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— Cecropia is a group of fast-growing pioneer trees that are important in forest regeneration and a common ant-plant mutualism in the Neotropics. To investigate the evolution of mutualism between Cecropia and associated ants, a phylogenetic framework is necessary. Cecropia species are difficult to distinguish morphologically and conventional genetic markers are insufficiently variable to resolve the phylogenetic relationships among species. Our study aimed to compare the phylogenetic utility of restriction site associated DNA (RAD) sequencing to prior work based on commonly sequenced gene regions. RAD sequence data resolved and supported species-level relationships better than previous studies. We identified a deeply divergent non-myrmecophytic clade including C. sciadophylla and African Musanga. Results from geographically widespread and morphologically heterogenous C. obtusifolia and C. angustifolia suggest that current synonymy has lumped phylogenetically divergent lineages. Reconstruction of ant associations on the highly supported Cecropia phylogeny inferred equal probability of the ancestor of Cecropia being myrmecophytic or not. More intensive genetic study is needed to refine species concepts in Cecropia.

Tree size shapes forest carbon dynamics and determines how trees interact with their environment, including a changing climate. Here, we conduct the first global analysis of among-site differences in how aboveground biomass stocks and fluxes are distributed with tree size. We analyzed repeat tree censuses from 25 large-scale (4-52 ha) forest plots spanning a broad climatic range over five continents to characterize how aboveground biomass, woody productivity, and woody mortality vary with tree diameter. We examined how the median, dispersion, and skewness of these size-related distributions vary with mean annual temperature and precipitation. In warmer forests, aboveground biomass, woody productivity, and woody mortality were more broadly distributed with respect to tree size. In warmer and wetter forests, aboveground biomass and woody productivity were more right skewed, with a long tail towards large trees. Small trees (1-10 cm diameter) contributed more to productivity and mortality than to biomass, highlighting the importance of including these trees in analyses of forest dynamics. Our findings provide an improved characterization of climate-driven forest differences in the size structure of aboveground biomass and dynamics of that biomass, as well as refined benchmarks for capturing climate influences in vegetation demographic models.

Summary Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance.A nanopore‐based assembly anchored to a high‐resolution linkage map provided a chromosome‐resolved genome for CBDRx, a potent CBD‐type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed.Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD‐type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio.Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.

Premise How genetic variation within a species affects phytochemical composition is a fundamental question in botany. The ratio of two specialized metabolites in Cannabis sativa, tetrahydrocannabinol (THC) and cannabidiol (CBD), can be grouped into three main classes (THC-type, CBD-type, and intermediate type). We tested a genetic model associating these three groups with functional and nonfunctional alleles of the cannabidiolic acid synthase gene (CBDAS). Methods We characterized cannabinoid content and assayed CBDAS genotypes of >300 feral C. sativa plants in Minnesota, United States. We performed a test cross to assess CBDAS inheritance. Twenty clinical cultivars obtained blindly from the National Institute on Drug Abuse and 12 Canadian-certified grain cultivars were also examined. Results Frequencies of CBD-type, intermediate-type, and THC-type feral plants were 0.88, 0.11, and 0.01, respectively. Although total cannabinoid content varied substantially, the three groupings were perfectly correlated with CBDAS genotypes. Genotype frequencies observed in the test cross were consistent with codominant Mendelian inheritance of the THC:CBD ratio. Despite significant mean differences in total cannabinoid content, CBDAS genotypes blindly predicted the THC:CBD ratio among clinical cultivars, and the same was true for industrial grain cultivars when plants exhibited >0.5% total cannabinoid content. Conclusions Our results extend the generality of the inheritance model for THC:CBD to diverse C. sativa accessions and demonstrate that CBDAS genotyping can predict the ratio in a variety of practical applications. Cannabinoid profiles and associated CBDAS segregation patterns suggest that feral C. sativa populations are potentially valuable experimental systems and sources of germplasm.

International audience; Figs and fig wasps are a classic example of an obligate pollination mutualism. Decades of work untangling the ecology and evolution of these organisms has simultaneously contributed to development of the fields of mutualism, coevolution and plant-insect interactions at large. With > 800 species, figs (Ficus, Moraceae) are among some of the larger genera of angiosperms. Phylogenetic studies of Moraceae have supported the clade Castilleae as the sister lineage of Ficus. Compared to Ficus, Castilleae have many fewer species (60 species in 11 genera), suggesting changes in rates of diversification along these two branches. Relatively little is known about Castilleae compared to Ficus, and we argue that defining the clade comprising Ficus and Castilleae, hereafter Involucrata, focuses attention on opportunities for comparative studies of pollination mutualisms and diversification rates. In this study, we define Involucrata and propose a revised classification scheme that accounts for the phylogenetic reconstruction based on the most comprehensive sampling of this group to date. Moving forward, this classification will better guide and support evolutionary, ecological and comparative pollination biology studies of this group. Additional Keyword: Asperae-external transcribed spacer-Involucrata-Mixtiflores-Noyera-paralogy-phylogenetic reconstruction.

