) test Pandanus subgeneric monophyly, (2) identify clade morphological synapomorphies, (3) investigate correlations between leaf anatomy of water storage tissue and climatic differentiation across clades, and (4) construct hypotheses on the genus' spatiotemporal history.

Speciation processes in plants can be difficult to evaluate, but are essential to understanding evolutionary processes that lead to diversification. Determining the juncture at which a genetically and/or morphologically divergent population can be reliably considered a separate species is often challenging. This is particularly so with respect to recent divergences amongst closely related taxa wherein factors such as incomplete lineage sorting may yield confounding results. Taxa in the Cymopterus terebinthinus (Apiaceae) species complex have long puzzled botanists. Named entities in this group display similar, yet apparently distinct morphologies that have been classified as varieties under various generic names highlighting long‐standing nomenclatural instability. Previous phylogenetic studies have challenged the monophyly of this complex. This study aims to clarify taxonomic boundaries and infer evolutionary relationships among the four C. terebinthinus varieties and C. petraeus by applying phylogenetic inference and incorporating ecological, morphological, and geographical evidence. We sampled from populations of all varieties of C. terebinthinus and C. petraeus for target capture with the Angiosperms353 bait kit. We performed phylogenetic analyses with maximum likelihood (RAxML and IQ‐TREE) and coalescent‐based phylogenetic analysis (ASTRAL). We also conducted principal component analysis of soil samples and climatic variables. We find that C. terebinthinus and its varietal infrataxa comprise a monophyletic clade that includes C. petraeus. Clade groupings correspond to previous taxonomic assignments and morphology. Clades are often closely associated with geographical variables and at times correlated with ecological variables. Exceptions to this are here attributed to various evolutionary factors that often confound other phylogenetic analyses such as incomplete lineage sorting, introgression, and paralogous loci. Our findings suggests that geographical factors might play a major role in genetic and morphological differentiation in this complex. Despite finding well‐supported clades that correspond to defined morphological characters; further sampling among C. petraeus populations is required to make taxonomic decisions.

Leaf traits are crucial to seedling growth and survival, and their plasticity can influence seedling fitness in changing environments. Seedlings of Artemisia tridentata, a keystone shrub of the western North American sagebrush steppe, show heteromorphic leaf development. Early leaves are larger and less pubescent than those produced later, suggesting a shift from characteristics favouring rapid growth to those increasing drought tolerance. To investigate this hypothesis, we determined the specific leaf area (SLA) and the osmotic potential at full turgor (π0) of early and late leaves, and measured their stomatal conductance and photosynthetic rates as leaf water potential (Ψl) declined under imposed drought. We also examined whether water stress could trigger late leaf development. At high Ψl and per area, early and late leaves had similar photosynthetic rates. However, the SLA of early leaves was three times higher than that of late leaves, yielding higher photosynthetic rates per unit mass in the former. Late leaves had lower π0 and were less sensitive to drought, exhibiting a lower Ψl at 50% of maximum photosynthesis than early leaves. Drought triggered the shedding of early leaves and the initiation of late-like leaves. Formation of these leaves continued upon return to well-watered conditions, possibly indicating stress memory. The overall results suggest that early leaves enhance growth during wet springs following germination, while late leaves prolong photosynthesis as water potentials decline during summer drought. The adaptive value of early leaves may be diminishing due to changing environmental conditions that are accelerating the onset of drought.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Pandanus ramromensis Callm., Y.W.Low & Buerki (Pandanaceae) from the summit of Khao Ram Rome (Nakhon Si Thammarat Province) in Peninsular Thailand is described here. The new species resembles Pandanus kedahensis H.St.John in its ecology and habit but differs by the dimensions of its leaves, leaf shape, syncarps and styles. The new species is provided with line drawings and field photographs, and is assigned a preliminary conservation status of Vulnerable (VU) using the IUCN Red List criteria.

In memory of Dr. Christopher Davidson

Abstract

Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf‐level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush (Artemisia tridentata), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to (1) determine whether leaf‐level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies‐cytotype relate to leaf‐level temperature. When considered across the whole season, stomatal conductance was negatively, non‐linearly correlated with crown‐level temperature derived from UAS. Subspecies identity best explained crown‐level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf‐level temperature. These results show how fine‐scale thermal mapping can decouple the contribution of genetic, phenotypic, and microclimate factors on leaf temperature dynamics. As climate‐change‐induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene‐by‐environment interactions.

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Abstract

Western North America has been experiencing persistent drought exacerbated by climate change for over two decades. This extreme climate event is a clear threat to native plant communities. Artemisia tridentata is a keystone shrub species in western North America and is threatened by climate change, urbanization, and wildfire. A drought Genotype × Environment (G × E) experiment was conducted to assess phenotypic plasticity and differential gene expression in A. tridentata. The G × E experiment was performed on diploid A. tridentata seedlings from two populations (one from Idaho, USA and one from Utah, USA), which experience differing levels of drought stress during the summer months. Photosynthetic data, leaf temperature, and gene expression levels were compared between treatments and populations. The Utah population maintained higher photosynthetic rates and photosynthetic efficiency than the Idaho population under drought stress. The Utah population also exhibited far greater transcriptional plasticity than the Idaho population and expressed genes of response pathways distinct from those of the Idaho population. Populations of A. tridentata differ greatly in their drought response pathways, likely due to differences in response pathways that have evolved under distinct climatic regimes. Epigenetic processes likely contribute to the observed differences between the populations.

