An extreme case of plant-insect codiversification: figs and fig-pollinating wasps

Characterisation of the fig-fig wasp holobiont

Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.

Enhanced and asymmetric signatures of hybridization at climatic margins: Evidence from closely related dioecious fig species

Hybridization plays a significant role in biological evolution. However, it is not clear whether ecological contingency differentially influences likelihood of hybridization, particularly at ecological margins where parental species may exhibit reduced fitnesses. Moreover, it is unknown whether future ecosystem change will increase the prevalence of hybridization. Ficus heterostyla and F. squamosa are closely related species co-distributed from southern Thailand to southwest China where hybridization, yielding viable seeds, has been documented. As a robust test of ecological factors driving hybridization, we investigated spatial hybridization signatures based on nuclear microsatellites from extensive population sampling across a widespread contact range. Both species showed high population differentiation and strong patterns of isolation by distance. Admixture estimates exposed asymmetric interspecific gene flow. Signatures of hybridization increase significantly towards higher latitude zones, peaking at the northern climatic margins. Geographic variation in reproductive phenology combined with ecologically challenging marginal habitats may promote this phenomenon. Our work is a first systematic evaluation of such patterns in a comprehensive, latitudinally-based clinal context, and indicates that tendency to hybridize appears strongly influenced by environmental conditions. Moreover, that future climate change scenarios will likely alter and possibly augment cases of hybridization at ecosystem scales.

Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies

Fig wasps (Agaonidae; Hymenoptera) are the only pollinating insects of fig trees (Ficus; Moraceae), forming the most closely and highly specific mutualism with the host. We used transcriptome sequences of 25 fig wasps from six genera to explore the evolution of key molecular components of fig wasp chemosensory genes: odorant-binding proteins (OBPs) and chemosensory proteins (CSPs). We identified a total 321 OBPs and 240 CSPs, with each species recording from 6 to 27 OBP genes and 6-19 CSP genes. 318 OBP genes are clustered into 17 orthologous groups and can be divided into two groups: PBP sensitive to pheromone and GOBP sensitive to general odor molecules, such as alcohols, esters, acids, ketones, and terpenoids. 240 CSP genes are clustered into 12 orthologous groups, which can be divided into three major groups and have functions, such as olfactory, tissue formation and/or regeneration, developmental, and some specific and unknown function. The gene sequences of most orthologous groups vary greatly among species and are consistent with the phylogenetic relationships between fig wasps. Strong purifying selection of both OBP and CSP genes was detected, as shown by low ω values. A positive selection was detected in one locus in CSP1. In conclusion, the evolution of chemosensory proteins OBPs and CSPs in fig wasps is relatively conservative, and they play an indispensable role in the life activities of fig wasps. Our results provide a starting point for understanding the molecular basis of the chemosensory systems of fig wasps.

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.

Local ecological factors, not interference competition, drive the foundress number of two species of fig wasp sharing Ficus septica figs

Recent studies have challenged assumptions about the classic fig-fig wasp pollination mutualism model, suggesting that further investigation into the receptive phase of fig development is needed. This study assessed the pollination mechanisms of Ficus septica in southern Taiwan and identified two species of wasps as the primary pollinators. Machine learning was used to identify and rank the factors that explain the relative abundance of these wasps. The two wasp species showed the highest level of cohabitation ever reported in the literature, with three-quarters of the figs containing multiple foundresses. The study also reported re-emerged foundresses and a 10% ratio of pollinated figs without foundresses. Local factors, such as the sampling period and tree identity, were the best predictors of the presence and number of each foundress species, with fig size also affecting the number of foundresses. The study highlights the variability in pollinator abundance between figs, crops, and trees. It also shows that the local environment of the trees and the availability of figs are crucial factors in determining which figs the pollinator wasps choose. These findings challenge assumptions about the classic mutualism model and suggest that long-term surveys are needed to estimate the relative contributions of each partner and provide data for evolutionary and ecological models. This study also provides valuable insights into the factors that affect the abundance and interactions of pollinator wasps during the receptive phase of fig development, with implications for understanding the behaviour of pollinating wasps and advancing our knowledge of population dynamics in Ficus species.

A telomere-to-telomere reference genome of ficus (Ficus hispida) provides new insights into sex determination

A high-quality reference genome is indispensable for resolving biologically essential traits. Ficus hispida is a dioecious plant. A complete Ficus reference genome will be crucial for understanding their sex evolution and important biological characteristics, such as aerial roots, mutualistic symbiosis with ficus-wasps, and fruiting from old stems. Here, we generated a telomere-to-telomere (T2T) genome for F. hispida using PacBio HiFi and Oxford Nanopore Ultra-long sequencing technologies. The genome contiguity and completeness has shown improvement compared with the previously released genome, with the annotation of six centromeres and 28 telomeres. We have refined our previously reported 2-Mb male-specific region into a 7.2-Mb genomic region containing 51 newly predicted genes and candidate sex-determination genes AG2 and AG3. Many of these genes showed extremely low expression, likely attributed to hypermethylation in the gene body and promoter regions. Gene regulatory networks (GRNs) revealed that AG2 and AG3 are related to the regulation of stamen development in male flowers, while the AG1 gene is responsible for regulating female flowers' defense responses and secondary metabolite processes. Comparative analysis of GRNs showed that the NAC, WRKY, and MYB transcription factor families dominate the female GRN, whereas the MADS and MYB transcription factor families are prevalent in the male GRN.

Evolution of Wolbachia reproductive and nutritional mutualism: insights from the genomes of two novel strains that double infect the pollinator of dioecious Ficus hirta

Wolbachia is a genus of maternally inherited endosymbionts that can affect reproduction of their hosts and influence metabolic processes. The pollinator, Valisia javana, is common in the male syconium of the dioecious fig Ficus hirta. Based on a high-quality chromosome-level V. javana genome with PacBio long-read and Illumina short-read sequencing, we discovered a sizeable proportion of Wolbachia sequences and used these to assemble two novel Wolbachia strains belonging to supergroup A. We explored its phylogenetic relationship with described Wolbachia strains based on MLST sequences and the possibility of induction of CI (cytoplasmic incompatibility) in this strain by examining the presence of cif genes known to be responsible for CI in other insects. We also identified mobile genetic elements including prophages and insertion sequences, genes related to biotin synthesis and metabolism. A total of two prophages and 256 insertion sequences were found. The prophage WOjav1 is cryptic (structure incomplete) and WOjav2 is relatively intact. IS5 is the dominant transposon family. At least three pairs of type I cif genes with three copies were found which may cause strong CI although this needs experimental verification; we also considered possible nutritional effects of the Wolbachia by identifying genes related to biotin production, absorption and metabolism. This study provides a resource for further studies of Wolbachia-pollinator-host plant interactions.

