Network analyses identify liver‐specific targets for treating liver diseases

We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co‐expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver‐specific genes co‐expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver‐specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver‐specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin‐like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.     

Parasite in peril? A new species of mite in the genus Ophiomegistus Banks (Parasitiformes: Paramegistidae) on an endangered host,the pygmy bluetongue lizard Tiliqua adelaidensis (Peters) (Squamata: Scincidae)

Host‐parasite relationships are generally understudied in wild populations but have a potential to influence host population dynamics and the broader ecosystem, which becomes particularly important when the host is endangered. Herein we describe a new species of parasitic mite from the genus Ophiomegistus (Parasitiformes: Mesostigmata: Paramegistidae) of an endangered South Australian skink; the pygmy bluetongue lizard (Tiliqua adelaidensis). Adult mites were observed on lizard hosts in three different host populations, among which prevalence varied. No temporal trend in prevalence was evident over two spring‐summer seasons of monitoring. We hypothesise that the reliance on burrows as refuges by T. adelaidensis may be essential for the completion of the mite life cycle and also for horizontal transmission. The conservation implications of not only its effect on the host, but also its potential status as an endangered species itself, are considered.     

Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next‐generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co‐correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co‐occurrence networks and thus investigate the presence of patterns in ecological networks.     

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics

Algal blooms are a worldwide phenomenon and the biological interactions that underlie their regulation are only just beginning to be understood. It is established that algal microorganisms associate with many other ubiquitous, oceanic organisms, but the interactions that lead to the dynamics of bloom formation are currently unknown. To address this gap, we used network approaches to investigate the association patterns among microeukaryotes and bacterioplankton in response to a natural Scrippsiella trochoidea bloom. This is the first study to apply network approaches to bloom dynamics. To this end, terminal restriction fragment (T‐RF) length polymorphism analysis showed dramatic changes in community compositions of microeukaryotes and bacterioplankton over the blooming period. A variance ratio test revealed significant positive overall associations both within and between microeukaryotic and bacterioplankton communities. An association network generated from significant correlations between T‐RFs revealed that S. trochoidea had few connections to other microeukaryotes and bacterioplankton and was placed on the edge. This lack of connectivity allowed for the S. trochoidea sub‐network to break off from the overall network. These results allowed us to propose a conceptual model for explaining how changes in microbial associations regulate the dynamics of an algal bloom. In addition, key T‐RFs were screened by principal components analysis, correlation coefficients, and network analysis. Dominant T‐RFs were then identified through 18S and 16S rRNA gene clone libraries. Results showed that microeukaryotes clustered predominantly with Dinophyceae and Perkinsea while the majority of bacterioplankton identified were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The ecologi‐cal roles of both were discussed in the context of these findings.     

Responses of the soil fungal communities to the co‐invasion of two invasive species with different cover classes

• Soil fungal communities play an important role in the successful invasion of non‐native species. It is common for two or more invasive plant species to co‐occur in invaded ecosystems.
• This study aimed to determine the effects of co‐invasion of two invasive species (Erigeron annuus and Solidago canadensis) with different cover classes on soil fungal communities using high‐throughput sequencing.
• Invasion of E. annuus and/or S. canadensis had positive effects on the sequence number, operational taxonomic unit (OTU) richness, Shannon diversity, abundance‐based cover estimator (ACE index) and Chao1 index of soil fungal communities, but negative effects on the Simpson index. Thus, invasion of E. annuus and/or S. canadensis could increase diversity and richness of soil fungal communities but decrease dominance of some members of these communities, in part to facilitate plant further invasion, because high soil microbial diversity could increase soil functions and plant nutrient acquisition. Some soil fungal species grow well, whereas others tend to extinction after non‐native plant invasion with increasing invasion degree and presumably time. The sequence number, OTU richness, Shannon diversity, ACE index and Chao1 index of soil fungal communities were higher under co‐invasion of E. annuus and S. canadensis than under independent invasion of either individual species.
• The co‐invasion of the two invasive species had a positive synergistic effect on diversity and abundance of soil fungal communities, partly to build a soil microenvironment to enhance competitiveness of the invaders. The changed diversity and community under co‐invasion could modify resource availability and niche differentiation within the soil fungal communities, mediated by differences in leaf litter quality and quantity, which can support different fungal/microbial species in the soil.

