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The early events in the vegetative development of the holoparasite Rafflesia have long remained a mystery. Because its entire vegetative growth occurs within the host body, very little is known about the developmental events prior to emergence of the floral shoot. The goal of this study was to describe the events that occur during the vegetative growth of R. consueloae, particularly in the early stages of infection. We performed extensive microtome sectioning of multiple root and stem segments from different Tetrastigma host individuals to examine the cytology, distribution, and development of the R. consueloae endophyte within the host tissues. We found that R. consueloae infection is restricted to the roots of its host. Infection begins within the vascular cambium where the endophyte appears to initially reside prior to their radial spread to the vascular tissues. The tissues obtained from different host individuals had varying degrees of infection alluding to a possible role of host resistance mechanisms and/or varying levels of parasite infectiousness. Endophyte presence in host vines without external manifestations of infection indicates that the parasite may dwell within the host tissues for prolonged periods as small cell clusters without transitioning to the reproductive stage. Furthermore, we found that floral shoots may develop in scarcely infected host tissues indicating that extensive endophyte growth within the host is not a prerequisite to the onset of reproductive development. Overall, our study describes for the first time the developmental events prior to emergence of R. consueloae buds from its host.

We describe and illustrate Begonia jurgenneae, a newly discovered species from Capiz and Iloilo Provinces, Panay Island, Philippines. A complete taxonomic treatment is here provided including a comprehensive morphological description, diagnostic comparisons with allied taxa, a phenological data, a distribution map, color images, and a preliminary conservation assessment.

Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.

Background Interspecific interactions have long been assumed to play an important role in diversification. Mutualistic interactions, such as nursery pollination mutualisms, have been proposed as good candidates for diversification through co-speciation because of their intricate nature. However, little is known about how speciation and diversification proceeds in emblematic nursery pollination systems such as figs and fig wasps. Here, we analyse diversification in connection with spatial structuring in the obligate mutualistic association between Ficus septica and its pollinating wasps throughout the Philippines and Taiwan. Results Ceratosolen wasps pollinating F. septica are structured into a set of three vicariant black coloured species, and a fourth yellow coloured species whose distribution overlaps with those of the black species. However, two black pollinator species were found to co-occur on Lanyu island. Microsatellite data on F. septica indicates the presence of three gene pools that broadly mirrors the distribution of the three black clades. Moreover, receptive fig odours, the specific message used by pollinating wasps to locate their host tree, varied among locations. Conclusions F. septica and its black pollinator clades exhibited similar geographic structuring. This could be due originally to geographic barriers leading to isolation, local adaptation, and finally co-structuring. Nevertheless, the co-occurrence of two black pollinator species on Lanyu island suggests that the parapatric distribution of the black clades is now maintained by the inability of migrating individuals of black pollinators to establish populations outside their range. On the other hand, the distribution of the yellow clade strongly suggests an initial case of character displacement followed by subsequent range extension: in our study system, phenotypic or microevolutionary plasticity has allowed the yellow clade to colonise hosts presenting distinct odours. Hence, while variation in receptive fig odours allows specificity in the interaction, this variation does not necessarily lead to coevolutionary plant-insect diversification. Globally, our results evidence evolutionary plasticity in the fig-fig wasp mutualism. This is the first documentation of the presence of two distinct processes in pollinating fig wasp diversification on a host species: the formation of vicariant species and the co-occurrence of other species over large parts of their ranges probably made possible by character displacement.

When Darwin visited the Galapagos archipelago, he observed that, in spite of the islands’ physical similarity, members of species that had dispersed to them recently were beginning to diverge from each other. He postulated that these divergences must have resulted primarily from interactions with sets of other species that had also diverged across these otherwise similar islands. By extrapolation, if Darwin is correct, such complex interactions must be driving species divergences across all ecosystems. However, many current general ecological theories that predict observed distributions of species in ecosystems do not take the details of between-species interactions into account. Here we quantify, in sixteen forest diversity plots (FDPs) worldwide, highly significant negative density-dependent (NDD) components of both conspecific and heterospecific between-tree interactions that affect the trees’ distributions, growth, recruitment, and mortality. These interactions decline smoothly in significance with increasing physical distance between trees. They also tend to decline in significance with increasing phylogenetic distance between the trees, but each FDP exhibits its own unique pattern of exceptions to this overall decline. Unique patterns of between-species interactions in ecosystems, of the general type that Darwin postulated, are likely to have contributed to the exceptions. We test the power of our null-model method by using a deliberately modified data set, and show that the method easily identifies the modifications. We examine how some of the exceptions, at the Wind River (USA) FDP, reveal new details of a known allelopathic effect of one of the Wind River gymnosperm species. Finally, we explore how similar analyses can be used to investigate details of many types of interactions in these complex ecosystems, and can provide clues to the evolution of these interactions.