Field sampling of fig pollinator wasps across host species and host developmental phase: Implications for host recognition and specificity

Previous genetic studies of pollinator wasps associated with a community of strangler figs (Ficus subgenus Urostigma, section Americana) in Central Panama suggest that the wasp species exhibit a range in host specificity across their host figs. To better understand factors that might contribute to this observed range of specificity, we used sticky traps to capture fig-pollinating wasp individuals at 13 Ficus species, sampling at different phases of the reproductive cycle of the host figs (e.g., trees with receptive inflorescences, or vegetative trees, bearing only leaves). We also sampled at other tree species, using them as non-Ficus controls. DNA barcoding allowed us to identify the wasps to species and therefore assign their presence and abundance to host fig species and the developmental phase of that individual tree. We found: (1) wasps were only very rarely captured at non-Ficus trees; (2) nonetheless, pollinators were captured often at vegetative individuals of some host species; (3) overwhelmingly, wasp individuals were captured at receptive host fig trees representing the fig species from which they usually emerge. Our results indicate that wasp occurrence is not random either spatially or temporally within the forest and across these hosts, and that wasp specificity is generally high, both at receptive and vegetative host trees. Therefore, in addition to studies that show chemicals produced by receptive fig inflorescences attract pollinator wasps, we suggest that other cues (e.g., chemicals produced by the leaves) can also play a role in host recognition. We discuss our results in the context of recent findings on the role of host shifts in diversification processes in the Ficus genus.

The genetic structuring in pollinating wasps of Ficus hispida in continental Asia

The interaction between figs and fig wasps provides a striking example of obligate brood site pollination mutualism. Monoecious figs, constituting independent radiations in each tropical biome, are present in significant proportions worldwide, but in continental Asia, dioecious figs have diverged into various niches, making the region's assemblage remarkably diverse. However, the reproductive success of figs and fig wasps largely depends on the fig wasp dispersal process. Monoecious fig pollinators in continental Asian tropical rain forests exhibit high gene flow of the plant, while many dioecious fig pollinators have a more restricted gene flow. However, there are limited studies on the genetic structure of dioecious Ficus pollinators that pollinate figs with intermediate gene flow. Here, we used molecular methods to investigate the genetic structure of pollinating wasps of the widely distributed dioecious Ficus hispida in China and Southeast Asia. Sequence data from two gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S genes. Both molecular and morphological results support two fig wasp species at our sampling sites. Our findings suggest that for widely sympatric Ficus species in continental Asia, monoecious figs presenting long gene glow have the fewest fig wasp species, followed by dioecious figs presenting intermediate gene flow, and dioecious figs presenting local gene flow have the most fig wasp species.

Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

East‒West genetic differentiation across the Indo-Burma hotspot: evidence from two closely related dioecious figs

BACKGROUND

Understanding biodiversity patterns and their underlying mechanisms is of interest to ecologists, biogeographers and conservationists and is critically important for conservation efforts. The Indo-Burma hotspot features high species diversity and endemism, yet it also faces significant threats and biodiversity losses; however, few studies have explored the genetic structure and underlying mechanisms of Indo-Burmese species. Here, we conducted a comparative phylogeographic analysis of two closely related dioecious Ficus species, F. hispida and F. heterostyla, based on wide and intensive population sampling across Indo-Burma ranges, using chloroplast (psbA-trnH, trnS-trnG) and nuclear microsatellite (nSSR) markers, as well as ecological niche modeling.

RESULTS

The results indicated large numbers of population-specific cpDNA haplotypes and nSSR alleles in the two species. F. hispida showed slightly higher chloroplast diversity but lower nuclear diversity than F. heterostyla. Low-altitude mountainous areas of northern Indo-Burma were revealed to have high genetic diversity and high habitat suitability, suggesting potential climate refugia and conservation priority areas. Strong phylogeographic structure and a marked east‒west differentiation pattern were observed in both species, due to the interactions between biotic and abiotic factors. Interspecific dissimilarities at fine-scale genetic structure and asynchronized historical dynamics of east‒west differentiation between species were also detected, which were attributed to different species-specific traits.

CONCLUSIONS

We confirm hypothesized predictions that interactions between biotic and abiotic factors largely determine the patterns of genetic diversity and phylogeographic structure of Indo-Burmese plants. The east‒west genetic differentiation pattern observed in two targeted figs can be generalized to some other Indo-Burmese plants. The results and findings of this work will contribute to the conservation of Indo-Burmese biodiversity and facilitate targeted conservation efforts for different species.

Metabolomics and genetics of reproductive bud development in Ficus carica var. sativa (edible fig) and in Ficus carica var. caprificus (caprifig): similarities and differences

In figs, reproductive biology comprises cultivars requiring or not pollination, with female trees (edible fig) and male trees (caprifig) bearing different types of fruits. Metabolomic and genetic studies may clarify bud differentiation mechanisms behind the different fruits. We used a targeted metabolomic analysis and genetic investigation through RNA sequence and candidate gene investigation to perform a deep analysis of buds of two fig cultivars, 'Petrelli' (San Pedro type) and 'Dottato' (Common type), and one caprifig. In this work, proton nuclear magnetic resonance (¹H NMR-based metabolomics) has been used to analyze and compare buds of the caprifig and the two fig cultivars collected at different times of the season. Metabolomic data of buds collected on the caprifig, 'Petrelli', and 'Dottato' were treated individually, building three separate orthogonal partial least squared (OPLS) models, using the "y" variable as the sampling time to allow the identification of the correlations among metabolomic profiles of buds. The sampling times revealed different patterns between caprifig and the two edible fig cultivars. A significant amount of glucose and fructose was found in 'Petrelli', differently from 'Dottato', in the buds in June, suggesting that these sugars not only are used by the ripening brebas of 'Petrelli' but also are directed toward the developing buds on the current year shoot for either a main crop (fruit in the current season) or a breba (fruit in the successive season). Genetic characterization through the RNA-seq of buds and comparison with the literature allowed the identification of 473 downregulated genes, with 22 only in profichi, and 391 upregulated genes, with 21 only in mammoni.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Evolutionary patterns of host switching, lifestyle mode, and the diversification history in symbiotic zoantharians