The establishment of Artemisia tridentata, a keystone species of the sagebrush steppe, is often limited by summer drought. Symbioses with arbuscular mycorrhizal fungi (AMF) can help plants to cope with drought. We investigated this possible effect on A. tridentata seedlings inoculated with native AMF and exposed to drought in greenhouse and field settings. In greenhouse experiments, AMF colonization increased intrinsic water use efficiency under water stress and delayed the decrease in photosynthesis caused by drought, or this decrease occurred at a lower soil water content. In the field, we evaluated the effect of AMF inoculation on colonization, leaf water potential, survival, and inflorescence development. Inoculation increased AMF colonization, and the seedlings experienced water stress, as evidenced by water potentials between −2 and −4 MPa and reduced stomatal conductance. However, survival remained high, and no differences in water potentials or survival occurred between treatments. Only the percentage of plants with inflorescence was higher in inoculated than non-inoculated seedlings. Overall, the greenhouse results support that AMF colonization enhances drought tolerance in A. tridentata seedlings. Yet, the significance of these results in increasing survival in nature remains to be tested under more severe drought than the plants experienced in our field experiment.

Abstract

Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products in a way that is easily findable and accessible. Consequently, scattered and incompatible metadata records create a barrier to scientific innovation, as researchers are burdened to find and link multidisciplinary datasets. One possible solution to increase data findability, accessibility, interoperability, reproducibility, and integrity within multi-institutional and interdisciplinary projects is a centralized and integrated data management platform. Overall, this type of interoperable framework supports reproducible open science and its dissemination to various stakeholders and the public in a FAIR manner by providing direct access to raw data and linking protocols, metadata and supporting workflow materials.

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.

Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated ‘Daphna’ genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change.

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways.

Biotic interactions can affect a plant’s ability to withstand drought. Such an effect may impact the restoration of the imperiled western North American sagebrush steppe, where seedlings are exposed to summer drought. This study investigated the impact of herbivory on seedlings’ drought tolerance for a keystone species in this steppe, the shrub Artemisia tridentata. Herbivory effects were investigated in two field experiments where seedlings were without tree protectors or within plastic or metal-mesh tree protectors. Treatment effects were statistically evaluated on herbivory, survival, leaf water potential, and inflorescence development. Herbivory occurrence was 80% higher in seedlings without protectors. This damage occurred in early spring and was likely caused by ground squirrels. Most plants recovered, but herbivory was associated with higher mortality during the summer when seedlings experienced water potentials between −2.5 and −7 MPa. However, there were no differences in water potential between treatments, suggesting that the browsed plants were less tolerant of the low water potentials experienced. Twenty months after outplanting, the survival of plants without protectors was 40 to 60% lower than those with protectors. The percentage of live plants developing inflorescences was approximately threefold higher in plants with protectors. Overall, spring herbivory amplified susceptibility to drought and delayed reproductive development.

A checklist of all species of bryophytes, lycophytes, ferns, gymnosperms and angiosperms that are found in the wild (native, naturalised and casual) in Singapore is presented. We have attempted to account for all names of species and infraspecific taxa that have ever been recorded for Singapore, along with the pertinent publications that reported each of these names. For each currently accepted name, the synonyms of relevance for Singapore are included. The native or non-native status for all taxa is given, along with the most recent national conservation assessment applied to each native taxon. If we were aware that the most recent assessment required an update, the taxon is newly assessed here. The checklist includes 2654 native taxa, 479 naturalised/casual taxa and 101 cryptogenic taxa.

Abstract

Otto Warburg (1859–1938) had a great interest in tropical botany. He travelled in South-East Asia and the South Pacific between 1885 and 1889 and brought back a considerable collection of plant specimens from this expedition later donated to the Royal Botanical Museum in Berlin. Warburg published the first comprehensive monograph on the family Pandanaceae in 1900 in the third issue of Das Pflanzenreich established and edited by Adolf Engler (1844–1930). The aim of this article is to clarify the taxonomy, nomenclature and typification of Warburg's contributions to the Pandanaceae. Considerable parts of Warburg's original material was destroyed in Berlin during World War II but duplicates survived, shared by Engler and Warburg with Ugolino Martelli (1860–1934). Martelli was an expert on the family and he assembled a precious herbarium of Pandanaceae that was later donated to the Museo di Storia Naturale dell'Università degli Studi di Firenze. Warburg published 86 new names in Pandanaceae between 1898 and 1909 (five new sections, 69 new species, five new varieties, two new combinations and five replacement names). A complete review of the material extant in B and FI led to the conclusion that 38 names needed a nomenclatural act: 34 lectotypes, three neotypes and one epitype are designated here. Twenty new synonyms are also proposed. One Freycinetia name and six Pandanus names are considered as incertae sedis. A total of 21 names published by Warburg are accepted: 11 in Freycinetia and ten in Pandanus. In addition, four names published in Pandanus by Warburg serve as the basionyms of accepted names in the genus Benstonea.

Premise

The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra‐familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework.

Abstract

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome‐to‐phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty‐one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought‐tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome‐to‐phenome work.

