Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine‐mapped region

Drosophila sechellia is a species of fruit fly endemic to the Seychelles islands. Unlike its generalist sister species, D. sechellia has evolved to be a specialist on the host plant Morinda citrifolia. This specialization is interesting because the plant's fruit contains secondary defence compounds, primarily octanoic acid (OA), that are lethal to most other Drosophilids. Although ecological and behavioural adaptations to this toxic fruit are known, the genetic basis for evolutionary changes in OA resistance is not. Prior work showed that a genomic region on chromosome 3R containing 18 genes has the greatest contribution to differences in OA resistance between D. sechellia and D. simulans. To determine which gene(s) in this region might be involved in the evolutionary change in OA resistance, we knocked down expression of each gene in this region in D. melanogaster with RNA interference (RNAi) (i) ubiquitously throughout development, (ii) during only the adult stage and (iii) within specific tissues. We identified three neighbouring genes in the Osiris family, Osiris 6 (Osi6), Osi7 and Osi8, that led to decreased OA resistance when ubiquitously knocked down. Tissue‐specific RNAi, however, showed that decreasing expression of Osi6 and Osi7 specifically in the fat body and/or salivary glands increased OA resistance. Gene expression analyses of Osi6 and Osi7 revealed that while standing levels of expression are higher in D. sechellia, Osi6 expression is significantly downregulated in salivary glands in response to OA exposure, suggesting that evolved tissue‐specific environmental plasticity of Osi6 expression may be responsible for OA resistance in D. sechellia.     

Dynamics of an ant-ant obligate mutualism: colony growth, density dependence and frequency dependence

In insect societies, worker vs. queen development (reproductive caste) is typically governed by environmental factors, but many Pogonomyrmex seed-harvester ants exhibit strict genetic caste determination, resulting in an obligate mutualism between two reproductively isolated lineages. Same-lineage matings produce fertile queens while alternate-lineage matings produce sterile workers. Because new virgin queens mate randomly with multiple males of each lineage type, and both worker and queen phenotypes are required for colony growth and future reproduction, fitness is influenced by the relative frequency of each lineage involved in the mutualistic breeding system. While models based solely on frequency-dependent selection predict the convergence of lineage frequencies towards equal (0.5/0.5), we surveyed the lineage ratios of 49 systems across the range of the mutualism and found that the global lineage frequency differed significantly from equal. Multiple regression analysis of our system survey data revealed that the density and relative frequency of one lineage decreases at lower elevations, while the frequency of the alternate lineage increases with total colony density. While the production of the first worker cohort is largely frequency dependent, relying on the random acquisition of worker-biased sperm stores, subsequent colony growth is independent of lineage frequency. We provide a simulation model showing that a net ecological advantage held by one lineage can lead to the maintenance of stable but asymmetric lineage frequencies. Collectively, these findings suggest that a combination of frequency-dependent and frequency-independent mechanisms can generate many different localized and independently evolving system equilibria.     

Bats join the ranks of oxpeckers and cleaner fish as partners in a pest‐reducing mutualism

While antagonistic species interactions such as predation or competition have a long history of study, positive inter‐species interactions have received comparatively little attention. Mutualisms and commensalisms appear to be widespread in the animal kingdom, with examples of mammals, birds, fish, and reptiles from around the world engaging with other species in evidentially beneficial ways. Cleaning mutualism is a specific type positive inter‐species interaction in which one species removes and feeds upon parasites infesting the other. Here, we document a new subset of positive inter‐species “cleaning” interactions, in which one partner benefits from and reduces the abundance of pest species attracted by but not attached to their host. We observed in person and in camera trap footage numerous instances of insectivorous bats associating with white‐tailed deer (Odocoileus virginianus) and feeding on the swarms of biting flies attracted to these large mammals. We call for the increased reporting of positive inter‐species associations to better our understanding of the mechanisms leading to the formation of these interactions and the effects that these relationships may for the structuring of ecological communities.     

Predation drives recurrent convergence of an interspecies mutualism

Mutualisms are important ecological interactions that underpin much of the world's biodiversity. Predation risk has been shown to regulate mutualism dynamics in species‐specific case studies; however, we lack studies which investigate whether predation can also explain broader patterns of mutualism evolution. We report that fish‐anemone mutualisms have evolved on at least 55 occasions across 16 fish families over the past 60 million years and that adult body size is associated with the ontogenetic stage of anemone mutualisms: larger‐bodied species partner with anemones as juveniles, while smaller‐bodied species partner with anemones throughout their lives. Field and laboratory studies show that predators target smaller prey, that smaller fishes associate more with anemones, and that these relationships confer protection to small fishes. Our results indicate that predation is likely driving the recurrent convergent evolution of fish‐anemone mutualisms and suggest that similar ecological processes may have selected convergence in interspecies interactions in other animal clades.     