Symbioses play important roles in forming the structural and distributional patterns of marine diversity. Understanding how interspecies interactions through symbioses contribute to biodiversity is an essential topic. Host switching has been considered as one of the main drivers of diversification in symbiotic systems. However, its process and patterns remain poorly investigated in the marine realm. Hexacoral species of the order Zoantharia (=zoantharians) are often epizoic on other marine invertebrates and generally use specific taxa as hosts. The present study investigates the patterns of host switching and the diversification history of zoantharians based on the most comprehensive molecular phylogenetic analyses to date, using sequences from three mitochondrial and three nuclear markers from representatives of 27 of 29 genera. Our results indicate that symbiotic zoantharians, in particular those within suborder Macrocnemina, diversified through repeated host switching. In addition, colonization of new host taxa appears to have driven morphological and ecological specialization in zoantharians. These findings have important implications for understanding the role of symbioses in the morphological and ecological evolution of marine invertebrates.

Host insect specificity and interspecific competition drive parasitoid diversification in a plant-insect community

Ecological interactions among plants, insect herbivores and parasitoids are pervasive in nature and play important roles in community assembling, but the codiversification of tri-trophic interactions has received less attention. Here we compare pairwise codiversification patterns between a set of 22 fig species, their herbivorous pollinating and galling wasps, and their parasitoids. The parasitoid phylogeny showed significant congruence and more cospeciation events with host insects phylogeny than with host plants. These results suggest that parasitoid phylogeny and speciation is more closely related to their host insects than to their host plants. The pollinating wasps hosted more parasitoid species than gallers and indicated a more intense interspecific competition among parasitoids associated with pollinators. Closer matching and fewer evolutionary host shifts were found between parasitoids and galler hosts than between parasitoids and pollinator hosts. These results suggest that interspecific competition among parasitoids, rather than resource availability of host wasps, is the main driver of the codiversification pattern in this community. Therefore, our study highlights the important role of interspecific competition among high trophic level insects in plant-insect tri-trophic community assembling. This article is protected by copyright. All rights reserved.

Key innovations and the diversification of Hymenoptera

The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.

Paleogene Ficus leaves from India and their implications for fig evolution and diversification

PREMISE

Ficus is a scientifically and economically important genus with abundant fossil records from the Paleocene to Pleistocene, but with an intriguing early evolutionary history that remains unresolved. Here, the foliage of three well-preserved figs is described from the early Paleogene succession of the Gurha mine, Rajasthan, India. These fossils provide new morphological data that strengthens our understanding of the past occurrences of Ficus and, alongside all validly published records of fossil figs, helps to trace the evolutionary history of figs.

METHODS

Fossils were identified and described by comparison with their closest modern analogs using the Nearest Living Relative (NLR) technique. Validated fig records are listed and categorized into six geological time frames. Modern precipitation data for the current distributions of NLRs were downloaded from the Climatic Research Unit Timeseries.

RESULTS

Fossil leaves assigned to three new species Ficus paleodicranostyla, F. paleovariegata, and F. paleoauriculata closely resemble their modern analogs based on leaf morphology. Reliable fossil records were used to hypothesize historical fig distributions and paleodispersal pathways. Precipitation data suggest higher precipitations at the fossil locality during the early Paleogene than at present.

CONCLUSIONS

The fossils described herein supplement fig fossil records known from other regions indicating that figs were widely diverse across low latitudes by the early Paleogene. These data support a Eurasian origin for figs, highlight a pivotal role for the Indian subcontinent during the early phase of fig diversification, and depict a perhumid-to-humid climate with high rainfall concordant with paleoclimate evidence from the Gurha mine.

Olfactory and gustatory receptor genes in fig wasps: Evolutionary insights from comparative studies

The mechanisms of chemoreception in fig wasps (Hymenoptera, Agaonidae) are of primary importance in their co-evolutionary relationship with the fig trees they pollinate. We used transcriptome sequences of 25 fig wasps in six genera that allowed a comparative approach to the evolution of key molecular components of fig wasp chemoreception: their odorant (OR) and gustatory (GR) receptor genes. In total, we identified 311 ORs and 47 GRs, with each species recording from 5 to 30 OR genes and 1-4 GR genes. 304 OR genes clustered into 18 orthologous groups known to be sensitive to cuticular hydrocarbons (CHC), pheromones, acids, alcohols and a variety of floral scents such as cineole, Linalool, and Heptanone. 45 GR genes clustered into 4 orthologous groups that contain sweet, bitter, CO₂ and undocumented receptors. Gene sequences in most orthologous groups varied greatly among species, except for ORco (60.0% conserved) and sweet receptors (30.7% conserved). Strong purifying selection of both odorant and gustatory genes was detected, as shown by low ω values. Signatures of positive selection were detected in loci from both OR and GR orthologous groups. Fig wasps have relatively few olfactory and especially gustatory receptors, reflecting the natural history of the system. Amino acid sequences nonetheless vary significantly between species and are consistent with the phylogenetic relationships among fig wasps. The differences in ORs within some orthologous groups from the same species, but different hosts and from closely related species from one host can reach as low as 49.3% and 9.8% respectively, implying the ORs of fig wasps can evolve rapidly to novel ecological environments. Our results provide a starting point for understanding the molecular basis of the chemosensory systems of fig wasps.

Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps

Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.

Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies

Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae)

Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

Diversity and metabolic potentials of microbial communities associated with pollinator and cheater fig wasps in fig-fig wasp mutualism system

Microbial symbionts can influence a myriad of insect behavioral and physiological traits. However, how microbial communities may shape or be shaped by insect interactions with plants and neighboring species remains underexplored. The fig-fig wasp mutualism system offers a unique model to study the roles of microbiome in the interactions between the plants and co-habiting insects because a confined fig environment is shared by two fig wasp species, the pollinator wasp (Eupristina altissima and Eupristina verticillata) and the cheater wasp (Eupristina sp1 and Eupristina sp2). Here, we performed whole genome resequencing (WGS) on 48 individual fig wasps (Eupristina spp.) from Yunnan, China, to reveal the phylogenetic relationship and genetic divergence between pollinator and congeneric cheater wasps associated with the Ficus trees. We then extracted metagenomic sequences to explore the compositions, network structures, and functional capabilities of microbial communities associated with these wasps. We found that the cheaters and pollinators from the same fig species are sister species, which are highly genetically divergent. Fig wasps harbor diverse but stable microbial communities. Fig species dominate over the fig wasp genotype in shaping the bacterial and fungal communities. Variation in microbial communities may be partially explained by the filtering effect from fig and phylogeny of fig wasps. It is worth noting that cheaters have similar microbial communities to their sister pollinators, which may allow cheaters to coexist and gain resources from the same fig species. In terms of metabolic capabilities, some bacteria such as Desulfovibrio and Lachnospiraceae are candidates involved in the nutritional uptake of fig wasps. Our results provide novel insights into how microbiome community and metabolic functions may couple with the fig-wasp mutualistic systems.

The roles of the ostiole in the fig-fig wasp mutualism from a morpho-anatomical perspective

The syconium is the urn-shaped inflorescence shared by all species of the genus Ficus. The orifice at the apex of the syconium is called the ostiole, and it is covered by interlocking bracts. The ostiolar bracts can have different arrangements, which only allow the entry of mutualist wasps and promote reproductive isolation among Ficus species. Here, we analyze the ostiolar structures that could play a role as selective filter and therefore impact the fig-fig wasp mutualism in the neotropical Ficus sections Americanae and Pharmacosycea. Samples of syconia with pistillate flowers during the receptive phase of seven species of Ficus were examined using light and scanning electron microscopy. Tests for histolocalization of substances were employed to detect secretory activity throughout the ostiolar tissues. Our results indicated that the ostiole has two components: ostiolar bracts and the periostiolar zone. Interspecies variation in ostiolar bract arrangement in both sections studied was broader than previously reported. We report for the first time for Ficus: (i) two types of ostiolar osmophores (mesophyll and diffuse), that could be a source of volatile compounds for attracting fig wasps; (ii) colleters in the axil of ostiolar bracts, which probably lubricate and facilitate the entry of pollinating wasps into the syconial cavity; (iii) secretory trichomes around the ostiolar bracts, and (iv) syconium basal bracts (F. isophlebia) covering the ostiole, which are the first physical barrier that the fig wasps must overcome to access receptive pistillate flowers. We describe the zones that compose the ostiole, which support the hypothesis that the ostiole is a selective filter in the interactions of fig trees with Agaonidae fig wasps. We also suggest that ostiolar osmophores, colleters, the periostiolar zone, and the arrangements of the ostiolar bracts may be informative with respect to Ficus systematics.

Plant‐associate interactions and diversification across trophic levels

Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates' population structure often paralleled their hosts' population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts' geographic distribution on mutualists' dispersal.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.

The complete chloroplast genome sequence of Ficus sarmentosa (Moraceae, Rosales), a widely distributed fig tree in East Asia

Ficus sarmentosa is a common climbing fig tree in East Asia in Moraceae, and its particular geographical distributed pattern and on-going radiation evolution make it significant to explore evolutionary history and biogeography of Ficus. In this work, the first complete chloroplast genome of F. sarmentosa was reported using Illumina NovaSeq high-throughput sequencing data. Totally, the whole chloroplast genome of F. sarmentosa is 160,183 bp in length, which includes large single-copy region of 88,307 bp, small single-copy region of 20,080 bp, and two pairs of inverted repeat regions of 25,898 bp. In addition, GC content and microsatellite makers of the genome were explored. Lastly, phylogenetic analysis demonstrated the closest relationship between F. sarmentosa and F. pumila.

Early diversifications of angiosperms and their insect pollinators: were they unlinked?

The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.

Rising temperatures threaten pollinators of fig trees-Keystone resources of tropical forests

Pollinating insects are decreasing worldwide in abundance, biomass, and species richness, affecting the plants that rely on pollinators for fruit production and seed set. Insects are often sensitive to high temperatures. The projected temperature increases may therefore severely affect plants that rely on insect pollinators. Highly specialized mutualisms are expected to be particularly vulnerable to change because they have fewer partner options should one partner become unavailable. In the highly specialized mutualism between fig trees and their pollinating fig wasp, each fig species is pollinated by only one or a few wasp species. Because of their year‐round fruit production, fig trees are considered a keystone resource for tropical forests. However, to produce fruits, wild fig trees need to be pollinated by fig wasps that typically travel a long one‐way trip from the tree donating pollen to the tree receiving pollen. In a few previous studies from China and Australia, increasing temperatures dramatically decreased fig wasp lifespan. Are these grim results generalizable to fig mutualisms globally? Here, we use survival experiments to determine the effect of increasing temperature on the lifespan of Neotropical fig wasps associated with five common Panamanian Ficus species. Experimental temperatures were based on the current daytime mean temperature of 26.8°C (2SD: 21.6–31.7°C) and the predicted local temperature increase of 1–4°C by the end of the 21st century. We found that all tested pollinator wasp species had a significantly shorter lifespan in 30, 32, 34, and 36°C compared to the current diurnal mean temperature of 26°C. At 36°C pollinator median lifespan decreased to merely 2–10 h (6%–19% of their median lifespan at 26°C). Unless wasps can adapt, such a dramatic reduction in lifespan is expected to reduce the number of pollinators that successfully disperse to flowering fig trees, and may therefore jeopardize both fruit set and eventually survival of the mutualism.

Overlaps in olfactive signalling coupled with geographic variation may result in localised pollinator sharing between closely related Ficus species

Background

In brood site pollination mutualisms, pollinators are attracted by odours emitted at anthesis. In Ficus, odours of receptive figs differ among species and the specific pollinators generally only enter figs of their host species ensuring a pre-zygotic barrier to plant interspecific hybridisation. However, field observations recorded that, in Guangdong province in China, Valisia javana hilli, the local pollinator of F. hirta, entered and reproduced successfully in the figs of the closely related F. triloba on a regular basis. We propose that closely related Ficus species produce similar receptive fig odours. Under particular contexts of odours locally present, the receptive fig odours of non-host figs of a Ficus species may become attractive to pollinators of closely related Ficus species. We used the headspace technique to collect in situ receptive fig odours of F. triloba in a series of locations in China. Under controlled conditions, we tested the attraction of fig pollinating wasps from F. hirta and F. triloba to host figs and non-host figs in Y tube experiments.