The fig (Moraceae) and pollinating fig wasp (Agaonidae) mutualism is best known as a model system for the study of coevolution in plant–pollinator interactions and its central role in shaping vertebrate communities in tropical forests. Figs also host myriad antagonistic parasitic fig wasps which impose costs on both partners threatening mutualism stability. Spatiotemporal variation in parasitic wasp abundance is a key factor in mitigating these effects. Because fig wasps are temperature sensitive and likely vary in their ability to traverse environmental gradients, we expect community assemblages and abundance of both pollinating and non‐pollinating fig wasps to respond to changes along an elevational gradient. In the present study, we compare the fig wasp communities and abundance of three fig species growing along the slopes of the Mount Wilhelm altitudinal gradient in Papua New Guinea. We quantified wasps from over 100 male fig trees and calculated seed set for 55 female trees along each of the species’ distribution on the transect. Our results show that the abundance of both pollinating and non‐pollinating fig wasps follow a mid‐elevation peak, consistent with fig species richness found in the same transect. The patterns, however, are different according to the host's species distribution. Seed set remained relatively constant along the gradient for all species with some decrease along higher elevations, potentially affecting connectivity along the gradient. As suggested for insects in general, temperature and habitat diversity appear to play a fundamental role in the species richness and abundance of fig wasps.

In the tropics, antagonistic seed predation networks may have different properties than mutualistic pollination and seed dispersal networks, but the former have been considerably less studied. We tested whether the structure of antagonistic tripartite networks composed of host plants, insects developing within seeds and fruits, and their insect parasitoids could be predicted from plant phylogenetic distance and plant traits. We considered subsets of the networks (“subnetworks”) at three rainforest locations (Panama, Thailand, Papua New Guinea), based on insect families, plant families or plant functional groups. We recorded 3,197 interactions and observed a low percentage of realized interactions, especially in Panama, where insect host specificity was higher than in Thailand or New Guinea. Several factors may explain this, including insect faunal composition, incidence of dry fruits, high fruit production and high occurrence of Fabaceae at the Panamanian site. Host specificity was greater among seed-eaters than pulp-eaters and for insects feeding on dry fruits as opposed to insects feeding on fleshy fruits. Plant species richness within plant families did not influence insect host specificity, but site characteristics may be important in this regard. Most subnetworks were extremely specialized, such as those including Tortricidae and Bruchinae in Panama. Plant phylogenetic distance, plant basal area and plant traits (fruit length, number of seeds per fruit) had important effects on several network statistics in regressions weighted by sampling effort. A path analysis revealed a weak direct influence of plant phylogenetic distance on parasitoid richness, indicating limited support for the “nasty host hypothesis”. Our study emphasizes the duality between seed dispersal and seed predation networks in the tropics, as key plant species differ and host specificity tends to be low in the former and higher in the latter. This underlines the need to study both types of networks for sound practices of forest regeneration and conservation.

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

Climbing plants form a substantial component of tropical forest diversity. Climbers are a diverse group comprising various ecological strategies dependent on tree support and are affected by biotic and abiotic forest conditions. In a lowland primary tropical rainforest in Papua New Guinea, we studied the distribution of root climbers from genus Piper in relation to topography (slope, convexity, altitude) and properties of vegetation and of individual host trees (basal area of trees, and host tree size, abundance and species identity). In total, 1,058 Piper climber individuals belonging to 8 species occupied 13.7% of tree trunks with a diameter at breast height (DBH) > 1 cm. All Piper species generally avoided similar habitat conditions – higher altitude, steeper slopes, more closed canopy layer and bigger total basal area of host vegetation. The preferences of Piper climbers for some tree species are primarily determined by properties of host trees, mainly their DBH. Therefore, the probability of Piper presence on a tree increased with individual host tree DBH. Piper species were more frequently found on rare than common tree species. However, this relationship might be also explained by their affinity for higher tree DBH. Our findings point to non-random association between climbers and their host trees, in a complicated interplay with local environmental conditions. These interactions have very probably consequences for forest vegetation dynamics and maintenance of diversity.

Arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) associations are critical for host-tree performance. However, how mycorrhizal associations correlate with the latitudinal tree beta-diversity remains untested. Using a global dataset of 45 forest plots representing 2,804,270 trees across 3840 species, we test how AM and EcM trees contribute to total beta-diversity and its components (turnover and nestedness) of all trees. We find AM rather than EcM trees predominantly contribute to decreasing total beta-diversity and turnover and increasing nestedness with increasing latitude, probably because wide distributions of EcM trees do not generate strong compositional differences among localities. Environmental variables, especially temperature and precipitation, are strongly correlated with beta-diversity patterns for both AM trees and all trees rather than EcM trees. Results support our hypotheses that latitudinal beta-diversity patterns and environmental effects on these patterns are highly dependent on mycorrhizal types. Our findings highlight the importance of AM-dominated forests for conserving global forest biodiversity., The relationship of mycorrhizal associations with latitudinal gradients in tree beta-diversity is unexplored. Using a global dataset approach, this study examines how trees with arbuscular mycorrhizal and ectomycorrhizal associations contribute to latitudinal beta-diversity patterns and the environmental controls of these patterns.

Papua New Guinea is home to >10% of the world’s languages and rich and varied biocultural knowledge, but the future of this diversity remains unclear. We measured language skills of 6,190 students speaking 392 languages (5.5% of the global total) and modelled their future trends, using individual-level variables characterizing family language use, socio-economic conditions, student’s skills, and language traits. This approach showed that only 58% of the students, compared to 91% of their parents, were fluent in indigenous languages, while the trends in key drivers of language skills (language use at home, proportion of mixed-language families, urbanization, students’ traditional skills) predicted accelerating decline of fluency, to an estimated 26% in the next generation of students. Ethnobiological knowledge declined in close parallel with language skills. Varied medicinal plant uses known to the students speaking indigenous languages are replaced by a few, mostly non-native species for the students speaking English or Tok Pisin, the national lingua franca. Most (88%) students want to teach indigenous language to their children. While crucial for keeping languages alive, this intention faces powerful external pressures as key factors (education, cash economy, road networks, urbanization) associated with language attrition are valued in contemporary society.Significance StatementAround the world, more than 7,000 languages are spoken, most of them by small populations of speakers in the tropics. Globalization puts small languages at a disadvantage, but our understanding of the drivers and rate of language loss remains incomplete. When we tested key factors causing language attrition among Papua New Guinean students speaking 392 different indigenous languages, we found an unexpectedly rapid decline in their language skills compared to their parents and predicted further acceleration of language loss in the next generation. Language attrition was accompanied by decline in the traditional knowledge of nature among the students, pointing to an uncertain future for languages and biocultural knowledge in the most linguistically diverse place on Earth.