Although vanilla is one of the most popular flavours in the world, there is still uncertainty concerning the native distribution of the species that produces it, Vanilla planifolia. To circumscribe the native geographical extent of this economically important species more precisely, we propose a new landscape-based approach to incorporate information from open-source databases and validate occurrences. In this approach, we include metrics to account for habitat suitability and population sustainability in terms of the biotic (co-occurrence of pollinators and dispersers) and abiotic (habitat quality) factors limiting plant distributions. To further validate occurrences within the resulting distribution, we compare the presence of morphologically similar wild relatives, assess the heterogeneity of ecological niches and verify the correct identification of herbarium specimens. Results from this approach suggest that V. planifolia has a larger geographical distribution than previously recognized; we hypothesize that populations naturally dispersed from Mesoamerica and became established in South America (with a south-eastern limit in Brazil). The recognition of an improved estimate of the distribution of this species will increase the accuracy of predictive models, promote further species circumscription, improve the efficacy of conservation strategies, and help to ensure the sustainability of a valuable, sought-after spice.

Abstract

Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152–161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome to phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and Fungi).

Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.

Phylogenetic analyses of the family Sapindaceae inferred from nuclear and plastid sequence data have revealed a high level of para- and polyphyly at the subfamilial, tribal, and generic levels. A phylogenetic study focusing on taxa in the southern Pacific belonging to tribe Cupanieae has shown that the two most species-rich genera, Arytera Blume and Cupaniopsis Radlk., are polyphyletic. This study aims to clarify generic limits among the taxa currently placed in these two genera by identifying morphological features that support monophyletic groups suitable for recognition at the generic level. Specimens deposited in major herbaria holding material of these taxa were examined to complement extensive field observations. Careful consideration of morphological features in light of previous taxonomic treatments and the results of phylogenetic analyses enabled us to propose a re-aligned generic framework for Cupanieae in which two new genera are described to accommodate species previously placed in Arytera and Cupaniopsis: viz., Lepidocupania Buerki, Callm., Munzinger & Lowry (21 species) and Neoarytera Callm., Buerki, Munzinger & Lowry (4 species). A total of 25 new combinations are made, lectotypes are designated for nine names (two first step and seven second-step), and one new synonym is established. A key to the newly circumscribed genera Arytera and Cupaniopsis, along with allied genera, is provided, accompanied by information on the distribution and ecology of each species.

Basin big sagebrush (Artemisia tridentata subsp. tridentata) is a keystone species of the sagebrush steppe, a widespread ecosystem of western North America threatened by climate change. The study’s goal was to develop an in vitro method of propagation for this taxon to support genome sequencing and genotype-by-environment research on drought tolerance. Such research may ultimately facilitate the reintroduction of big sagebrush in degraded habitats. Seedlings were generated from two diploid mother plants (2n = 2x = 18) collected in environments with contrasting precipitation regimes. The effects of IBA and NAA on rooting of shoot tips were tested on 45 individuals and 15 shoot tips per individual. Growth regulator and individual-seedling effects on percent rooting and roots per shoot tip were evaluated using statistical and clustering analyses. Furthermore, rooted shoot tips were transferred into new media to ascertain their continued growth in vitro. The results suggest that A. tridentata is an outbred species, as shown by individuals’ effect on rooting and growth. IBA addition was the most effective method for promoting adventitious rooting, especially in top-performing individuals. These individuals also have high survival and growth rates upon transferring to new media, making them suitable candidates for generating biomass for genome sequencing and producing clones for genotype-by-environment research.

• Despite broad recognition that water is a major limiting factor in arid ecosystems, we lack an empirical understanding of how this resource is shared and distributed among neighbouring plants. Intraspecific variability can further contribute to this variation via divergent life‐history traits, including root architecture. We investigated these questions in the shrub Artemisia tridentata and hypothesized that the ability to access and utilize surface water varies among subspecies and cytotypes.

• We used an isotope tracer to quantify below‐ground zone of influence in A. tridentata, and tested whether spatial neighbourhood characteristics can alter plant water uptake. We introduced deuterium‐enriched water to the soil in plant interspaces in a common garden experiment and measured deuterium composition of plant stems. We then applied spatially explicit models to test for differential water uptake by A. tridentata, including intermingled populations of three subspecies and two ploidy levels.

• The results suggest that lateral root functioning in A. tridentata is associated with intraspecific identity and ploidy level. Subspecies adapted to habitats with deep soils generally had a smaller horizontal reach, and polyploid cytotypes were associated with greater water uptake compared to their diploid variants. We also found that plant crown volume was a weak predictor of water uptake, and that neighbourhood crowding had no discernable effect on water uptake.

• Intraspecific variation in lateral root functioning can lead to differential patterns of resource acquisition, an essential process in arid ecosystems in the contexts of changing climate and seasonal patterns of precipitation. Altogether, we found that lateral root development and activity are more strongly related to genetic variability within A. tridentata than to plant size. Our study highlights how intraspecific variation in life strategies is linked to mechanisms of resource acquisition.