Results

Receptive fig odours of F. triloba though different from those of F. hirta, were mainly composed of a same set of volatile organic compounds. When given the choice between receptive fig odours and air, the pollinating wasps were only attracted by their host’s odours. However, when given a choice between host and non-host figs the pollinators of F. hirta were equally attracted by the two odours while the pollinators of F. triloba tended to be more attracted by their host’s fig odours.

Conclusions

Receptive fig odours vary geographically within species and the differentiation of receptive fig odours between closely related Ficus species is often incomplete. This allows localised or occasional pollinator sharing following different modalities. Cross stimulation when wasps are exposed simultaneously to odours of host and non-host species may be important. While occasional pollinator sharing may play a marginal role when wasp populations are robust, it may ensure the provisioning of new pollinators from the closest relative of a Ficus species if its pollinators go extinct.

Evolution of andrenine bees reveals a long and complex history of faunal interchanges through the Americas during the Mesozoic and Cenozoic

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Here, we apply DNA sequences from multiple genes to recover a dated phylogeny and historical biogeographic of andrenine bees, a large group of 3000 species mainly distributed in arid areas of North America, South America, and the Palearctic region. Our results corroborate the monophyly of Andreninae and points toward a South America origin for the group during the Late Cretaceous. Overall, we provide strong evidence of amphitropical distributional pattern currently observed in the American continent as result of faunal interchange in at least three historical periods, much prior to the Panama Isthmus closure. The Palearctic diversity is shown to have arisen from North America during the Eocene and Miocene, and the Afrotropical lineages likely originated from the Palearctic region in the Miocene when the Sahara Desert was mostly vegetated. The incursions from South to North America and then onto the Old World are chronological congruent with periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

The obligate pollination mutualism between figs (Ficus, Moraceae) and pollinator wasps (Agaonidae, Hymenoptera) is a classic example of cospeciation. However, examples of phylogenetic incongruencies between figs and their pollinators suggest that pollinators may speciate by host shifting. To investigate the mechanism of speciation by host shifting, we examined the phylogenetic relationships and population genetic structures of six closely related fig species and their pollinators from southern China and Taiwan-Ryukyu islands using various molecular markers. The results revealed 1) an extraordinary case of pollinator sharing, in which five distinct fig species share a single pollinator species in southern China; 2) two types of copollination, namely, sympatric copollination by pollinator duplication or pollinator migration, and allopatric copollination by host migration and new pollinator acquisition; 3) fig species from southern China have colonized Taiwan repeatedly and one of these events has been followed by host shifting, reestablishment of host specificity, and pollinator speciation, in order. Based on our results, we propose a model for pollinator speciation by host shifting in which the reestablishment of host-specificity plays a central role in the speciation process. These findings provide important insights into understanding the mechanisms underlying pollinator speciation and host specificity in obligate pollination mutualism.

Phylogenetic and population genetic analyses reveal mechanisms of pollinator sharing, copollination and speciation by host-shift in fig-wasp mutualism.

Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants

More than 95% of phytophagous true bug (Hemiptera: Heteroptera) species belong to four superfamilies: Miroidea (Cimicomorpha), Pentatomoidea, Coreoidea, and Lygaeoidea (all Pentatomomorpha). These iconic groups of highly diverse, overwhelmingly phytophagous insects include several economically prominent agricultural and silvicultural pest species, though their evolutionary history has not yet been well resolved. In particular, superfamily- and family-level phylogenetic relationships of these four lineages have remained controversial, and the divergence times of some crucial nodes for phytophagous true bugs have hitherto been little known, which hampers a better understanding of the evolutionary processes and patterns of phytophagous insects. In the present study, we used 150 species and concatenated nuclear and mitochondrial protein-coding genes and rRNA genes to infer the phylogenetic relationships within the Terheteroptera (Cimicomorpha + Pentatomomorpha) and estimated their divergence times. Our results support the monophyly of Cimicomorpha, Pentatomomorpha, Miroidea, Pentatomoidea, Pyrrhocoroidea, Coreoidea, and Lygaeoidea. The phylogenetic relationships across phytophagous lineages are largely congruent at deep nodes across the analyses based on different datasets and tree-reconstructing methods with just a few exceptions. Estimated divergence times and ancestral state reconstructions for feeding habit indicate that phytophagous true bugs explosively radiated in the Early Cretaceous-shortly after the angiosperm radiation-with the subsequent diversification of the most speciose clades (Mirinae, Pentatomidae, Coreinae, and Rhyparochromidae) in the Late Cretaceous.

Asymmetric sharing of pollinator fig wasps between two sympatric dioecious fig trees: a reflection of supply and demand or differences in the size of their figs?

BACKGROUND

Host specificity among pollinator fig wasps (Agaonidae) depends on host plant specific volatile cues, but fig wasps must also pass through a narrow physical barrier (the ostiole) if they are to pollinate and oviposit. Across South East Asia the dioecious shrub Ficus hirta is associated with at least ten pollinator species allied to Valisia javana. Ficus triloba has a single recorded pollinator, Valisia esquirolianae. Receptive figs of F. hirta are usually much smaller than those of F. triloba, but at a mainland site where F. hirta has atypically large figs we identified both V. esquirolianae and V. javana from both Ficus species using COI and ITS2 sequencing. To investigate whether this host overlap was exceptional we reared fig wasps from the two trees elsewhere and recorded features that may facilitate host transfer between them, including attractant volatiles, reproductive phenology and the sizes of their figs and fig wasps.

RESULTS

The two Ficus species were found to support both Valisia species at several of the sites, suggesting that the differences we detected in volatile profiles, ostiole sizes and pollinator head sizes are not strict barriers to host sharing. Valisia javana colonised F. triloba more frequently than V. esquirolianae colonised F. hirta.

CONCLUSIONS

This asymmetric sharing of pollinators may reflect the relative abundance of the two species of fig wasps and differences in host reproductive phenology. Asynchronous flowering of individual F. hirta may favor local retention of pollinators, in contrast to the tree-wide synchrony of F. triloba figs, which can generate local shortages of V. esquirolianae. If the pollinator sharing by male figs of F. triloba and F. hirta also occurs in female figs then this could result in gene flow between them.