Barriers to gene-flow within populations, typically in response to divergent selection, are often mediated via third-party interactions. Under these conditions speciation is inextricably linked to ecological context. We present a novel framework for studying arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI) via alternative strain associations. Building on empirical findings, our model predicts that sympatric host sister-species harbour paraphyletic strains that provide CI, while well-defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia may provide an adaptive advantage when coupled with reduced hybrid fitness (via trait mismatching), by facilitating assortative mating between co-occurring divergent phenotypes – the contact contingency hypothesis. To test this, we applied a custom-built predictive algorithm to empirical data from host-specific pollinating fig wasps, achieving ≤88.46% accuracy. We then considered post-zygotic offspring mortality during CI matings by developing a model featuring fitness clines across oviposition resources. This oviposition trade-off model, tested through simulation, favoured CI at realistic conspecific mating frequencies despite fecundity losses. We demonstrate that a rules-based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely-related sympatric species encounter adaptive disadvantage through hybridisation.

The ant mosaic is a concept of the non-random spatial distribution of individual ant species in trees built upon the assumption of interspecific behavioural associations. However, colony identity and environmental variance may also play a role in species distribution. Here we assess the presence of ant mosaics in a primary forest ecosystem and whether they are structured by species' aggressive behaviours or by habitat filtering. We sampled arboreal ants from vertically stratified baits exposed in 225 canopy trees in a 9-ha plot of primary lowland forest in Papua New Guinea, the largest forest area surveyed to detect ant mosaics. We performed behavioural tests on conspecific ants from adjacent trees to determine the territories of individual colonies. We explored the environmental effects on the ant communities using information on the plot vegetation structure and topography. Furthermore, we created a novel statistical method to test for the community non-random spatial structure across the plot via spatial randomisation of individual colony territories. Finally, we linked spatial segregation among the four most common species to experimentally assessed rates of interspecies aggression. The ant communities comprised 57 species of highly variable abundance and vertical stratification. Ant community composition was spatially dependent, but it was not affected by tree species composition or canopy connectivity. Only local elevation had a significant but rather small effect. Individual colony territories ranged from one tree to 0.7 ha. Species were significantly over-dispersed, with their territory overlap significantly reduced. The level of aggression between pairs of the four most common species was positively correlated with their spatial segregation. Our study demonstrates the presence of ant mosaics in tropical pristine forest, which are maintained by interspecific aggression rather than habitat filtering, with vegetation structure having a rather small and indirect effect, probably linked to microclimate variability. publishedVersion

ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimensions, censusing of all stems ≥1 cm in diameter, inclusion of tropical, temperate and boreal forests, and investigation of additional biotic (e.g., arthropods) and abiotic (e.g., soils) drivers, which together provide a holistic view of forest functioning. The 71 FDPs in 27 countries include approximately 7.33 million living trees and about 12,000 species, representing 20% of the world's known tree diversity. With >1300 published papers, ForestGEO researchers have made significant contributions in two fundamental areas: species coexistence and diversity, and ecosystem functioning. Specifically, defining the major biotic and abiotic controls on the distribution and coexistence of species and functional types and on variation in species' demography has led to improved understanding of how the multiple dimensions of forest diversity are structured across space and time and how this diversity relates to the processes controlling the role of forests in the Earth system. Nevertheless, knowledge gaps remain that impede our ability to predict how forest diversity and function will respond to climate change and other stressors. Meeting these global research challenges requires major advances in standardizing taxonomy of tropical species, resolving the main drivers of forest dynamics, and integrating plot-based ground and remote sensing observations to scale up estimates of forest diversity and function, coupled with improved predictive models. However, they cannot be met without greater financial commitment to sustain the long-term research of ForestGEO and other forest plot networks, greatly expanded scientific capacity across the world's forested nations, and increased collaboration and integration among research networks and disciplines addressing forest science.

Legumes provide an essential service to ecosystems by capturing nitrogen from the atmosphere and delivering it to the soil, where it may then be available to other plants. However, this facilitation by legumes has not been widely studied in global tropical forests. Demographic data from 11 large forest plots (16–60 ha) ranging from 5.25° S to 29.25° N latitude show that within forests, leguminous trees have a larger effect on neighbor diversity than non-legumes. Where soil nitrogen is high, most legume species have higher neighbor diversity than non-legumes. Where soil nitrogen is low, most legumes have lower neighbor diversity than non-legumes. No facilitation effect on neighbor basal area was observed in either high or low soil N conditions. The legume–soil nitrogen positive feedback that promotes tree diversity has both theoretical implications for understanding species coexistence in diverse forests, and practical implications for the utilization of legumes in forest restoration., Xu et al. examine the effect of leguminous trees on neighbor diversity across 11 plots in tropical forests around the world, and find that in high soil nitrogen conditions, most legume species have higher neighbor diversity than non-legumes, and vice versa where soil nitrogen is low. Their results have practical implications for the utilization of legumes in forest restoration.

