Neutral Models of Microbiome Evolution

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.     

PHYTOPHAGOUS INSECT–MICROBE MUTUALISMS AND ADAPTIVE EVOLUTIONARY DIVERSIFICATION

Adaptive diversification is a process intrinsically tied to species interactions. Yet, the influence of most types of interspecific interactions on adaptive evolutionary diversification remains poorly understood. In particular, the role of mutualistic interactions in shaping adaptive radiations has been largely unexplored, despite the ubiquity of mutualisms and increasing evidence of their ecological and evolutionary importance. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification, using herbivorous insects and their microbial mutualists as exemplars. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. In this perspective, we examine microbial mutualist mediation of ecological opportunity and ecologically based divergent natural selection for their insect hosts. We also explore the conditions and mechanisms by which microbial mutualists may either facilitate or impede adaptive evolutionary diversification. These include effects on the availability of novel host plants or adaptive zones, modifying host-associated fitness trade-offs during host shifts, creating or reducing enemy-free space, and, overall, shaping the evolution of ecological (host plant) specialization. Although the conceptual framework presented here is built on phytophagous insect–microbe mutualisms, many of the processes and predictions are broadly applicable to other mutualisms in which host ecology is altered by mutualistic interactions.     

Variability and its implications for host-parasite interactions

Variability in host-parasite interactions has considerable impact on the ecology and evolution of parasites and on the epidemiology of disease. The nature of the impact depends largely on the level of ecological organization where variability occurs: variability of parasites within their individual hosts, variability of host individuals within populations, or variability of hosts and parasites among populations. In this review, Paul Schmid-Hempel and Jacob Koella give some examples of variability at each of these levels, with particular emphasis on microparasites (defined broadly as viruses, bacteria and protozoa), consider the maintenance of the variability, and describe the implications of variability for the epidemiology of disease and the ecology of host parasite associations. In particular, they describe how variability at each level of ecological organization can affect the perception of AIDS and the evolution of virulence.     

Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity

Biodiversity is fundamental to both eukaryote and prokaryote ecology, yet investigations of diversity often differ markedly between the two disciplines. Host specificity - the association of organisms with only a few (specialism) or many (generalism) host species - is recognized within eukaryote ecology as a key determinant of diversity. In contrast, its implications for microbial diversity have received relatively little attention. Here we explore the relationship between microbial diversity and host specificity using marine sponge-bacteria associations. We used a replicated, hierarchical sampling design and both 16S rDNA- and rpoB-based denaturing gradient gel electrophoresis (DGGE) to examine whether three co-occurring sponges from temperate Australia -Cymbastela concentrica, Callyspongia sp. and Stylinos sp. - contained unique, specialized communities of microbes. Microbial communities varied little within each species of sponge, but variability among species was substantial. Over five seasons, the microbial community in C. concentrica differed significantly from other sponges, which were more similar to seawater. Overall, three types of sponge-associated bacteria were identified via 16S rDNA sequencing of excised DGGE bands: 'specialists'- found on only one host species, 'sponge associates'- found on multiple hosts but not in seawater, and 'generalists' from multiple hosts and seawater. Analogous to other high diversity systems, the degree of specificity of prokaryotes to host eukaryotes could have a potentially significant effect on estimates of marine microbial diversity.     

The phylogeny of a mutualism: evolution and coadaptation between Trollius and its seed-parasitic pollinators

Interactions between seed-parasitic pollinators and their hosts provide useful model systems for the analysis of evolution of mutualism and potential coevolution between plants and insects. Here I present the systematics, pollination ecology and evolution of one of these interactions. I have documented and analysed the phylogenetic and geographic associations between Trollius (Ranunculaceae: 18 spp.) and Chiastocheta (Diptera: Anthomyiidae; 17 spp.), a host-specific genus of seed-parasitic flies that pollinate their host plants to varying extent. Their interactions are usually facultative mutualisms, but in the specialized T. europaeus three fly species are obligate mutualists and a fourth species is an antagonist. The distribution patterns of fly species among Trollius species suggest that the flies evolved in associations with five highly derived Trollius species, and secondarily colonized four more primitive taxa in the parts of their ranges that overlapped with primary hosts. In general, host specificity is maintained primarily through allopatry, with colonization occurring in regions of overlap between parapatric taxa. Fly speciation has occurred in allopatry, both within and among host taxa. Cospeciation is not evident, but convergent evolution in Trollius flowers of several traits, viz. orange sepals, elongated staminodia and increased carpel number per flower, may be the result of mutualism with Chiastocheta.     

The parasitism of immature stages of <Emphasis Type="Italic">Ixodes loricatus</Emphasis> (Acari: Ixodidae) on wild rodents in Argentina

Ixodes loricatus has long been considered with strict-total specificity to New World Marsupials. However, frequent findings of its immature stages on rodents suggest that these vertebrates play an important role in the tick’s life cycle. Aspects dealing with the ecology of Sigmodontinae rodents infestation by I. loricatus are unknown. To contribute to the knowledge of the ecology of this tick species, environmental factors, as well as host species, sex and age, were evaluated to find associations of immature I. loricatus infestation of the most abundant wild rodent species from riparian locations of Buenos Aires province (Argentina). A total of 290 hosts belonging to the subfamily Sigmodontinae were captured and examined for ticks at six locations. The data analysis showed that there was a preference of I. loricatus towards Akodon azarae, but only for those hosts captured in lands not prone to flooding. The results suggest that the host preference of I. loricatus is mainly related to factors such as habitat type and host density.     