Macroevolutionary patterns in the origin of mutualisms involving ants

Ants are a diverse and abundant insect group that form mutualistic associations with a number of different organisms from fungi to insects and plants. Here, we use a phylogenetic approach to identify ecological factors that explain macroevolutionary trends in the mutualism between ants and honeydew-producing Homoptera. We also consider association between ant-Homoptera, ant-fungi and ant-plant mutualisms. Homoptera-tending ants are more likely to be forest dwelling, polygynous, ecologically dominant and arboreal nesting with large colonies of 10(4)-10(5) individuals. Mutualistic ants (including those that garden fungi and inhabit ant-plants) are found in under half of the formicid subfamilies. At the genus level, however, we find a negative association between ant-Homoptera and ant-fungi mutualisms, whereas there is a positive association between ant-Homoptera and ant-plant mutualisms. We suggest that species can only specialize in multiple mutualisms simultaneously when there is no trade-off in requirements from the different partners and no redundancy of rewards.     

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.     

Interactions of the ant Crematogaster scutellaris with the fig/fig wasp mutualism

Abstract. 1. A classical example of specialised pollination mutualisms is the relationship between fig trees and their pollinating wasps, in which each partner depends completely on the other for its reproduction; however the fig/fig wasp association is also the target of a great diversity of other species, ranging from specialised parasites to opportunistic foragers, among them ants.
2. The ant community and the sources of ant attraction observed on the Mediterranean fig tree Ficus carica were characterised.
3. A guild of ants attracted by homopterans tended on the plant was distinguished from a second guild composed of two co-dominant ant species ( Crematogaster scutellaris and Pheidole pallidula ) that prey mostly on pollinating wasps, abundant during certain parts of the fig cycle.
4. Foraging workers of C. scutellaris search for prey on the fig inflorescence (syconium), capturing pollinating wasps mostly at the peak of wasp emergence and at a rate estimated to reach 600 prey per day for an entire tree.
5. Detailed study of the predatory sequences displayed under experimental conditions showed that ant workers captured 100% of the pollinating wasps offered, while they captured only 5.5% of the parasitoid wasp specific to the pollinator. The respective impacts of the interaction on ants and on the figs are discussed, as well as several behavioural traits of predation by the dominant ant on pollinators.     

Cohabitation and roommate bias of symbiotic bacteria in insect hosts

Symbiotic interactions between insects and bacteria have long fascinated ecologists. Aphids have emerged as the model system on which to study the effect of endosymbiotic bacteria on their hosts. Aphid‐symbiont interactions are ecologically interesting as aphids host multiple secondary symbionts that can provide broad benefits, such as protection against heat stress or specialist natural enemies (parasitic wasps and entomopathogenic fungi). There are nine common aphid secondary symbionts and individual aphids host on average 1–2 symbionts. A cost‐benefit trade‐off for hosting symbionts is thought to explain why not all aphids host every possible symbiont in a population. Both positive and negative associations between various symbionts occur, and this could happen due to increased costs when cohosting certain combinations or as a consequence of competitive interactions between the symbionts within a host. In this issue of Molecular Ecology, Mathé‐Hubert, Kaech, Hertaeg, Jaenike, and Vorburger (2019) use data on the symbiont status of field‐collected aphids to inform a model on the evolution of symbiont co‐occurrence. They vary the effective female population size as well as the rate of horizontal and maternal transmission to infer the relative impact of symbiont‐symbiont interactions versus random drift. Additional data analysis revisits an association between two symbionts in a fruit fly species using a long‐term data set to highlight that such interactions are not limited to aphids.     

Dating the fungus-growing termites' mutualism shows a mixture between ancient codiversification and recent symbiont dispersal across divergent hosts

The mutualistic symbiosis between fungus-growing termites and Termitomyces fungi originated in Africa and shows a moderate degree of interaction specificity. Here we estimate the age of the mutualism and test the hypothesis that the major splits have occurred simultaneously in the host and in the symbiont. We present a scenario where fungus-growing termites originated in the African rainforest just before the expansion of the savanna, about 31 Ma (19-49 Ma). Whereas rough age correspondence is observed for the four main clades of host and symbiont, the analysis reveals several recent events of host switching followed by dispersal of the symbiont throughout large areas and throughout different host genera. The most spectacular of these is a group of closely related fungi (the maximum age of which is estimated to be 2.4 Ma), shared between the divergent genera Microtermes, Ancistrotermes, Acanthotermes and Synacanthotermes (which diverged at least 16.7 Ma), and found throughout the African continent and on Madagascar. The lack of geographical differentiation of fungal symbionts shows that continuous exchange has occurred between regions and across host species.     