The complete chloroplast genome of the Chinese banyan tree Ficus microcarpa

Banyan tree or Ficus microcarpa is a large perennial plant with extraordinary aerial roots from the Moraceae family. In this study, the complete chloroplast genome sequence of F. microcarpa was assembled using PacBio data. The chloroplast genome size is 141,611 bp, consisting of a large single-copy (LSC) region and a small single-copy (SSC) region of 101,835 bp and 9,676 bp, respectively, which are separated by a pair of 15,050 bp inverted repeat (IR) regions. The genome includes 74 protein-coding genes, 43 tRNA genes, and 8 rRNA genes. A phylogenetic tree reconstructed by 25 complete chloroplast genomes reveals that F. microcarpa is mostly related to Ficus racemosa.

The complete chloroplast genome of two related fig species Ficus squamosa and Ficus heterostyla

The Ficus squamosa and Ficus heterostyla share an undescribed pollinating fig wasp Ceratosolen sp. in Xishuangbanna region, which constitutes the most excellent model to study the role of convergent evolution and hybridization in the species-specific fig-wasp mutualism. The plastomes were 160,350 bp for Ficus squamosa and 160,300 bp for F. heterostyla, both in length with the typical quadripartite structure. In the two genomes, the LSC region was 88,615 bp (F. squamosa) and 88,535 bp (F. heterostyla), the SSC region was 20,071 bp (F. squamosa) and 20,101 bp (F. heterostyla), and the IR regions of both figs were 25,832 bp. They contained 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). Phylogenetic analysis based on the complete chloroplast (cp) genomes within the Ficus genus suggests that they are closely related sister species.

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here, we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome‐wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well‐delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g. yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.

Pollinating fig wasps' simple solutions to complex sex ratio problems: a review

Local mate competition (LMC) favours female biased clutch sex ratios because it reduces competition between brothers and provides extra mating opportunities for sons. Fig wasps seem to fit LMC model assumptions and lay female-biased sex ratios as predicted. These female biased sex ratios increase fitness greatly. In line with predictions, their sex ratios become less female-biased as the number of mothers laying in the same fig increases. However, this variation results in comparatively small fitness benefits compared to just biased ratios and data suggest substantial mismatches with LMC theory. The mismatches are due to several factors. (1) Multiple foundresses typically lay too many daughters. (2) Single foundress sex ratios are explained by sequential oviposition and ladies-last models. (3) Mortality that typically exceeds 10% may decouple the link between primary sex ratios, the focus of model predictions, and secondary sex ratios of adult wasps that are counted by researchers. (4) Model assumptions are frequently violated: (a) clutch sizes are unequal, (b) oviposition may not be simultaneous (c) cryptic/multiple wasp species inhabit the same host, (d) foundress numbers are systematically undercounted, (e) inbreeding coefficient calculations are inaccurate, and (f) male wasps sometimes disperse. These data and calculations suggest that alternative explanations must be considered seriously. Substantial data show that wasps typically lay most of their male eggs first followed by mostly female eggs require a new approach. These "slope" strategies result in more accurate sex ratios that are automatically adjusted to foundress number, own and relative clutch sizes and to sequential clutches. This effect will alter sex ratios in all species once the egg capacity of a fig is crossed or when interference reduces clutch sizes. In addition to this passive response, the females of about half the studied species have a conditional response that reduces female bias under higher foundress numbers by laying more sons. Therefore, wasps seem to use a very simple strategy that increases their fitness. Natural selection could have optimized parameters of the slope strategy and possibly the existence of the slope strategy itself. Variation in the slope strategy that is the result of natural selection is adaptive. Research should therefore focus on quantifying variables of this slope strategy. Currently, it is unclear how much of the variation is adaptive as opposed to being coincidental by-products.

Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.

Regeneration and Endogenous Phytohormone Responses to High-Temperature Stress Drive Recruitment Success in Hemiepiphytic Fig Species

Exposure to high-temperature stress (HTS) during early regeneration in plants can profoundly shape seed germination, seedling growth, and development, thereby providing stress resilience. In this study, we assessed how the timing of HTS, which was implemented as 8 h in 40°C, could affect the early regeneration stages and phytohormone concentration of four hemiepiphytic (Hs) and four non-hemiepiphytic (NHs) Ficus species. Their seed germination, seedling emergence, and seedling survival probabilities and the concentrations of three endogenous phytohormones, abscisic acid (ABA), indole-3-acetic acid (IAA), and salicylic acid (SA) were assessed after HTS imposed during imbibition, germination, and emergence. In both groups, seeds were more sensitive to HTS in the early regeneration process; stress experienced during imbibition affected emergence and survival, and stress experienced during germination affected subsequent emergence. There was no effect from HTS when received after emergence. Survival was highest in hemiepiphytes regardless of the HTS treatment. The phytohormones showed growth form- and regeneration stage-specific responses to HTS. Due to the HTS treatment, both SA and ABA levels decreased in non-hemiepiphytes during imbibition and germination; during germination, IAA increased in hemiepiphytes but was reduced in non-hemiepiphytes. Due to the HTS treatment experienced during emergence ABA and IAA concentrations were greater for hemiepiphytes but an opposite effect was seen in the two growth forms for the SA concentration. Our study showed that the two growth forms have different strategies for regulating their growth and development in the early regeneration stages in order to respond to HTS. The ability to respond to HTS is an ecologically important functional trait that allows plant species to appropriately time their seed germination and seedling development. Flexibility in modulating species regeneration in response to HTS in these subtropical and tropical Ficus species could provide greater community resilience under climate change.

Specialization on Ficus Supported by Genetic Divergence and Morphometrics in Sympatric Host-Populations of the Camellia Aphid, Aphis aurantii

Adaptation to different host plants is considered to be an important driver of the divergence and speciation of herbivorous insects. The application of molecular data and integrated taxonomic practices in recent years may contribute to our understanding of population divergence and speciation, especially for herbivorous insects considered to be polyphagous. Aphis aurantii is an important agricultural and forestry pest with a broad range of host plants. In this study, samples of A. aurantii feeding on different host plants in the same geographical area were collected, and their population genetic divergence and morphological difference were analyzed. Phylogenetic analysis and haplotype network analysis based on five genes revealed that the population on Ficus exhibited significantly genetic divergence from populations on other host plants, which was also supported by the statistical analysis based on measurements of 38 morphological characters. Our results suggest that A. aurantii has undergone specialized evolution on Ficus, and the Ficus population may represent a lineage that is experiencing ongoing sympatric speciation.