Aim: Plants distributed between southern Taiwan and the north of the Philippines are spread among numerous small islands in an area crossed by the powerful Kuroshio current. Oceanic currents can be effective seed-dispersal agents for coastal plant species. Moreover, the Luzon Strait is an area prone to tropical cyclones. The aim of this study is to look at the dispersal capability of an endangered coastal plant species, the Mearns fig (Ficus pedunculosa var. mearnsii), using both experimental and population genetics methods. Location: Southern Taiwan, the Philippines, and the islands between Luzon and Taiwan Island. Methods: This study combined two types of analysis, i.e., buoyancy experiments on syconia and double digest restriction-associated DNA sequencing (ddRAD), to analyze the population genetics of the Mearns fig. Results: We first discovered that mature Mearns fig syconia could float in seawater. They have a mean float duration of 10 days to a maximum of 21 days. Germination rates varied significantly between Mearns fig seeds that had undergone different durations of flotation treatment. Population genetic analysis shows a high degree of inbreeding among various Mearns fig populations. Moreover, no isolation by distance was found between the populations and individuals. Main conclusions: From our analysis of the genetic structure of the Mearns fig populations, we can clearly highlight the effect of the Kuroshio oceanic current on the seed dispersal of this fig tree. Comprehensive analysis has shown that Mearns fig seeds are still viable before the mature syconium sinks into the seawater, and so they could use the Kuroshio Current to float to the current population locations in Taiwan.

Aim: Plants distributed between southern Taiwan and the north of the Philippines are spread among numerous small islands in an area crossed by the powerful Kuroshio current. Oceanic currents can be effective seed-dispersal agents for coastal plant species. Moreover, the Luzon Strait is an area prone to tropical cyclones. The aim of this study is to look at the dispersal capability of an endangered coastal plant species, the Mearns fig (Ficus pedunculosa var. mearnsii ), using both experimental and population genetics methods. Location: Southern Taiwan, the Philippines, and the islands between Luzon and Taiwan Island. Methods: This study combined two types of analysis, i.e., buoyancy experiments on syconia and double digest restriction-associated DNA sequencing (ddRAD), to analyze the population genetics of the Mearns fig. Results: We first discovered that mature Mearns fig syconia could float in seawater. They have a mean float duration of 10 days to a maximum of 21 days. Germination rates varied significantly between Mearns fig seeds that had undergone different durations of flotation treatment. Population genetic analysis shows a high degree of inbreeding among various Mearns fig populations. Moreover, no isolation by distance was found between the populations and individuals. Main conclusions: From our analysis of the genetic structure of the Mearns fig populations, we can clearly highlight the effect of the Kuroshio oceanic current on the seed dispersal of this fig tree. Comprehensive analysis has shown that Mearns fig seeds are still viable before the mature syconium sinks into the seawater, and so they could use the Kuroshio Current to float to the current population locations in Taiwan.

Despite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets. Competing Interest Statement The authors have declared no competing interest.

Despite their ecological and evolutionary importance, fig trees still lack a resolved phylogeny. We used multiple analytical approaches and 600 conserved RAD-seq loci collected across 40 representative species to infer phylogenetic relationships among the major clades of Ficus. Our results converged on a fully resolved phylogeny that contradicts previous hypotheses by not placing section Pharmacosycea sister to all other fig trees. Instead, we find that subgenus Sycomorus is sister to two clades, one comprising all other gynodioecious sections, and the other containing all monoecious sections. Our results corroborate earlier botanist hypotheses and provide a baseline for future classification. We infer the evolution of key traits (growth form, breeding system and pollination mode) and find that, contrary to previous hypotheses, the ancestor of extant fig trees was likely a gynodioecious and actively pollinated tree. Our results open new opportunities to explore diversification patterns in fig trees and better understand their mutualistic interaction with wasps.