A free Plain Language Summary

Abstract

Synima Radlk. is a small genus of Sapindaceae distributed in Australia, Indonesia (Moluccas and Western New Guinea) and Papua New Guinea with three species currently accepted. The genus can be recognized by its crested scales on the petals, a pericarp that dries thin and wrinkled, and the seed which has a fleshy, yellow-orange sarcotesta that is either small and basal or ± enclosing the seed. Previous taxonomic studies expressed doubts regarding the generic placement of two species belonging to the genus Sarcotoechia Radlk.: Sarcotoechia serrata S.T. Reynolds and Sarcotoechia heterophylla S.T. Reynolds. A phylogenetic framework has shown that Sarcotoechia is paraphyletic and Sarcotoechia serrata is sister to Synima. Further morphological evidence (e.g., crested petals) support the transfer of the latter two species to Synima and the new combinations are proposed here: Synima heterophylla (S.T. Reynolds) Callm. & Buerki and Synima serrata (S.T. Reynolds) Callm. & Buerki. A key to all species of Synima is presented.

Premise of the Study

While brinjal eggplant (Solanum melongena L.) is the second most important solanaceous fruit crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step‐wise expansion of the eggplant group from Africa to Asia.

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary distinctiveness and the extinction risks they face. EDGE is applied to gymnosperms using a phylogenetic tree comprising DNA sequence data for 85% of gymnosperm species (923 out of 1090 species), to which the 167 missing species were added, and IUCN Red List assessments available for 92% of species. The effect of different extinction probability transformations and the handling of IUCN data deficient species on the resulting rankings is investigated. Although top entries in our ranking comprise species that were expected to score well (e.g. Wollemia nobilis, Ginkgo biloba), many were unexpected (e.g. Araucaria araucana). These results highlight the necessity of using approaches that integrate evolutionary information in conservation science.

Abstract

Tropical mountains are usually characterized by a vertically-arranged sequence of ecological belts, which, in contrast to temperate habitats, have remained relatively stable in space across the Quaternary. Such long-lasting patterning of habitats makes them ideal to test the role of environmental pressure in driving ecological and evolutionary processes. Using Sumatran freshwater mayfly communities, we test whether elevation, rather than other spatial factors (i.e. volcanoes, watersheds) structures both species within communities and genes within species. Based on the analysis of 31 mayfly (Ephemeroptera) communities and restriction-site-associated-DNA sequencing in the four most ubiquitous species, we found elevation as the major spatial component structuring both species and genes in the landscape. In other words, similar elevations across different mountains or watersheds harbor more similar species and genes than different elevations within the same mountain or watershed. Tropical elevation gradients characterized by environmental conditions that are both steep and relatively stable seasonally and over geological time scales, are thus responsible for both ecological and genetic differentiation. Our results demonstrate howin situecological diversification at the micro-evolutionary level might fuel alpha- and beta- components of diversity in tropical sky islands.

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of PalaearcticPyrgusbutterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses.

This study focuses on reconstructing the time‐calibrated phylogeny of the nine families comprising the order Sapindales, representing a diverse and economically important group of eudicots including citrus, mahogany, tree‐of‐heaven, cashew, mango, pistachio, frankincense, myrrh, lychee, rambutan, maple, and buckeye. We sampled three molecular markers, plastid genes rbcL and atpB, and the trnL‐trnLF spacer region, and covered one‐third of the generic diversity of Sapindales. All three markers produced congruent phylogenies using maximum likelihood and Bayesian methods for a set of taxa that included outgroups, i.e., members of the closely related orders Brassicales and Malvales, and the more distantly related Crossosomatales, Ranunculales, and Ceratophyllales. All results confirmed the current delimitation of the families within Sapindales, and the monophyly of the order. Concerning inter‐familial relationships, Biebersteiniaceae and Nitrariaceae formed a basal grade (or sister clade) to the rest of Sapindales with moderate support. The sister relationship of Kirkiaceae to Anacardiaceae and Burseraceae was strongly supported. The clade combining Anacardiaceae and Burseraceae as well as the clade combining Meliaceae, Simaroubaceae, and Rutaceae each received strong support. The sister relationship between Meliaceae and Simaroubaceae was moderately supported. The position of Sapindaceae could not be resolved with confidence. The Sapindales separated from their sister clade, comprising Brassicales and Malvales, in the Early Cretaceous at ca. 112 Ma, and diversified into the nine families from ca. 105 Ma until ca. 87 Ma during Early to Late Cretaceous times. Biebersteiniaceae and Nitrariaceae have the longest stem lineages observed in Sapindales, possibly indicating that extinction may have had a greater role in shaping their extant diversity than elsewhere within the order. Divergence within the larger families (Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, Sapindaceae, Simaroubaceae) started during the Late Cretaceous, extending into the Paleogene and Neogene.

Abstract

This study investigates the biogeography, evolution and systematics of Benstonea Callm. & Buerki (Pandanaceae) based on six plastid DNA regions and 54 specimens representing 36 species (60% of species generic diversity). Our maximum likelihood and Bayesian phylogenetic inferences support the monophyly of Benstonea and its close relationship with the speciose Pandanus Parkinson. Benstonea is subdivided into three clades exhibiting contrasting species diversities. Clades I and II have seven species each, whereas most of the species diversity occurs in clade III with 21 species. None of the sections defined by Stone in Pandanus subgenus Acrostigma (Kurz) B.C. Stone (now Benstonea) are retrieved monophyletic by our analyses. Biogeographical inference supports the origin of Benstonea on the Sunda shelf during the Miocene and shows several subsequent exchanges between Peninsular Malaysia and Borneo. Species in Indochina and the Indian continent originated in Peninsular Malaysia and all belong to clade I. Wallacea was colonized at least twice from Borneo sometimes during the Miocene and no back-dispersals were inferred. The Sunda shelf was colonized once, most likely from Halmahera. Finally, our analyses suggest that the Fijian endemic Benstonea thurstonii (C.H. Wright) Callm. & Buerki dispersed from either Australia or New Guinea during the Pleistocene.