Biotic interactions hold the key to understanding metacommunity organisation

Biotic interactions are fundamental drivers governing biodiversity locally, yet their effects on geographical variation in community composition (i.e. incidence-based) and community structure (i.e. abundance-based) at regional scales remain controversial. Ecologists have only recently started to integrate different types of biotic interactions into community assembly in a spatial context, a theme that merits further empirical quantification. Here, we applied partial correlation networks to infer the strength of spatial dependencies between pairs of organismal groups and mapped the imprints of biotic interactions on the assembly of pond metacommunities. To do this, we used a comprehensive empirical dataset from Mediterranean landscapes and adopted the perspective that community assembly is best represented as a network of interacting organismal groups. Our results revealed that the co-variation among the beta diversities of multiple organismal groups is primarily driven by biotic interactions and, to a lesser extent, by the abiotic environment. These results suggest that ignoring biotic interactions may undermine our understanding of assembly mechanisms in spatially extensive areas and decrease the accuracy and performance of predictive models. We further found strong spatial dependencies in our analyses which can be interpreted as functional relationships among several pairs of organismal groups (e.g. macrophytes–macroinvertebrates, fish–zooplankton). Perhaps more importantly, our results support the notion that biotic interactions make crucial contributions to the species sorting paradigm of metacommunity theory and raise the question of whether these biologically-driven signals have been equally underappreciated in other aquatic and terrestrial ecosystems. Although more research is still required to empirically capture the importance of biotic interactions across ecosystems and at different spatial resolutions and extents, our findings may allow decision makers to better foresee the main consequences of human-driven impacts on inland waters, particularly those associated with the addition or removal of key species.     

Applying landscape genetics to the microbial world

Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as ‘the invisible regulators’ of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro‐ and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in ‘macro’‐landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro‐ and macroecological processes and expand our knowledge of species’ distributions, adaptive mechanisms and species’ interactions in changing environments.     

Putting the genes into community genetics

As part of the long‐term fusion of evolutionary biology and ecology (Ford, 1964), the field of community genetics has made tremendous progress in describing the impacts of plant genetic variation on community and ecosystem processes. In the “genes‐to‐ecosystems” framework (Whitham et al., 2003), genetically based traits of plant species have ecological consequences, but previous studies have not identified specific plant genes responsible for community phenotypes. The study by Barker et al. (2019) in this issue of Molecular Ecology uses an impressive common garden experiment of trembling aspen (Figure 1) to test for the genetic basis of tree traits that shape the insect community composition. Using a Genome‐Wide Association Study (GWAS), they found that genomic regions associated with phytochemical traits best explain variation in herbivore community composition, and identified specific genes associated with different types of leaf‐modifying herbivores and ants. This is one of the first studies to identify candidate genes underlying the heritable plant traits that explain patterns of insect biodiversity.     

Insect life history and the evolution of bacterial mutualism

Bacterial symbiosis has played a fundamental role in the evolution of eukaryotes. However, we still know little about how cooperative relationships with bacteria originate, and why they form in some host species but not others. Facultative symbionts that are beneficial, but not essential, provide unique insights into these processes. We use data from over a hundred aphid species to test if host life history is associated with the presence of facultative symbionts. We find that aphid species that have mutualistic associations with ants that protect them from natural enemies are less likely to carry symbionts that provide similar benefits. We also find one symbiont species occurs more frequently in unrelated aphid species that specialise on certain plant genera. In addition, aphid species that attack multiple plants often carry different symbiont complements. Our findings provide evidence of the ecological conditions that facilitate stable, mutually beneficial relationships between microbes and eukaryotic hosts.     

Inferring coevolution in a plant–pollinator network

Mutualistic interactions are at the core of community dynamics, determining dispersal, colonization and differential survival and reproduction among individuals and species. Mutualistic interactions therefore affect the fitness of interaction partners, hence modifying their respective evolutionary trajectories reciprocally, potentially leading to coevolution. Although mathematical models predict coevolution in mutualistic interaction networks, no empirical data are available. By taking into account the patterns of interactions and reconstructing evolutionary change in plant and pollinator traits, we tested the hypothesis that coevolution occurs between plants and insects that interact more frequently, or more symmetrically. To test this hypothesis, we built an interaction network with data from five flowering seasons, measured plant and insect morphology, mapped morphology on the plant and insect phylogenies, and reconstructed ancestral character changes based on maximum parsimony. We calculated an index, called the coevolutionary ratio, which represents the amount of correlated change in traits that mediate the interaction between plants and pollinators (i.e. proboscis versus corolla length, and body width and corolla aperture). Our results suggest that high frequency of interaction, i.e. the number of times two species interact, does not lead to coevolution. Instead, symmetry of interaction strength, i.e. the reciprocal similarity in the mutual effect of interaction partners, may lead to coevolution, in spite of a pervasive lack of reciprocal specialization and high interaction frequency. Although the statistical signal is quite weak, our results hold for three statistical tests of very different nature. The most specialized species, expected to be under directional selection, do not show more evolutionary change than do generalist species, expected to be under different, perhaps opposing, selective pressures. By dissecting the complexity of an interaction network we show that coevolution may partially shape functional morphology of interaction partners, thus providing the closest evidence to date of mutualistic adaptation of organisms within a community.     