     

Tracking the elusive history of diversification in plant–herbivorous insect–parasitoid food webs: insights from figs and fig wasps

The food webs consisting of plants, herbivorous insects and their insect parasitoids are a major component of terrestrial biodiversity. They play a central role in the functioning of all terrestrial ecosystems, and the number of species involved is mind‐blowing (Nyman et al. 2015 ). Nevertheless, our understanding of the evolutionary and ecological determinants of their diversity is still in its infancy. In this issue of Molecular Ecology, Sutton et al. ( 2016 ) open a window into the comparative analysis of spatial genetic structuring in a set of comparable multitrophic models, involving highly species‐specific interactions: figs and fig wasps. This is the first study to compare genetic structure using population genetics tools in a fig‐pollinating wasp (Pleistodontes imperialis sp1) and its main parasitoid (Sycoscapter sp.A). The fig‐pollinating wasp has a discontinuous spatial distribution that correlates with genetic differentiation, while the parasitoid bridges the discontinuity by parasitizing other pollinator species on the same host fig tree and presents basically no spatial genetic structure. The full implications of these results for our general understanding of plant–herbivorous insect–insect parasitoids diversification become apparent when envisioned within the framework of recent advances in fig and fig wasp biology.     

Co‐occurrence of bobcats,coyotes, and ocelots in Texas

Interspecific competition among carnivores has been linked to differences in behavior, morphology, and resource use. Insights into these interactions can enhance understanding of local ecological processes that can have impacts on the recovery of endangered species, such as the ocelot (Leopardus pardalis). Ocelots, bobcats (Lynx rufus), and coyotes (Canis latrans) share a small geographic range overlap from South Texas to south‐central Mexico but relationships among the three are poorly understood. From May 2011 to March 2018, we conducted a camera trap study to examine co‐occurrence patterns among ocelots, bobcats, and coyotes on the East Foundation's El Sauz Ranch in South Texas. We used a novel multiseason extension to multispecies occupancy models with ≥2 interacting species to conduct an exploratory analysis to examine interspecific interactions and examine the potential effects of patch‐level and landscape‐level metrics relative to the occurrence of these carnivores. We found strong evidence of seasonal mutual coexistence among all three species and observed a species‐specific seasonal trend in detection. Seasonal coexistence patterns were also explained by increasing distance from a high‐speed roadway. However, these results have important ecological implications for planning ocelot recovery in the rangelands of South Texas. This study suggests a coexistence among ocelots, bobcats, and coyotes under the environmental conditions on the El Sauz Ranch. Further research would provide a better understanding of the ecological mechanisms that facilitate coexistence within this community. As road networks in the region expand over the next few decades, large private working ranches will be needed to provide important habitat for ocelots and other carnivore species.     

Competing for blood: the ecology of parasite resource competition in human malaria–helminth co‐infections

Ecological theory suggests that co‐infecting parasite species can interact within hosts directly, via host immunity and/or via resource competition. In mice, competition for red blood cells (RBCs) between malaria and bloodsucking helminths can regulate malaria population dynamics, but the importance of RBC competition in human hosts was unknown. We analysed infection density (i.e. the concentration of parasites in infected hosts), from a 2‐year deworming study of over 4000 human subjects. After accounting for resource‐use differences among parasites, we find evidence of resource competition, priority effects and a competitive hierarchy within co‐infected individuals. For example reducing competition via deworming increased Plasmodium vivax densities 2.8‐fold, and this effect is limited to bloodsucking hookworms. Our ecological, resource‐based perspective sheds new light into decades of conflicting outcomes of malaria–helminth co‐infection studies with significant health and transmission consequences. Beyond blood, investigating within‐human resource competition may bring new insights for improving human health.     