New Guinea is one of the centres of diversity of Benstonea (Pandanaceae), a genus distributed from India to Fiji. Ten species were previously recognised on this island and further field observations, accompanied by the study of available herbarium material have brought new insights into species delimitations within a group of caespitose species with a solitary terminal infructescence. The taxonomical identity of Benstonea odoardoi is elucidated and is considered here as a synonym of Benstonea lauterbachii. Three new combinations and a new name—based on names of Pandanus species previously treated as synonyms of Benstonea odoardoi—are proposed for four distinct species belonging to this group of caespitose species and restricted to Indonesian New Guinea and Papua New Guinea. Finally, Pandanus bintuniensis is here considered as a synonym of Benstonea permicron.

Aim

To test for and describe the genetic structure of the Pandanus tectorius complex, a group of closely related ocean‐dispersed plants and members of the Indo‐Pacific coastal strand community.

Abstract

Summary

• Crassulacean acid metabolism (

  CAM
  ) photosynthesis is an adaptation to water and atmospheric
  CO
  ₂ deficits that has been linked to diversification in dry‐adapted plants. We investigated whether
  CAM
  evolution can be associated with the availability of new or alternative niches, using Eulophiinae orchids as a case study.

• Carbon isotope ratios, geographical and climate data, fossil records and

  DNA
  sequences were used to: assess the prevalence of
  CAM
  in Eulophiinae orchids; characterize the ecological niche of extant taxa; infer divergence times; and estimate whether
  CAM
  is associated with niche shifts.

• CAM
  evolved in four terrestrial lineages during the late Miocene/Pliocene, which have uneven diversification patterns. These lineages originated in humid habitats and colonized dry/seasonally dry environments in Africa and Madagascar. Additional key features (variegation, heterophylly) evolved in the most species‐rich
  CAM
  lineages. Dry habitats were also colonized by a lineage that includes putative mycoheterotrophic taxa.

• These findings indicate that the switch to

  CAM
  is associated with environmental change. With its suite of adaptive traits, this group of orchids represents a unique opportunity to study the adaptations to dry environments, especially in the face of projected global aridification.

There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar.

Biological collections are at the front line of biodiversity research, informing taxonomy, evolution, conservation and sustainable livelihoods. In April 2014, we organised a meeting at the Linnean Society (UK) discussing the impact of next-generation sequencing (NGS) methods on collections-based research. Here, we explore the main themes of this meeting and outline the incredible potential of NGS to reinvent collections-based research. Among the many opportunities at the interface of genomics and collections, we focus specifically on (1) the genomic characterisation of biological collections, (2) the enhancement and development of DNA-based identification, (3) the tree of life and (4) interdisciplinary research addressing the most pressing environmental challenges of our times. Across the world, biological collections are at risk, primarily due to declining funding and shifts in scientific fashions. We encourage all users of collections to embrace the genomic era, not only because of the unparalleled scientific potential that it presents, but also because new cross-disciplinary synergies will reinvigorate and secure the collections for future generations.

Halmahera is the largest (c. 18,000 km2) island of the Moluccan archipelago, but naturalists have only sporadically visited Halmahera and it has remained very poorly explored botanically. However, an intensive botanical inventory project was undertaken between 2012 and 2014 in part of the island to inform flora biodiversity management for certain proposed mining activities. This effort has contributed over 3600 plant collections and nearly doubled the number of Pandanus Parkinson (Pandanaceae) specimens (bringing the total to 55) available for Halmahera. After careful examination of all available material and comparison with other material from the region, we are able to present the first overview of the genus for the island. We have identified ten species from the island of which three are new to science and not known elsewhere, while the other seven are all representatives of species already described from other localities. The new species are formally described here as Pandanus beguinii Callm. & A. P. Keim, Pandanus benstoneoides Callm., Buerki & Phillipson and Pandanus halmaherensis Callm. & A. P. Keim. The new species are provided with notes on their respective morphology and known distributional and ecological ranges, line drawings. Those three new species are assigned a preliminary status of Endangered following IUCN Red List Categories and Criteria. All ten species are illustrated with colour photographs and a key to the species is provided.

Abstract

New Caledonia is a remote archipelago of the South-West Pacific, whose flora is rich, distinctive, and disharmonic. The interest of botanists has long been attracted by the spatio-temporal origin of this flora, but little attention has been paid to the modes of colonization and the diversification processes that have led to the archipelago’s modern flora. To date, no explosive plant radiation has yet been highlighted for New Caledonia. A dated phylogenetic framework on the second richest New Caledonian genus – Psychotria s.l. and its allied genera (tribes Psychotrieae and Palicoureeae, Rubiaceae; ca. 85 species) – is provided in this study to explore its patterns of colonization and diversification in the archipelago. This study is based on a comprehensive species sampling, two nuclear and four plastid loci. Results show that New Caledonia was colonized four times by Psychotria and its allied genera during the Neogene long after its mid-Eocene re-emergence from the sea. The Pacific clade of Psychotrieae, one of the largest plant diversifications in the Pacific islands and the Indo-Pacific region, is absent from New Caledonia, possibly due to niche competition. Although the four lineages colonized New Caledonia relatively simultaneously during the Neogene, they express different evolutionary histories, as revealed by unevenness in species richness and net diversification rates. The genus Geophila has not diversified on New Caledonia, as a non-endemic single species has been documented in the archipelago. The genus Margaritopsis had a moderate level of diversification (four species) similar to that on other Pacific islands. The Psychotria clade NC1 appears to be a relictual lineage, which probably underwent a drastic extinction, with a narrow ecological habitat and dispersal limitations. The Psychotria clade NC2 is the largest and youngest New Caledonian plant radiation, and has undergone the fastest recorded diversification of any endemic lineage in the archipelago, and could be the result of a ‘non-adaptive radiation’, originating from Australian rainforests.