Long-term forest dynamics plots in the tropics tend to be situated on stable terrain. This study investigated forest dynamics on the north coast of New Guinea where active subduction zones are uplifting lowland basins and exposing relatively young sediments to rapid weathering. We examined forest dynamics in relation to disturbance history, topography and soil nutrients based on partial re-census of the 50-ha Wanang Forest Dynamics Plot in Papua New Guinea. The plot is relatively high in cations and phosphorus but low in nitrogen. Soil nutrients and topography accounted for 29% of variation in species composition but only 4% of variation in basal area. There were few areas of high biomass and most of the forest was comprised of small-diameter stems. Approximately 18% of the forest was less than 30 y old and the annual tree mortality rate of nearly 4% was higher than in other tropical forests in South-East Asia and the neotropics. These results support the reputation of New Guinea's forests as highly dynamic, with frequent natural disturbance. Empirical documentation of this hypothesis expands our understanding of tropical forest dynamics and suggests that geomorphology might be incorporated in models of global carbon storage especially in regions of unstable terrain.

Escalation (macroevolutionary increase) or divergence (disparity between relatives) in trait values are two frequent outcomes of the plant-herbivore arms race. We studied the defences and caterpillars associated with 21 sympatric New Guinean figs. Herbivore generalists were concentrated on hosts with low protease and oxidative activity. The distribution of specialists correlated with phylogeny, protease and trichomes. Additionally, highly specialised Asota moths used alkaloid rich plants. The evolution of proteases was conserved, alkaloid diversity has escalated across the studied species, oxidative activity has escalated within one clade, and trichomes have diverged across the phylogeny. Herbivore specificity correlated with their response to host defences: escalating traits largely affected generalists and divergent traits specialists; but the effect of escalating traits on extreme specialists was positive. In turn, the evolution of defences in Ficus can be driven towards both escalation and divergence in individual traits, in combination providing protection against a broad spectrum of herbivores.

Maintaining tree diversity Negative interaction among plant species is known as conspecific negative density dependence (CNDD). This ecological pattern is thought to maintain higher species diversity in the tropics. LaManna et al. tested this hypothesis by comparing how tree species diversity changes with the intensity of local biotic interactions in tropical and temperate latitudes (see the Perspective by Comita). Stronger local specialized biotic interactions seem to prevent erosion of biodiversity in tropical forests, not only by limiting populations of common species, but also by strongly stabilizing populations of rare species, which tend to show higher CNDD in the tropics. Science , this issue p. 1389 ; see also p. 1328

Elevational gradients affect the production of plant secondary metabolites through changes in both biotic and abiotic conditions. Previous studies have suggested both elevational increases and decreases in host-plant chemical defences. We analysed the correlation of alkaloids and polyphenols with elevation in a community of nine Ficus species along a continuously forested elevational gradient in Papua New Guinea. We sampled 204 insect species feeding on the leaves of these hosts and correlated their community structure to the focal compounds. Additionally, we explored species richness of folivorous mammals along the gradient. When we accounted for Ficus species identity, we found a general elevational increase in flavonoids and alkaloids. Elevational trends in non-flavonol polyphenols were less pronounced or showed non-linear correlations with elevation. Polyphenols responded more strongly to changes in temperature and humidity than alkaloids. The abundance of insect herbivores decreased with elevation, while the species richness of folivorous mammals showed an elevational increase. Insect community structure was affected mainly by alkaloid concentration and diversity. Although our results show an elevational increase in several groups of metabolites, the drivers behind these trends likely differ. Flavonoids may provide figs with protection against abiotic stressors. In contrast, alkaloids affect insect herbivores and may provide protection against mammalian herbivores and pathogens. Concurrent analysis of multiple compound groups alongside ecological data is an important approach for understanding the selective landscape that shapes plant defences.

In arthropod community ecology, species richness studies tend to be prioritised over those investigating patterns of abundance. Consequently, the biotic and abiotic drivers of arboreal arthropod abundance are still relatively poorly known. In this cross-continental study, we employ a theoretical framework in order to examine patterns of covariance among herbivorous and predatory arthropod guilds. Leaf-chewing and leaf-mining herbivores, and predatory ants and spiders, were censused on > 1000 trees in nine 0.1 ha forest plots. After controlling for tree size and season, we found no negative pairwise correlations between guild abundances per plot, suggestive of weak signals of both inter-guild competition and top-down regulation of herbivores by predators. Inter-guild interaction strengths did not vary with mean annual temperature, thus opposing the hypothesis that biotic interactions intensify towards the equator. We find evidence for the bottom-up limitation of arthropod abundances via resources and abiotic factors, rather than for competition and predation. publishedVersion