Nonlinear frequency‐dependent selection promotes long‐term coexistence between bacteria species

Negative frequency‐dependent selection (NFDS) is an important mechanism for species coexistence and for the maintenance of genetic polymorphism. Long‐term coexistence nevertheless requires NFDS interactions to be resilient to further evolution of the interacting species or genotypes. For closely related genotypes, NFDS interactions have been shown to be preserved through successive rounds of evolution in coexisting lineages. On the contrary, the evolution of NFDS interactions between distantly related species has received less attention. Here, we tracked the co‐evolution of Escherichia coli and Citrobacter freundii that initially differ in their ecological characteristics. We showed that these two bacterial species engaged in an NFDS interaction particularly resilient to further evolution: despite a very strong asymmetric rate of adaptation, their coexistence was maintained owing to an NFDS pattern where fitness increases steeply as the frequency decreases towards zero. Using a model, we showed how and why such NFDS pattern can emerge. These findings provide a robust explanation for the long‐term maintenance of species at very low frequencies.     

Comparative genetics of Na+/K+‐ATPase in monarch butterfly populations with varying host plant toxicity

Herbivores have evolved numerous behavioural and physiological adaptations to host plants; however, molecular adaptations are still poorly understood. One well‐studied case comprises the specialist insects that feed on cardenolide‐containing plants. Here, convergent molecular evolution in the Na⁺/K⁺‐ATPase results in a reduced sensitivity to cardenolides across four insect orders. Because different plant species and genotypes differ in toxicity, Na⁺/K⁺‐ATPase may be under differential selection from geographically varying host plants. We examined the α subunit of Na⁺/K⁺‐ATPase in monarch butterflies (Danaus plexippus) from six worldwide populations to test whether differences in their host plant chemistry result in local adaptation at the molecular level. Although our study revealed multiple synonymous changes, we did not find these to be population‐specific, nor did we identify nonsynonymous changes. Additionally, we compared the amino acid sequence of this subunit across 19 species. We identified two novel changes at sites 836 (K836N) and 840 (E840R) in the αM7‐αM8 regions in the genus Danaus. Although previous studies focused on the first two trans‐membrane domains, C‐terminal domains may also interact with cardenolides. These results reveal a lack of molecular evolution of Na⁺/K⁺‐ATPase at the population level, and call for additional attention regarding the C‐terminal regions of this important enzyme.     

Uncovering symbiont‐driven genetic diversity across North American pea aphids

Heritable genetic variation is required for evolution, and while typically encoded within nuclear and organellar genomes, several groups of invertebrates harbour heritable microbes serving as additional sources of genetic variation. Hailing from the symbiont‐rich insect order Hemiptera, pea aphids (Acyrthosiphon pisum) possess several heritable symbionts with roles in host plant utilization, thermotolerance and protection against natural enemies. As pea aphids vary in the numbers and types of harboured symbionts, these bacteria provide heritable and functionally important variation within field populations. In this study, we quantified the cytoplasmically inherited genetic variation contributed by symbionts within North American pea aphids. Through the use of Denaturing Gradient Gel Electrophoresis (DGGE) and 454 amplicon pyrosequencing of 16S rRNA genes, we explored the diversity of bacteria harboured by pea aphids from five populations, spanning three locations and three host plants. We also characterized strain variation by analysing 16S rRNA, housekeeping and symbiont‐associated bacteriophage genes. Our results identified eight species of facultative symbionts, which often varied in frequency between locations and host plants. We detected 28 cytoplasmic genotypes across 318 surveyed aphids, considering only the various combinations of secondary symbiont species infecting single hosts. Yet the detection of multiple Regiella insecticola, Hamiltonella defensa and Rickettsia strains, and diverse bacteriophage genotypes from H. defensa, suggest even greater diversity. Combined, these findings reveal that heritable bacteria contribute substantially to genetic variation in A. pisum. Given the costs and benefits of these symbionts, it is likely that fluctuating selective forces play a role in the maintenance of this diversity.     