Recent molecular phylogenetic studies in Chrysobalanaceae as well as new analyses presented in this study cast doubt on the monophyly of the three largest genera in the family, Couepia, Hirtella and Licania. Couepia, a Neotropical genus, had species appearing in four separate clades, the majority of species sequenced, however, form a highly supported clade, referred to here as core Couepia (including the type species). These results lend support to a revised taxonomy of the genus, and to resolve Couepia as monophyletic the following taxonomic changes are here proposed: Couepia recurva should be transferred to Hirtella, C. platycalyx transferred to Licania, C. longipendula and C. dolichopoda transferred to Acioa, and a new genus, Gaulettia, is proposed to accommodate species of the Gaulettia clade and allies.

Benstonea (Pandanaceae) was circumscribed to include 57 species formerly placed in the genus Pandanus. Field observations, accompanied by the study of available herbarium material have brought new insights for the delimitation of certain problematic species, especially in the difficult group of species characterized by an axillary infructescence on a short peduncle covered by prophylls and the abscission of the basal portion of the drupe at maturity. New combinations, based on names in Pandanus previously treated as synonyms of Benstonea stenocarpa, are proposed for three distinct species of this group from Halmahera (Indonesia) and Papua New Guinea. The identity of Benstonea celebica, endemic to Sulawesi (Indonesia), is also elucidated and an epitype is designated for this species.

After the publication of our Update on the systematics of Benstonea (Pandanaceae): When a visionary taxonomist foresees phylogenetic relationships (Callmander, Booth, Beentje & Buerki 2013), an error was brought to our attention: 

Aim

The biogeography of the grass genera Festuca (subgenus Schedonorus) and Lolium, which form one of the world main forage groups, is here reconstructed for the first time using nuclear and plastid

The paleotropical monocot Pandanaceae family comprises c. 700 species distributed into five genera: Benstonea (c. 60 spp.), Freycinetia (c. 250 spp.), Martellidendron (6 spp.), Pandanus (c. 450 spp.) and Sararanga (2 spp.). Benstonea was circumscribed to include species previously placed in Pandanus section Acrostigma (one of the four sections of Pandanus subgenus Acrostigma). New phylogenetic data show that the six species of the remaining three sections of subgenus Acrostigma (sections Epiphytica, Fusiforma and Platystigma) and a seventh species doubtfully placed in section Acrostigma (Pandanus microglottis) also belonged to Benstonea. This genus is therefore characterized by a suite of morphological characters, viz. stigmatic groove on the adaxial side of the stigma and a staminate flower reduced to 1 to 3 free stamens (sometimes joined at base). We therefore make here the necessary seven new combinations accompanied by one lectotypification in Benstonea, a genus that now reflects the view of the visionary Benjamin Stone who had already grouped these species in Pandanus subgenus Acrostigma based solely on morphology.

• Premise of the study: Tribe Cardueae (thistles) forms one of the largest tribes in the family Compositae (2400 species), with representatives in almost every continent. The greatest species richness of Cardueae occurs in the Mediterranean region where it forms an important element of its flora. New fossil evidence and a nearly resolved phylogeny of Cardueae are used here to reconstruct the spatiotemporal evolution of this group.

• Methods: We performed maximum parsimony and Bayesian phylogenetic inference based on nuclear ribosomal DNA and chloroplast DNA markers. Divergence times and ancestral area reconstructions for main lineages were estimated using penalized likelihood and dispersal–vicariance analyses, respectively, and integrated over the posterior distribution of the phylogeny from the Bayesian Markov chain Monte Carlo analysis to accommodate uncertainty in phylogenetic relationships.

• Key results: The phylogeny shows that subtribe Cardopatiinae is sister to the remaining subtribes, and subtribes Carlininae and Echinopsinae appear as consecutive sister‐clades to the Carduinae/Centaureinae. Tribe Cardueae is inferred to have originated around the Mid Eocene in West Asia, which is also the ancestral area of most subtribes within Cardueae. Diversification within each subtribe began during the Oligocene‐Miocene period.

• Conclusions: Most diversification events within Cardueae are related to the continuous cycles of area connection and division between the Anatolian microplate and the western Mediterranean Basin during the Oligocene‐Miocene and with the uplift of the Himalayan range from the Miocene onward. From these two regions, thistles dispersed and colonized the rest of the continents (e.g., the New World, Africa, and Australia), most likely during the colder Pliocene‐Pleistocene period.