The ecology and phylogeny of oomycete infections in Asplanchna rotifers

1. Recently, the potential for parasites to influence the ecology and evolution of their zooplankton hosts has been the subject of increasing study. However, most research to date has focussed on Daphnia hosts, and the potential for parasites to influence other zooplankton taxa remains largely unstudied. 2. During routine sampling of zooplankton in a eutrophic lake, we observed that the rotifer Asplanchna girodi was often infected with a parasitic oomycete. Epidemics of this parasite occurred frequently, with three separate events in a single year. Prevalence at peak infection ranged from 29 to 41% and epidemics lasted from 17 to 56 days. Our data indicate that high densities of the host population are required for epidemics to occur. 3. Our morphological and molecular analyses suggest that this parasite is in the genus Pythium. Most Pythium spp. are plant pathogens, but our study supports recent work on Daphnia, suggesting that Pythium spp. are also important parasites of zooplankton. 4. As the parasite in this study was recalcitrant to cultivation, we developed an alternative method to verify its identity. Our approach used quantitative PCR to show that the ribosomal sequences identified increased with increasing density of infected hosts and, thus, were associated with the parasite. This approach should be generally applicable to other plankton parasites that are difficult to cultivate outside their hosts. 5. Infections significantly reduced host fecundity, lifespan and population growth rate. As a result of the virulence of this parasite, it is likely to influence the population ecology and evolution of its Asplanchna host, and may be a useful model system for studies on host–parasite coevolutionary dynamics.     

Host manipulation by parasites: a multidimensional phenomenon

The diversity of ways in which parasites manipulate the phenotype of their hosts to increase their transmission has been well‐documented during the past decades. Parasites clearly have the potential to alter a broad range of phenotypic traits in their hosts, extending from behaviour and colour to morphology and physiology. While the vast majority of studies have concentrated on few, often only one, host characters, there is increasing evidence that manipulative parasites alter multiple characteristics of their host's phenotype. These alterations can occur simultaneously and/or successively through time, making parasitically modified organisms undoubtedly more complex than traditionally viewed. Here, we briefly review the multidimensionality of host manipulation by parasites, discuss its possible significance and evolution, and propose directions for further research. This view should prove to be an extremely useful approach, generating a series of testable hypotheses regarding the ecology of parasitized hosts, and leading to a better comprehension of complex host–parasite relationships.     

Mock communities highlight the diversity of host‐associated eukaryotes

Host‐associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High‐throughput sequencing (HTS) tools have illuminated the vast diversity of host‐associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall‐Ngai et al. 2013 ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. 2011 ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host‐associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host‐associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. 2014 ; Simon et al. 2015 ; de Vargas et al. 2015 ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. 2014 )]. In this issue of Molecular Ecology, Geisen et al. ( 2015 ) use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free‐living. By isolating the host‐associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high‐throughput sequencing (HTS) and reinforce the ubiquity of these host‐associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free‐living, but instead need to design studies that specifically enumerate the diversity and function of host‐associated eukaryotes. Doing so will allow the field to determine the role host‐associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host‐associated communities, disease ecology and more.     

PHYLOGENESIS OF INSECT/PLANT INTERACTIONS: HAVE PHYLLOBROTICA LEAF BEETLES (CHRYSOMELIDAE) AND THE LAMIALES DIVERSIFIED IN PARALLEL?

The relative importance of conservative versus locally adapted traits for species interactions is an increasingly common theme in evolutionary ecology. Obligate interactions such as those between parasites and hosts often exhibit such strong phylogenetic conservatism that current associations may reflect diversification in parallel. Parallel phylogenesis, documented for animal parasites, has been doubted for insect/plant interactions, but phylogenetic studies of highly specific insect/plant associations are very few. A comparison of phylogeny estimates for the strictly monophagous Phyllobrotica leaf beetles and their lamialean hostplants shows nearly complete concordance, strongly supporting the hypothesis of parallel diversification. The cladogram concordance is significant or nearly so (consensus index values equalling or exceeding the critical value) under randomization distributions based on Adams (though not Nelson) consensus trees. The one clear exception shows unusual natural history, suggesting an isolated host transfer. Insect distributions and plant fossil ages are consistent with a mid-Tertiary age for both clades, further disfavoring the alternative hypothesis of entirely subsequent evolution. The dependence of both larval and adult beetles on the hostplants, larval endophagy, and possible dependence of beetles on toxic host compounds for defense against predators are suggested to underlie the evolutionary persistence of this interaction. Current host use in these beetles appears to reflect primarily the phylogeny of the interaction, strengthening the thesis that history can play a major role in structuring insect/plant relationships.     