Made available in DSpace on 2020-12-10T17:39:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-08-05 Royal Society International Exchanges Carlsberg Foundation Danish Research Council National Natural Science Foundation of China Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) US National Science Foundation National Parks Board, Singapore Deutsche Forschungsgemeinschaft Synthesys Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Edinburgh Botanic Garden (Sibbald) Trust M. L. MacIntyre Begonia Trust Scottish Government's Rural and Environmental Science and Analytical Services Division New Guinea is the world's largest tropical island and has fascinated naturalists for centuries(1,2). Home to some of the best-preserved ecosystems on the planet(3)and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region(4,5), it is a globally recognized centre of biological and cultural diversity(6,7). So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families-suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the 'Last Unknown'(8). A catalogue of the vascular flora of New Guinea indicates that this island is the most floristically diverse in the world, and that 68% of the species identified are endemic to New Guinea. Royal Bot Gardens, London, England Nat Biodivers Ctr, Leiden, Netherlands Univ Michigan Herbarium, Ann Arbor, MI USA Univ Gottingen, Dept Systemat Biodivers & Evolut Plants, Albrecht von Haller Inst Plant Sci, Gottingen, Germany Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland Aarhus Univ, Dept Biosci, Aarhus, Denmark Univ Vermont, Dept Plant Biol, Pringle Herbarium, Burlington, VT USA Boise State Univ, Dept Biol Sci, Boise, ID 83725 USA Conservatoire & Jardin Bot Ville Geneve, Chambesy, Switzerland Univ Sydney, Sch Life & Environm Sci, Sydney, NSW, Australia Natl Museum Nat & Sci, Dept Bot, Tsukuba, Ibaraki, Japan Univ Minnesota, Dept Plant & Microbial Biol, St Paul, MN 55108 USA New Guinea Binatang Res Ctr, Madang, Papua N Guinea Guangxi Zhuang Autonomous Reg & Chinese Acad Sci, Guangxi Key Lab Plant Conservat & Restorat Ecol K, Guangxi Inst Bot, Guilin, Peoples R China Papua New Guinea Univ Technol, Lae, Papua N Guinea Herbarium Bogoriense, Bogor, Indonesia Univ Fed Mato Grosso do Sul, Tres Lagoas Campus, Tres Lagoas, Brazil Royal Bot Garden Sydney, Sydney, NSW, Australia Univ Papua, Fak Kehutanan, Manokwari, Indonesia Baden Penelitian & Pengembangan Daerah Prov Papua, Manokwari, Indonesia Missouri Bot Garden, St Louis, MO USA Papua New Guinea Forest Res Inst, Lae, Papua N Guinea Natl Bot Gardens Ireland, Glasnevin, Ireland Univ Zurich, Dept Systemat & Evolutionary Bot, Zurich, Switzerland Forest Res Inst Malaysia, Kepong, Malaysia Nat Hist Museum, Dept Life Sci, London, England Univ Bonn, Nees Inst Biodivers Plants, Bonn, Germany Martin Luther Univ Halle Wittenberg, Inst Biol, Herbarium, Halle, Germany Natl Pk Board, Nat Plants Ctr, Singapore, Singapore Natl Pk Board, Singapore Bot Gardens, Singapore, Singapore Univ Aberdeen, Sch Biol Sci, Aberdeen, Scotland Univ Philippines Manila, Coll Arts & Sci, Dept Biol, Manila, Philippines Kyoto Univ, Kyoto Univ Museum, Kyoto, Japan Sao Paulo State Univ, Inst Biosci, Rio Claro, Brazil Royal Bot Gardens Victoria, South Yarra, Vic, Australia Univ Melbourne, Sch BioSci, Parkville, Vic, Australia Univ Oxford, Dept Plant Sci, Oxford, England Queens Univ Belfast, Marine Lab, Portaferry, North Ireland Fern Res Fdn, Kerikeri, New Zealand Univ N Carolina, Wilmington, NC USA Museum New Zealand Papa Tongarewa, Wellington, New Zealand Western Michigan Univ, Dept Biol Sci, Kalamazoo, MI 49008 USA New Mexico State Univ, Dept Anim & Range Sci, Las Cruces, NM 88003 USA Univ Fed Vicosa, Dept Biol Vegetal, Vicosa, MG, Brazil Colorado State Univ, Dept Biol, Ft Collins, CO 80523 USA Trinity Coll Dublin, Sch Nat Sci, Dept Bot, Dublin, Ireland Univ Florida, Dept Biol, Gainesville, FL USA CSIRO Land & Water, Floreat, WA, Australia Univ Western Australia, Sch Biol Sci, Crawley, WA, Australia Chinese Acad Sci, Inst Bot, Beijing, Peoples R China Univ Minnesota, Bell Museum, St Paul, MN 55108 USA Univ Glasgow, Inst Biodivers Anim Hlth & Comparat Med, Glasgow, Lanark, Scotland Chinese Acad Sci, Chengdu Inst Biol, Chengdu, Peoples R China Leiden Univ, Inst Biol Leiden, Leiden, Netherlands Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland Sao Paulo State Univ, Inst Biosci, Rio Claro, Brazil Royal Society International Exchanges: IE 170241 National Natural Science Foundation of China: 31570307 CNPq: 153430/2018-4 US National Science Foundation: DEB-1457366 US National Science Foundation: DEB-1754667 US National Science Foundation: DEB-0515678 US National Science Foundation: DEB-0816749 US National Science Foundation: DEB-0841885 Deutsche Forschungsgemeinschaft: LE 1826/3-1 Synthesys: GB-TAF-6305 FAPESP: 2015/13112-7 FAPESP: 2018/09379-6

A community of frugivorous insects was studied by rearing of 25 565 individual insects representing three orders (Coleoptera, Lepidoptera and Diptera except Drosophilidae) from 326 woody plant species in a lowland rainforest in Papua New Guinea. Fruits from 19.3% of plant species were not attacked by any insect order, 33.4% of plant species were attacked by a single order, 30% by two orders and 17.2% by all three orders. The likelihood of attack by individual orders was positively correlated so that a higher proportion of plant species than expected suffered either no attack at all or was attacked by all three insect orders. Fruits from most of the plant species exhibited low rates of attack and low densities of insects. One kilogram of fruit was attacked on average by 11 insects, including three to four Coleoptera, six Diptera and one Lepidoptera. Thus, we reared on average one insect from 10 fruits, including one Diptera from 14 fruits, one Coleoptera from 22 fruits and one Lepidoptera from 100 fruits. Only 72 out of the 326 plant species hosted more than one insect per 10 fruits, and only seven species supported a density of greater than one insect per fruit. Our results suggest that specialized insect seed predators are probably too rare to maintain the diversity of vegetation by density-dependent mortality of seeds as suggested by the Janzen–Connell hypothesis. Fruit weight, fruit volume, mesocarp volume, seed volume and fleshiness had no significant effect on the probability that a fruit would be attacked by an insect frugivore. However, fruits attacked by Diptera were significantly larger and had larger volume of both mesocarp and seeds than fruits attacked by Coleoptera and Lepidoptera.