Aim

We examined phylogenetic relationships and spatio‐temporal diversification in Indian Ocean Primulaceae, assessing correlations between speciation rates, geographical expansion and ecomorphological specialization.

Abstract

The Paleotropical monocot family Pandanaceae includes ca. 700 species assigned to four genera: Pandanus (ca. 500 spp.), Freycinetia (ca. 200 spp.), Martellidendron (6 spp.) and Sararanga (2 spp.). The most speciose genus, Pandanus, was classically subdivided into eight subgenera. Previous cladistic analyses revealed that several key morphological characters might have evolved independently several times, thus highlighting the need for a robust molecular phylogenetic framework to elucidate phylogenetic relationships and infrafamilial and infrageneric classification within this group. In this study, three plastid DNA regions (matK, trnQ­rps16, trnL­trnF) and 200 individuals (representing 134 species and 609 newly produced sequences)—spanning the taxonomic and biogeographic diversity of the family—are analyzed to test the monophyly at the familial and generic levels, and to infer phylogenetic relationships within the family. Particular emphasis is devoted to Pandanus with the aim of recognizing key morphological characters that reflect the evolutionary history of the genus. Phylogenetic inferences support the monophyly of Pandanaceae and establish Sararanga as sister to the rest of the family, with Freycinetia as sister to the Pandanus­Martellidendron pair. Although relationships are not well­resolved within the latter clade, three supported lineages are retrieved: (1) the Acrostigma clade comprising taxa of P. subg. Acrostigma, (2) the Martellidendron clade including taxa assigned to the genus Martellidendron and (3) the core Pandanus clade including taxa of all other subgenera of Pandanus. Morphological and biogeographic evidence supporting clade definitions are discussed in detail. This study provides the first phylogenetic backbone for Pandanaceae, which is sufficiently robust to serve as a springboard for future research into the evolutionary history of this neglected family.

In the past, the circumscription of the large genus Psychotria (Rubiaceae) was difficult, until molecular phylogenetic studies revealed its considerable paraphyly, enabling the delimitation of its major lineages and the grouping of related genera, and most notably the separation of Psychotria and its relatives (former Psychotrieae) into two tribes: Psychotrieae and Palicoureeae. The genus Margaritopsis, which is included in Palicoureeae, encompasses 27 Neotropical species, and in previous studies these have been shown to be close relatives of a group of eight Psychotria species that occur over a large region extending from South‐East Asia to tropical South Pacific through Malesia (= the AMP region, defined as including South‐East Asia, Malesia, tropical Australia, Melanesia, Micronesia, New Caledonia and Polynesia). A molecular phylogenetic study, using one nuclear DNA region (ITS) and four plastid DNA regions (ndhF, rps16, trnH‐psbA, trnT‐F), is undertaken in order to test the placement of 17 AMP Psychotria species within Palicoureeae. The phylogenetic results show that they form a monophyletic clade (= clade G), which also includes the monotypic Fijian genus Readea and Hodgkinsonia frutescens from Australia. Clade G is embedded in a well‐supported grade with five Neotropical representatives of Margaritopsis. A morphological survey based on twenty characters, with the potential to circumscribe generic entities, shows that the monophyly of clade G is supported by a character combination that is similar to species of Neotropical Margaritopsis, confirming their inclusion in this genus. Taxonomic and nomenclatural work on these species is required to formalize nomenclatural implications. Based on the same set of morphological characters, but in absence of molecular data, 28 other Psychotria species from the AMP region were detected as likely candidates for inclusion in Margaritopsis, allowing the estimation of species richness of clade G to be a minimum of 47 species. Within clade G, five well‐supported subclades and a Readea lineage are delimited and each of these is generally supported by unique morphological features. Phylogenetic topologies reveal biogeographical patterns, including a main route of dispersal from western to eastern parts of the AMP region, with subsequent dispersals between archipelagos in the region.

Aim  To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host plant as a case study.

Location  The Alps.

Methods  We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host‐plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern.

Results  Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice‐based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago.

Main conclusions  Species‐specific interactions are scarce in alpine habitats because glacial cycles have limited the opportunities for co‐evolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at a large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host dependence of the beetle, which locally limits the establishment of dispersing insects.

Sapindaceae (Sapindales) are a conspicuous and diversified element of the New Caledonian flora, with ca. 67 species (ca. 90 % endemic) in 13 genera (four endemic: Gongrodiscus, Loxodiscus, Podonephelium, Storthocalyx). The phylogeny of New Caledonian Sapindaceae is inferred by adding 97 new samples, encompassing the full distributional and morphological range of the archipelago's genera, to a broad plastid and nuclear DNA sequence dataset that is representative of the family worldwide. Results from phylogenetic analyses indicate that members of the family on New Caledonia belong to two major clades, the Dodonaea group (placed within subfamily Dodonaeoideae) and the Cupania group (subfamily Sapindoideae), which exhibit strikingly different species diversities (ca. 89% of the species on New Caledonia belong to the Cupania group). Results support the monophyly of all four endemic genera and most of those that also occur elsewhere, with the exception of the morphologically similar Austro‐Pacific genera Arytera and Cupaniopsis, both of which have representatives in each of two well‐supported subclades within the Cupania group, suggesting at least two dispersals to New Caledonia (most likely from Australia). The results provide a robust phylogenetic framework for ongoing taxonomic revisions of Sapindaceae genera on New Caledonia and for investigating the spatio‐temporal history of the family in this biogeographically intriguing archipelago, although expanded sampling (including from other areas) and further analyses will be required to resolve generic limits among the taxa currently placed in Arytera and Cupaniopsis.