Intraspecies Genomic Divergence of a Fig Wasp Species Is Due to Geographical Barrier and Adaptation

Understanding how intraspecies divergence results in speciation has great importance for our knowledge of evolutionary biology. Here we applied population genomics approaches to a fig wasp species (Valisia javana complex sp 1) to reveal its intraspecies differentiation and the underlying evolutionary dynamics. With re-sequencing data, we prove the Hainan Island population (DA) of sp1 genetically differ from the continental ones, then reveal the differed divergence pattern. DA has reduced SNP diversity but a higher proportion of population-specific structural variations (SVs), implying a restricted gene exchange. Based on SNPs, 32 differentiated islands containing 204 genes were detected, along with 1,532 population-specific SVs of DA overlapping 4,141 genes. The gene ontology (GO) enrichment analysis performed on differentiated islands linked to three significant GO terms on a basic metabolism process, with most of the genes failing to enrich. In contrast, population-specific SVs contributed more to the adaptation than the SNPs by linking to 59 terms that are crucial for wasp speciation, such as host reorganization and development regulation. In addition, the generalized dissimilarity modeling confirms the importance of environment difference on the genetic divergence within sp1. Hence, we assume the genetic divergence between DA and the continent due to not only the strait as a geographic barrier, but also adaptation. We reconstruct the demographic history within sp1. DA shares a similar population history with the nearby continental population, suggesting an incomplete divergence. Summarily, our results reveal how geographic barriers and adaptation both influence the genetic divergence at population-level, thereby increasing our knowledge on the potential speciation of non-model organisms.

More examples of breakdown the 1:1 partner specificity between figs and fig wasps

BACKGROUND

The obligate mutualism between fig trees (Ficus, Moraceae) and pollinating fig wasps (Agaonidae) is a model system for studying co-evolution due to its perceived extreme specificity, but recent studies have reported a number of examples of trees pollinated by more than one fig wasp or sharing pollinators with other trees. This will make the potential of pollen flow between species and hybridization more likely though only few fig hybrids in nature have been found. We reared pollinator fig wasps from figs of 13 Chinese fig tree species and established their identity using genetic methods in order to investigate the extent to which they were supporting more than one species of pollinator (co-pollinator).

RESULTS

Our results showed (1) pollinator sharing was frequent among closely-related dioecious species (where pollinator offspring and seeds develop on different trees); (2) that where two pollinator species were developing in figs of one host species there was usually one fig wasp with prominent rate than the other. An exception was F. triloba, where its two pollinators were equally abundant; (3) the extent of co-pollinator within one fig species is related to the dispersal ability of them which is stronger in dioecious figs, especially in small species.

CONCLUSIONS

Our results gave more examples to the breakdown of extreme specificity, which suggest that host expansion events where pollinators reproduce in figs other than those of their usual hosts are not uncommon among fig wasps associated with dioecious hosts. Because closely related trees typically have closely related pollinators that have a very similar appearance, the extent of pollinator-sharing has probably been underestimated. Any pollinators that enter female figs carrying heterospecific pollen could potentially generate hybrid seed, and the extent of hybridization and its significance may also have been underestimated.

Ultraconserved elements-based systematics reveals evolutionary patterns of host-plant family shifts and phytophagy within the predominantly parasitoid braconid wasp subfamily Doryctinae

Phytophagy has promoted species diversification in many insect groups, including Hymenoptera, one of the most diverse animal orders on Earth. In the predominantly parasitoid family Braconidae, an association with insect-induced, plant galls in angiosperms have been reported in three subfamilies, but in particular in the Doryctinae, where it has been recorded to occur in species of ten genera. Allorhogas Gahan is the most species-rich of these genera, with its species having different phytophagous strategies. Here we conducted a comprehensive phylogenomic study for the doryctine gall-associated genera, with an emphasis on Allorhogas, using ultraconserved elements (UCEs). Based on this estimate of phylogeny we: (1) evaluated their taxonomic composition, (2) estimated the timing of origin of the gall-associated clade and divergence of its main subclades, and (3) performed ancestral state reconstruction analyses for life history traits related to their host-plant association. Our phylogenetic hypothesis confirmed Allorhogas as polyphyletic, with most of its members being nested in a main clade composed of various subclades, each comprising species with a particular host-plant family and herbivorous feeding habit. The origin of gall-association was estimated to have occurred during the late Oligocene to early Miocene, with a subsequent diversification of subclades during the middle to late Miocene and Pliocene. Overlap in divergence timing appears to occur between some taxa and their host-associated plant lineages. Evolution of the feeding strategies in the group shows "inquilinism-feeding" as the likely ancestral state, with gall-formation in different plant organs and seed predation having independently evolved on multiple occasions.

Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data

Simple Summary

Research on fig wasps has made a considerable contribution to the understanding of insect–plant interactions. However, the molecular mechanisms underlying fig wasp host specificity are poorly understood. This study reports on a relatively large-scale transcriptomic dataset of 25 fig wasp species. We outline potential genetic mechanisms underlying the specific host adaptation by investigating changes in a gene family, in evolutionary rates, and in genes under positive selection. The transcriptome datasets reported here (1) provide new insights into the evolutionary diversification and host specificity of fig wasps and (2) contribute to a growing dataset on fig wasp genomics.

Abstract

Figs and fig wasps are highly species-specific and comprise a model system for studying co-evolution and co-speciation. The evolutionary relationships and molecular adaptations of fig wasps to their fig hosts are poorly understood, and this is in part due to limited sequence data. Here, we present large-scale transcriptomic datasets of 25 fig wasp species with the aim of uncovering the genetic basis for host specificity. Our phylogenetic results support the monophyly of all genera associated with dioecious figs, and two genera associated with monoecious figs, Eupristina and Platyscapa, were revealed to be close relatives. We identified gene loss and gain, potentially rapidly evolving genes, and genes under positive selection. Potentially functional changes were documented and we hypothesize as to how these may determine host specificity. Overall, our study provides new insights into the evolutionary diversification of fig wasps and contributes to our understanding of adaptation in this group.

Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase phylogenetic information for higher-level relationships, we targeted conserved regions and assembled paired reads into long loci to enable the retrieval of homologous loci in outgroup genomes. We compared morphological and molecular results to highlight discrepancies and reveal possible inference bias. For the first time, we recovered a monophyletic subgenus Urostigma (stranglers) and a clade with all gynodioecious Ficus. However, we show, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference. Four competing positions for the root of the molecular tree are possible. The placement of section Pharmacosycea as sister to other fig trees is not supported by morphological data and considered 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 Ficus into monoecious versus gynodioecious species appears most plausible. It seems most likely that the ancestor of fig trees was a freestanding tree and active pollination is inferred as the ancestral state, contrary to previous hypotheses. However, ambiguity remains on the ancestral breeding system. Despite morphological plasticity, we advocate restoring a central role to morphology in our understanding of the evolution of Ficus, as it can help detect systematic errors that appear more pronounced with larger molecular datasets.

Interactions Between Figs and Gall-Inducing Fig Wasps: Adaptations, Constraints, and Unanswered Questions

The ancient interaction between figs (Ficus, Moraceae) and their pollinating fig wasps is an unusual example of a mutualism between plants and gall-inducing insects. This review intends to offer fresh perspectives into the relationship between figs and the diversity of gall-inducing sycophiles which inhabit their enclosed globular inflorescences that function as microcosms. Besides gall-inducing pollinators, fig inflorescences are also inhabited by other gall-inducing wasps. This review evaluates the state of current knowledge on gall-induction by fig wasps and exposes the many lacunae in this area. This review makes connections between fig and gall-inducing wasp traits, and suggests relatively unexplored research avenues. This manuscript calls for an integrated approach that incorporates such diverse fields as life-history theory, plant mate choice, wasp sexual selection and local mate competition, plant embryology as well as seed and fruit dispersal. It calls for collaboration between researchers such as plant developmental biologists, insect physiologists, chemical ecologists and sensory biologists to jointly solve the many valuable questions that can be addressed in community ecology, co-evolution and species interaction biology using the fig inflorescence microcosm, that is inhabited by gall-inducing mutualistic and parasitic wasps, as a model system.

Source-sink dynamics assists the maintenance of a pollinating wasp

Dispersal that unites spatially subdivided populations into a metapopulation with source-sink dynamics is crucial for species persistence in fragmented landscapes. Understanding such dynamics for pollinators is particularly urgent owing to the ongoing global pollination crisis. Here, we investigated the population structure and source-sink dynamics of a pollinating wasp (Wiebesia sp. 3) of Ficus pumila in the Zhoushan Archipelago of China. We found significant asymmetry in the pairwise migrant numbers for 22 of 28 cases on the historical timescale, but only two on the contemporary timescale. Despite a small population size, the sole island not colonized by a superior competitor wasp (Wiebesia sp. 1) consistently behaved as a net exporter of migrants, supplying large sinks. Comparable levels of genetic diversity, with few private alleles and low genetic differentiation (total F_st : 0.03; pairwise F_st : 0.0005-0.0791), were revealed among all the islands. There was a significant isolation-by-distance pattern caused mainly by migration between the competition-free island and other islands, otherwise the pattern was negligible. The clustering analysis failed to detect multiple gene pools for the whole region. Thus, the sinks were most probably organized into a patchy population. Moreover, the estimates of effective population sizes were comparable between the two timescales. Thus the source-sink dynamics embedded within a well-connected population network may allow Wiebesia sp. 3 to persist at a competitive disadvantage. This study provides evidence that metapopulations in the real world may be complicated and changeable over time, highlighting the necessity to study such metapopulations in detail.

The evolution of parasitism from mutualism in wasps pollinating the fig, Ficus microcarpa, in Yunnan Province, China

Theory identifies factors that can undermine the evolutionary stability of mutualisms. However, theory's relevance to mutualism stability in nature is controversial. Detailed comparative studies of parasitic species that are embedded within otherwise mutualistic taxa (e.g., fig pollinator wasps) can identify factors that potentially promote or undermine mutualism stability. We describe results from behavioral, morphological, phylogenetic, and experimental studies of two functionally distinct, but closely related, Eupristina wasp species associated with the monoecious host fig, Ficus microcarpa, in Yunnan Province, China. One (Eupristina verticillata) is a competent pollinator exhibiting morphologies and behaviors consistent with observed seed production. The other (Eupristina sp.) lacks these traits, and dramatically reduces both female and male reproductive success of its host. Furthermore, observations and experiments indicate that individuals of this parasitic species exhibit greater relative fitness than the pollinators, in both indirect competition (individual wasps in separate fig inflorescences) and direct competition (wasps of both species within the same fig). Moreover, phylogenetic analyses suggest that these two Eupristina species are sister taxa. By the strictest definition, the nonpollinating species represents a "cheater" that has descended from a beneficial pollinating mutualist. In sharp contrast to all 15 existing studies of actively pollinated figs and their wasps, the local F. microcarpa exhibit no evidence for host sanctions that effectively reduce the relative fitness of wasps that do not pollinate. We suggest that the lack of sanctions in the local hosts promotes the loss of specialized morphologies and behaviors crucial for pollination and, thereby, the evolution of cheating.

Fitness costs for fig wasps that fail to pollinate their host Ficus perforata

Mutualisms are of fundamental ecological importance, but risk breaking down if one partner stops paying the costs yet still takes the benefits of the interaction. To prevent such cheating, many mutualisms have mechanisms that lower the fitness of uncooperative symbionts, often termed host sanctions. In mutualisms where the interacting partners are species-specific, we would expect to see coevolution of the levels of host sanctions and partner cooperation across species-pairs. In the mutualism between fig trees and their species-specific pollinating fig wasps, host sanctions vary greatly in strength, and wasp cooperation levels vary accordingly. Here I show experimentally that in Panamanian Ficus perforata (section Urostigma, Americana) there are fitness costs for wasps that do not pollinate. These fitness costs are caused by a combination of abortions of unpollinated figs and reduced proportion of wasp larvae that successfully develop to adults. The relative fitness of wasps that do not pollinate compared to wasps that pollinate is 0.59, leading to the intermediate sanction strength 0.41. Next, by screening pollinators of F. perforata I found that 1.9% of wasp individuals in natural populations failed to carry pollen. Across five actively pollinated Neotropical fig species and their pollinators, fig species with stronger host sanctions had fewer uncooperative wasps, as would be expected if sanctions promote cooperation.