Questions How do spatial patterns of tree distribution and species co-occurrence differ between primary and secondary tropical rain forests? What signatures of ecological processes might be discerned by comparing the spatial patterns of trees between primary and secondary forest plots? Location Tropical rain forest vegetation, lowlands of Papua New Guinea. Methods All trees over 5 cm DBH were surveyed in two non-replicated 1-ha plots situated in primary and secondary forest. Grid location, DBH, height and species identity were recorded for all surveyed trees. Analysis of the spatial pattern and the autocorrelation of tree sizes and identities were used to assess the structure of the forest found within the plots. Functions combining Ripley's K and the individual species–area relationship were applied to study the spatial distribution of trees and species diversity. Results The spatial distribution of common species, and all stems collectively, was aggregated in the secondary forest plot but not different from random in the primary forest plot. Diameter and height were also strongly spatially auto-correlated in the secondary forest plot but not in the primary forest plot. Conspecific aggregations were more common in the secondary forest plot. Finally, the secondary forest plot was characterized by the presence of diversity-repelling species and lower diversity than the primary forest plot, where diversity-accumulating species were present. Conclusions We attribute the weaker autocorrelation of tree size in the primary forest to the development of size hierarchies throughout the course of stand aging. The conspecific aggregation and low local diversity within the secondary forest plot are likely caused by dispersal limitation during a brief period of establishment after disturbance. The higher local diversity of the primary forest can be explained by the reduction of species aggregation through increased mortality of conspecifics. This is caused by strong intraspecific competition, supporting the spatial segregation hypothesis (interspecific spatial segregation).

Ant-plant mutualisms are abundant in the tropics and are popular models for ecological study, but investigating the origin and evolution of such systems requires a phylogenetic framework. A common ant-plant mutualism in the Neotropics involves the genus Cecropia, a group of fast-growing pioneer trees that are important in forest regeneration. Relationships between genera in the tribe Cecropieae (Urticaceae), including Cecropia, Coussapoa, Musanga, Myrianthus, and Pourouma, are unknown and are necessary to investigate the evolutionary history of the Cecropia-ant mutualism. Bayesian phylogenetic analyses of the NADH dehydrogenase (ndhF) chloroplast gene region, the 26S region of nuclear ribosomal DNA, and an exon-primed intron-crossing DNA region support the position of non-myrmecophytic African Musanga within a paraphyletic Cecropia. Neotropical Pourouma and Coussapoa are supported as sister taxa with African Myrianthus as their closest relative. Although it remains uncertain whether myrmecophytis...

We propose a new classification of rain forest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit‐feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand), and Wanang (Papua New Guinea). The three plots differed widely in fruit syndrome composition. Plant species with fleshy, indehiscent fruits containing multiple seeds were important at all three sites. However, in Panama, a high proportion of species had dry fruits, while in New Guinea and Thailand, species with fleshy drupes and thin mesocarps were dominant. Species with dry, winged seeds that do not develop as capsules were important in Thailand, reflecting the local importance of Dipterocarpaceae. These differences can also determine differences among frugivorous insect communities. Fruit syndromes and colors were phylogenetically flexible traits at the scale studied, as only three of the eight seed syndromes, and one of the 10 colors, showed significant phylogenetic clustering at either genus or family levels. Plant phylogeny was, however, the most important factor explaining differences in overall fruit syndrome composition among individual plant families or genera across the three study sites.

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Cannabis has been cultivated for millennia with distinct cultivars providing either fiber and grain or tetrahydrocannabinol. Recent demand for cannabidiol rather than tetrahydrocannabinol has favored the breeding of admixed cultivars with extremely high cannabidiol content. Despite several draft Cannabis genomes, the genomic structure of cannabinoid synthase loci has remained elusive. A genetic map derived from a tetrahydrocannabinol/cannabidiol segregating population and a complete chromosome assembly from a high-cannabidiol cultivar together resolve the linkage of cannabidiolic and tetrahydrocannabinolic acid synthase gene clusters which are associated with transposable elements. High-cannabidiol cultivars appear to have been generated by integrating hemp-type cannabidiolic acid synthase gene clusters into a background of marijuana-type cannabis. Quantitative trait locus mapping suggests that overall drug potency, however, is associated with other genomic regions needing additional study.Resources available online at: http://cannabisgenome.orgSummaryA complete chromosome assembly and an ultra-high-density linkage map together identify the genetic mechanism responsible for the ratio of tetrahydrocannabinol (THC) to cannabidiol (CBD) in Cannabis cultivars, allowing paradigms for the evolution and inheritance of drug potency to be evaluated.