Background and Aims

Tecophilaeaceae (27 species distributed in eight genera) have a disjunct distribution in California, Chile and southern and tropical mainland Africa. Moreover, although the family mainly occurs in arid ecosystems, it has colonized three Mediterranean-type ecosystems. In this study, the spatio-temporal history of the family is examined using DNA sequence data from six plastid regions.

Methods

Modern methods in divergence time estimation (BEAST), diversification (LTT and GeoSSE) and biogeography (LAGRANGE) are applied to infer the evolutionary history of Tecophilaeaceae. To take into account dating and phylogenetic uncertainty, the biogeographical inferences were run over a set of dated Bayesian trees and the analyses were constrained according to palaeogeographical evidence.

Key Results

The analyses showed that the current distribution and diversification of the family were influenced primarily by the break up of Gondwana, separating the family into two main clades, and the establishment of a Mediterranean climate in Chile, coinciding with the radiation of Conanthera. Finally, unlike many other groups, no shifts in diversification rates were observed associated with the dispersals in the Cape region of South Africa.

Conclusions

Although modest in size, Tecophilaeaceae have a complex spatio-temporal history. The family is now most diverse in arid ecosystems in southern Africa, but is expected to have originated in sub-tropical Africa. It has subsequently colonized Mediterranean-type ecosystems in both the Northern and Southern Hemispheres, but well before the onset of the Mediterranean climate in these regions. Only one lineage, genus Conanthera, has apparently diversified to any extent under the impetus of a Mediterranean climate.

Abstract

Pandanaceae, a palaeotropical monocot family of c. 700 species, comprises four currently recognized genera: Freycinetia Gaudich., Martellidendron (Pic. Serm.) Callm. & Chassot, Pandanus Parkinson and Sararanga Helms. Within Pandanus (c. 500 spp.), species of sect. Acrostigma Kurz [one of four sections comprising subg. Acrostigma (Kurz) B. C. Stone] possess highly distinctive morphological features (viz. sharp spiniform, linear styles with the stigmatic groove on the abaxial side of the style and a staminate flower reduced to 1 to 3 stamens) shared with two other species (likewise belonging to subg. Acrostigma but originally placed in sect. Fusiforma B. C. Stone) that separate them from all other congeners. Based on morphology, biogeography, and recent inferences from plastid DNA sequence data, we place these distinctive species in a new genus, Benstonea Callm. & Buerki, making the necessary new combinations for the 50 recognized species, accompanied by six lectotypifications, one epitytification and two neotypifications, and placing seventeen names in synonymy. A generic key is provided to facilitate distinguishing Benstonea from the four other genera of Pandanaceae. Comments are provided on the distribution, ecology and typification of each accepted species.

Background

Within the Coleoptera, the largest order in the animal kingdom, the exclusively herbivorous Chrysomelidae are recognized as one of the most species rich beetle families. The evolutionary processes that have fueled radiation into the more than thirty-five thousand currently recognized leaf beetle species remain partly unresolved. The prominent role of leaf beetles in the insect world, their omnipresence across all terrestrial biomes and their economic importance as common agricultural pest organisms make this family particularly interesting for studying the mechanisms that drive diversification. Here we specifically focus on two ecotypes of the alpine leaf beetleOreina speciosissima(Scop.), which have been shown to exhibit morphological differences in male genitalia roughly corresponding to the subspeciesOreina speciosissima sensu strictoandOreina speciosissima troglodytes. In general the two ecotypes segregate along an elevation gradient and by host plants:Oreina speciosissima sensu strictocolonizes high forb vegetation at low altitude andOreina speciosissima troglodytesis found in stone run vegetation at higher elevations. Both host plants and leaf beetles have a patchy geographical distribution. Through use of gene sequencing and genome fingerprinting (AFLP) we analyzed the genetic structure and habitat use ofOreina speciosissimapopulations from the Swiss Alps to examine whether the two ecotypes have a genetic basis. By investigating a wide range of altitudes and focusing on the structuring effect of habitat types, we aim to provide answers regarding the factors that drive adaptive radiation in this phytophagous leaf beetle.

This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species.

We combined chloroplast DNA (cpDNA) sequencing, analysed using statistical parsimony network, with nonhierarchical K-means clustering of amplified fragment length polymorphism (AFLP) genotyping, to unravel patterns of genetic structure across the native range of Ae. geniculata. The AFLP dataset was further explored by measurement of the regional genetic diversity and the detection of isolation by distance patterns.

Both cpDNA and AFLP suggest an eastern Mediterranean origin of Ae. geniculata. Two lineages have spread independently over northern and southern Mediterranean areas. Northern populations show low genetic diversity but strong phylogeographical structure among the main peninsulas, indicating a major influence of glacial cycles. By contrast, low genetic structuring and a high genetic diversity are detected in southern Mediterranean populations. Finally, we highlight human-mediated dispersal resulting in substantial introgression between resident and migrant populations.

We have shown that the evolutionary trajectories of ruderal plants can be similar to those of wild species, but are interfered by human activities, promoting range expansions through increased long-distance dispersal and the creation of suitable habitats.