Resource predictability and specialization in avian malaria parasites

We tested the hypothesis that avian haemosporidian (malaria) parasites specialize on hosts that can be characterized as predictable resources at a site in Amazonian Ecuador. We incorporated host phylogenetic relationship and relative abundance in assessing parasite specialization, and we examined associations between parasite specialization and three host characteristics – abundance, mass and longevity – using quantile regression, phylogenetic logistic regression and t‐tests. Hosts of specialist malaria parasite lineages were on average more abundant than hosts of generalist parasite lineages, but the relationship between host abundance and parasite specialization was not consistent across analyses. We also found support for a positive association between parasite specialization and host longevity, but this also was not consistent across analyses. Nonetheless, our findings suggest that the predictability of a host resource may play a role in the evolution of specialization. However, we also discuss two alternative explanations to the resource predictability hypothesis for specialization: (i) that interspecific interactions among the parasites themselves might constrain some parasites to a specialist strategy, and (ii) that frequent encounters with multiple host species, mediated by blood‐sucking insects, might promote generalization within this system.     

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host

Bacterial endosymbionts have been detected in some groups of plant‐parasitic nematodes, but few cases have been reported compared to other groups in the phylum Nematoda, such as animal‐parasitic or free‐living nematodes. This study was performed on a wide variety of plant‐parasitic nematode families and species from different host plants and nematode populations. A total of 124 nematode populations (previously identified morphologically and molecularly) were screened for the presence of potential bacterial endosymbionts using the partial 16S rRNA gene and fluorescence in situ hybridization (FISH) and confocal microscopy. Potential bacterial endosymbionts were only detected in nematode species belonging to the genus Xiphinema and specifically in the X. americanum group. Fifty‐seven partial 16S rRNA sequences were obtained from bacterial endosymbionts in this study. One group of sequences was closely related to the genus ‘Candidatus Xiphinematobacter’ (19 bacterial endosymbiont sequences were associated with seven nematode host species, including two that have already been described and three unknown bacterial endosymbionts). The second bacterial endosymbiont group (38 bacterial endosymbiont sequences associated with six nematode species) was related to the family Burkholderiaceae, which includes fungal and soil–plant bacterial endosymbionts. These endosymbionts were reported for the first time in the phylum Nematoda. Our findings suggest that there is a highly specific symbiotic relationship between nematode host and bacterial endosymbionts. Overall, these results were corroborated by a phylogeny of nematode host and bacterial endosymbionts that suggested that there was a high degree of phylogenetic congruence and long‐term evolutionary persistence between hosts and endosymbionts.     

Progressive sensitivity of trophic levels to warming underlies an elevational gradient in ant–aphid mutualism strength

Although species interactions are often proposed to be stronger at lower latitudes and elevations, few studies have evaluated the mechanisms driving such patterns. In this study, we assessed whether, and by which mechanisms, abiotic changes associated with elevation altered the outcome of an ant–aphid protection mutualism. To do so, we characterized the multi‐trophic interactions among the ant Formica podzolica, the aphid Aphis varians, and aphid natural enemies occurring on the plant Chamerion angustifolium within replicate high and low elevation valleys. Low (versus high) elevation sites had longer summers (snowmelt 13 days earlier) and were on average 1.1°C warmer and 41% drier throughout the year. At low elevations, individual ant colonies consumed approximately double the volume of carbohydrate baits, likely due to a higher foraging tempo, and possibly due to a greater demand for sugar‐ versus protein‐rich resources (as indicated by stable isotope analysis). Wild aphid colonies at low elevations were visited by 1.4‐fold more natural enemies (controlling for variation in aphid abundance), while experimental aphid colonies on potted plants were tended 52% more frequently by ants. As a result, ants increased aphid colony survival by 66% at low elevations but had no detectable effect at high elevations; at low (versus high) elevations aphid colonies without ants had lower survival, demonstrating stronger predator effects, while aphid colonies with ants had higher survival, demonstrating even stronger ant benefits. Analyses for the effects of mean summer temperature yielded qualitatively identical results to those based on elevation. Collectively, these findings support predictions for a greater sensitivity of higher trophic levels to warming and demonstrate how species interactions can vary across environmental gradients due to simultaneous changes in species traits and abundances across multiple trophic levels.