The relationship between β-diversity and latitude still remains to be a core question in ecology because of the lack of consensus between studies. One hypothesis for the lack of consensus between studies is that spatial scale changes the relationship between latitude and β-diversity. Here, we test this hypothesis using tree data from 15 large-scale forest plots (greater than or equal to 15 ha, diameter at breast height ≥ 1 cm) across a latitudinal gradient (3–30 o ) in the Asia-Pacific region. We found that the observed β-diversity decreased with increasing latitude when sampling local tree communities at small spatial scale (grain size ≤0.1 ha), but the observed β-diversity did not change with latitude when sampling at large spatial scales (greater than or equal to 0.25 ha). Differences in latitudinal β-diversity gradients across spatial scales were caused by pooled species richness (γ-diversity), which influenced observed β-diversity values at small spatial scales, but not at large spatial scales. Therefore, spatial scale changes the relationship between β-diversity, γ-diversity and latitude, and improving sample representativeness avoids the γ-dependence of β-diversity.

Hülsmann and Hartig suggest that ecological mechanisms other than specialized natural enemies or intraspecific competition contribute to our estimates of conspecific negative density dependence (CNDD). To address their concern, we show that our results are not the result of a methodological artifact and present a null-model analysis that demonstrates that our original findings—(i) stronger CNDD at tropical relative to temperate latitudes and (ii) a latitudinal shift in the relationship between CNDD and species abundance—persist even after controlling for other processes that might influence spatial relationships between adults and recruits.

Aim Insects feeding on seeds and fruits represent interesting study systems, potentially able to lower the fitness of their host plants. In addition to true seed eaters, a suite of insects feed on the fleshy parts of fruits. We examined the likelihood of community convergence in whole insect assemblages attacking seeds/fruits in three tropical rainforests. Location Three ForestGEO permanent forest plots within different biogeographical regions: Barro Colorado Island (Panama), Khao Chong (Thailand) and Wanang (Papua New Guinea). Methods We surveyed 1,186 plant species and reared 1.1 ton of seeds/fruits that yielded 80,600 insects representing at least 1,678 species. We assigned seeds/fruits to predation syndromes on the basis of plant traits relevant to insects, seed/fruit appearance and mesocarp thickness. Results We observed large differences in insect faunal composition, species richness and guild structure between our three study sites. We hypothesize that the high species richness of insect feeding on seeds/fruits in Panama may result from a conjunction of low plant species richness and high availability of dry fruits. Insect assemblages were weakly influenced by seed predation syndromes, both at the local and regional scale, and the effect of host phylogeny varied also among sites. At the driest site (Panama), the probability of seeds of a plant species being attacked depended more on seed availability than on the measured seed traits of that plant species. However when seeds were attacked, plant traits shaping insect assemblages were difficult to identify and not related to seed availability. Main conclusions We observed only weak evidence of community convergence at the intercontinental scale among these assemblages. Our study suggests that seed eaters may be most commonly associated with dry fruits at relatively dry tropical sites where fleshy fruits may be less prevalent.

Summary � Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. � Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. � Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/ CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. � Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency.

Climate is widely recognised as an important determinant of the latitudinal diversity gradient. However, most existing studies make no distinction between direct and indirect effects of climate, which substantially hinders our understanding of how climate constrains biodiversity globally. Using data from 35 large forest plots, we test hypothesised relationships amongst climate, topography, forest structural attributes (stem abundance, tree size variation and stand basal area) and tree species richness to better understand drivers of latitudinal tree diversity patterns. Climate influences tree richness both directly, with more species in warm, moist, aseasonal climates and indirectly, with more species at higher stem abundance. These results imply direct limitation of species diversity by climatic stress and more rapid (co-)evolution and narrower niche partitioning in warm climates. They also support the idea that increased numbers of individuals associated with high primary productivity are partitioned to support a greater number of species.

Secondary succession is well-understood, to the point of being predictable for plant com-munities, but the successional changes in plant-herbivore interactions remains poorly explored. This is particularly true for tropical forests despite the increasing importance of early successional stages in tropical landscapes. Deriving expectations from successional theory, we examine properties of plant-herbivore interaction networks while accounting for host phylogenetic structure along a succession chronosequence in montane rainforest in Papua New Guinea. We present one of the most comprehensive successional inves-tigations of interaction networks, equating to > 40 person years of field sampling, and one of the few focused on montane tropical forests. We use a series of nine 0.2 ha for-est plots across young secondary, mature secondary and primary montane forest, sampled almost completely for woody plants and larval leaf chewers (Lepidoptera) using forest fell-ing. These networks comprised of 12 357 plant-herbivore interactions and were analysed using quantitative network metrics, a phylogenetically controlled host-use index and a qualitative network beta diversity measure. Network structural changes were low and spe-cialisation metrics surprisingly similar throughout succession, despite high network beta diversity. Herbivore abundance was greatest in the earliest stages, and hosts here had more species-rich herbivore assemblages, presumably reflecting higher palatability due to lower defensive investment. All herbivore communities were highly specialised, using a phylo-genetically narrow set of hosts, while host phylogenetic diversity itself decreased through-out the chronosequence. Relatively high phylogenetic diversity, and thus high diversity of plant defenses, in early succession forest may result in herbivores feeding on fewer hosts than expected. Successional theory, derived primarily from temperate systems, is limited in predicting tropical host-herbivore interactions. All succession stages harbour diverse and unique interaction networks, which together with largely similar network structures and consistent host use patterns, suggests general rules of assembly may apply to these systems.