High efficiency Agrobacterium‐mediated site‐specific gene integration in maize utilizing the FLP‐FRT recombination system

An efficient Agrobacterium‐mediated site‐specific integration (SSI) technology using the flipase/flipase recognition target (FLP/FRT) system in elite maize inbred lines is described. The system allows precise integration of a single copy of a donor DNA flanked by heterologous FRT sites into a predefined recombinant target line (RTL) containing the corresponding heterologous FRT sites. A promoter‐trap system consisting of a pre‐integrated promoter followed by an FRT site enables efficient selection of events. The efficiency of this system is dependent on several factors including Agrobacterium tumefaciens strain, expression of morphogenic genes Babyboom (Bbm) and Wuschel2 (Wus2) and choice of heterologous FRT pairs. Of the Agrobacterium strains tested, strain AGL1 resulted in higher transformation frequency than strain LBA4404 THY‐ (0.27% vs. 0.05%; per cent of infected embryos producing events). The addition of morphogenic genes increased transformation frequency (2.65% in AGL1; 0.65% in LBA4404 THY‐). Following further optimization, including the choice of FRT pairs, a method was developed that achieved 19%–22.5% transformation frequency. Importantly, >50% of T0 transformants contain the desired full‐length site‐specific insertion. The frequencies reported here establish a new benchmark for generating targeted quality events compatible with commercial product development.     

Contrasting genetic responses to population fragmentation in a coevolving fig and fig wasp across a mainland–island archipelago

Interacting species of pollinator–host systems, especially the obligate ones, are sensitive to habitat fragmentation, due to the nature of mutual dependence. Comparative studies of genetic structure can provide insights into how habitat fragmentation contributes to patterns of genetic divergence among populations of the interacting species. In this study, we used microsatellites to analyse genetic variation in Chinese populations of a typical mutualistic system – Ficus pumila and its obligate pollinator Wiebesia sp. 1 – in a naturally fragmented landscape. The plants and wasps showed discordant patterns of genetic variation and geographical divergence. There was no significant positive relationship in genetic diversity between the two species. Significant isolation‐by‐distance (IBD) patterns occurred across the populations of F. pumila and Wiebesia sp. 1 as whole, and IBD also occurred among island populations of the wasps, but not the plants. However, there was no significant positive relationship in genetic differentiation between them. The pollinator populations had significantly lower genetic variation in small habitat patches than in larger patches, and three island pollinator populations showed evidence of a recent bottleneck event. No effects of patch size or genetic bottlenecks were evident in the plant populations. Collectively, the results indicate that, in more fragmented habitats, the pollinators, but not the plants, have experienced reduced genetic variation. The contrasting patterns have multiple potential causes, including differences in longevity and hence number of generations experiencing fragmentation; different dispersal patterns, with the host's genes dispersed as seeds as well as a result of pollen dispersal via the pollinator; asymmetrical responses to fluctuations in partner populations; and co‐existence of a rare second pollinating wasp on some islands. These results indicate that strongly interdependent species may respond in markedly different ways to habitat fragmentation.     

Bacterial influence on alkenones in live microalgae

The microalga Emiliania huxleyi produces alkenone lipids that are important proxies for estimating past sea surface temperatures. Field calibrations of this proxy are robust but highly variable results are obtained in culture. Here, we present results suggesting that algal‐bacterial interactions may be responsible for some of this variability. Co‐cultures of E. huxleyi and the bacterium Phaeobacter inhibens resulted in a 2.5‐fold decrease in algal alkenone‐containing lipid bodies. In addition levels of unsaturated alkenones increase in co‐cultures. These changes result in an increase in the reconstructed growth temperature of up to 2°C relative to axenic algal cultures.