A long-term goal in evolutionary ecology is to explain the incredible diversity of insect herbivores and patterns of host plant use in speciose groups like tropical Lepidoptera. Here, we used standardized food-web data, multigene phylogenies of both trophic levels and plant chemistry data to model interactions between Lepidoptera larvae (caterpillars) from two lineages (Geometridae and Pyraloidea) and plants in a species-rich lowland rainforest in New Guinea. Model parameters were used to make and test blind predictions for two hectares of an exhaustively sampled forest. For pyraloids, we relied on phylogeny alone and predicted 54% of species-level interactions, translating to 79% of all trophic links for individual insects, by sampling insects from only 15% of local woody plant diversity. The phylogenetic distribution of host-plant associations in polyphagous geometrids was less conserved, reducing accuracy. In a truly quantitative food web, only 40% of pair-wise interactions were described correctly in geometrids. Polyphenol oxidative activity (but not protein precipitation capacity) was important for understanding the occurrence of geometrids (but not pyraloids) across their hosts. When both foliar chemistry and plant phylogeny were included, we predicted geometrid–plant occurrence with 89% concordance. Such models help to test macroevolutionary hypotheses at the community level.

Efforts to incentivize the reduction of carbon emissions from deforestation and forest degradation require accurate carbon accounting. The extensive tropical forest of Papua New Guinea (PNG) is a target for such efforts and yet local carbon estimates are few. Previous estimates, based on models of neotropical vegetation applied to PNG forest plots, did not consider such factors as the unique species composition of New Guinea vegetation, local variation in forest biomass, or the contribution of small trees. We analysed all trees >1 cm in diameter at breast height (DBH) in Melanesia's largest forest plot (Wanang) to assess local spatial variation and the role of small trees in carbon storage. Above-ground living biomass (AGLB) of trees averaged 210.72 Mg ha−1 at Wanang. Carbon storage at Wanang was somewhat lower than in other lowland tropical forests, whereas local variation among 1-ha subplots and the contribution of small trees to total AGLB were substantially higher. We speculate that these differences may be attributed to the dynamics of Wanang forest where erosion of a recently uplifted and unstable terrain appears to be a major source of natural disturbance. These findings emphasize the need for locally calibrated forest carbon estimates if accurate landscape level valuation and monetization of carbon is to be achieved. Such estimates aim to situate PNG forests in the global carbon context and provide baseline information needed to improve the accuracy of PNG carbon monitoring schemes.

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

A community of frugivorous weevils was studied by quantitative rearing of 57 weevil species represented by 10485 individuals from 326 woody plant species in lowland rain forest in Papua New Guinea. Only fruits from 35% of plant species were attacked by weevils. On average, weevils were reared from only 1 in 33 fruits and 1 kg of fruit was attacked by 2.51 individuals. Weevil host specificity was relatively high: 42% of weevil species fed on a single plant genus, 19% on a single plant family and only 16% were reared from more than one family. However, monophagous specialists represented only 23% of all reared individuals. The average 1 kg of fruits was infested by 1.84 individuals of generalist weevils (feeding on allogeneric or allofamilial host species), 0.52 individual of specialists (feeding on a single or several congeneric species), and 0.15 individual of unknown host specificity. Large-seeded fruits with thin mesocarp tended to host specialist species whereas those with thick, fleshy mesocarp were often infested with both specialists and generalists. Weevils tended to avoid small-seeded, fleshy fruits. The low incidence of seed damage (3% of seeds) suggests that weevils are unlikely to play a major role in regulating plant populations via density-dependent mortality processes outlined by the Janzen–Connell hypothesis.

We documented one of the most species-rich assemblages of tropical rain-forest Auchenorrhyncha, comprising 402 phloem- and xylem-feeding species, by sampling adults from forest vegetation. Further, we reared 106 species from larvae sampled on 14 plant species. Both xylem- and phloem-feeding guilds exhibited wide host-plant ranges, as 74% of species fed on more than one plant family. In comparison, using data extracted from the temperate-zone literature, phloem-feeders exhibited lower host specificity in Papua New Guinea than in Germany, because in Papua New Guinea they were dominated by generalist Fulgoroidea while in Germany by specialist Membracoidea. The similarity of Auchenorrhyncha assemblages from different plant species was unrelated to the phylogenetic distance between their hosts. Host specificity, abundance and species composition of Auchenorrhyncha assemblages were unrelated to the optimum of their host plant species on succession gradient from secondary to primary forest. Higher host specificity did not lead to greater species richness in Auchenorrhyncha assemblages feeding on different plant species, but the number of species feeding on a particular plant species was a strong predictor of the Auchenorrhyncha abundance on that plant. These patterns suggest that Auchenorrhyncha assemblages on these plant species are not saturated with species and determined by division of limited resources among competitors, but instead are dependent on the number of colonizers from the regional species pool.

Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the Medicago truncatula reference genome to confidently identify 87 596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago .( Medicago; phylogenomics; whole-genome resequencing.)

The demand for knowledge about the tree of life is steadily rising in ecology and other fields, but bioinformatic resources designed to meet these needs remain poorly developed. Ecologists pursuing phylogenetic insights into the organization of communities have come to rely on relatively conservative reference trees that, in general, are poorly resolved and documented. New methods for inferring very large trees by mining data from DNA sequence repositories will undoubtedly be useful in community phylogenetics, but are not without limitations. Here we argue that the collective phylogenetic knowledge embodied in the literature of systematics is a valuable resource that can be tapped in assembling synthetic trees. Assembling a composite ''literature-based'' tree by the judicious grafting of clades is one way to achieve a synthesis of current knowledge, and could, under some circumstances, better represent ''what we know'' about phylogenetic relationships than results obtained from automated pipelines. We describe an approach and new software for storing and annotating trees from published studies and grafting clades together in a documented and repeatable manner. Using this agglomerative approach, we are in the process of assembling a literature- based tree for land plants, which presently contains 14 423 species from over 259 sources. For this strategy to be maximally effective, improvements in digital infrastructure are needed to capture and deploy advances in phylogenetic knowledge as they are published.