Climate variation influences host specificity in avian malaria parasites

Parasites with low host specificity (e.g. infecting a large diversity of host species) are of special interest in disease ecology, as they are likely more capable of circumventing ecological or evolutionary barriers to infect new hosts than are specialist parasites. Yet for many parasites, host specificity is not fixed and can vary in response to environmental conditions. Using data on host associations for avian malaria parasites (Apicomplexa: Haemosporida), we develop a hierarchical model that quantifies this environmental dependency by partitioning host specificity variation into region‐ and parasite‐level effects. Parasites were generally phylogenetic host specialists, infecting phylogenetically clustered subsets of available avian hosts. However, the magnitude of this specialisation varied biogeographically, with parasites exhibiting higher host specificity in regions with more pronounced rainfall seasonality and wetter dry seasons. Recognising the environmental dependency of parasite specialisation can provide useful leverage for improving predictions of infection risk in response to global climate change.     

Characterizing symbiont inheritance during host–microbiota evolution: Application to the great apes gut microbiota

Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes’ diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model‐based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high‐throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.     

THE ORIGIN OF SPECIFICITY BY MEANS OF NATURAL SELECTION: EVOLVED AND NONHOST RESISTANCE IN HOST–PATHOGEN INTERACTIONS

Most species seem to be completely resistant to most pathogens and parasites. This resistance has been called “nonhost resistance” because it is exhibited by species that are considered not to be part of the normal host range of the pathogen. A conceptual model is presented suggesting that failure of infection on nonhosts may be an incidental by‐product of pathogen evolution leading to specialization on their source hosts. This model is contrasted with resistance that results from hosts evolving to resist challenge by their pathogens, either as a result of coevolution with a persistent pathogen or as the result of one‐sided evolution by the host against pathogens that are not self‐sustaining on those hosts. Distinguishing evolved from nonevolved resistance leads to contrasting predictions regarding the relationship between resistance and genetic distance. An analysis of cross‐inoculation experiments suggests that the resistance is often the product of pathogen specialization. Understanding the contrasting evolutionary origins of resistance is critical for studies on the genetics and evolution of host–pathogen interactions in human, agricultural, and natural populations. Research on human infectious disease using animal models may often study resistances that have quite contrasting evolutionary origins, and therefore very different underlying genetic mechanisms.     

Gut microbial ecology of lizards: insights into diversity in the wild,effects of captivity,variation across gut regions and transmission

Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in‐depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host‐specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.     

Black box of phage–bacterium interactions: exploring alternative phage infection strategies

The canonical lytic–lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms ‘pseudolysogeny’ and ‘productive or non-productive chronic infection’, and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage–host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.     

Phytophagous insect-microbe mutualisms and adaptive evolutionary diversification.

Adaptive diversification is a process intrinsically tied to species interactions. Yet, the influence of most types of interspecific interactions on adaptive evolutionary diversification remains poorly understood. In particular, the role of mutualistic interactions in shaping adaptive radiations has been largely unexplored, despite the ubiquity of mutualisms and increasing evidence of their ecological and evolutionary importance. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification, using herbivorous insects and their microbial mutualists as exemplars. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. In this perspective, we examine microbial mutualist mediation of ecological opportunity and ecologically based divergent natural selection for their insect hosts. We also explore the conditions and mechanisms by which microbial mutualists may either facilitate or impede adaptive evolutionary diversification. These include effects on the availability of novel host plants or adaptive zones, modifying host-associated fitness trade-offs during host shifts, creating or reducing enemy-free space, and, overall, shaping the evolution of ecological (host plant) specialization. Although the conceptual framework presented here is built on phytophagous insect-microbe mutualisms, many of the processes and predictions are broadly applicable to other mutualisms in which host ecology is altered by mutualistic interactions.     

Evolution of host resistance: looking for coevolutionary hotspots at small spatial scales

Natural plant populations are often found to be extremely diverse in their resistance to pathogens. While the potential of pathogens in driving the evolution of resistance in hosts has been widely recognized, empirical evidence linking disease dynamics to host population genetic structure has remained scarce. Here I show that current coevolutionary selection for resistance can be divergent even on a very fine spatial scale. In a natural plant-pathogen metapopulation, disease occurrence patterns were highly aggregated over space and time within host populations. A laboratory inoculation experiment showed higher resistance within areas of the host populations where encounter rates with the pathogen have been high. Higher resistance to sympatric than to allopatric strains of the pathogen suggests that this change has taken place as a response to local selection. These results constitute evidence of adaptive microevolution of resistance resulting from disease epidemics in natural plant-pathogen associations, and highlight the importance of finding the relevant scale at which to address questions of current coevolutionary selection.     

Nestedness of hoopoes' bacterial communities: symbionts from the uropygial gland to the eggshell

How microbial symbionts are established and maintain on their hosts is a leading question with important consequences for the understanding of the evolution and functioning of mutualistic relationships. The acquisition by hosts of mutualistic microbial symbionts can be considered as colonization processes of environments (i.e., host) by symbionts. Colonization processes can be explored by characterizing the nestedness of communities, but this approach has rarely been applied to communities of microbial symbionts. We used this approach here, and estimated the nestedness of bacterial communities of hoopoes (Upupa epops), a species with symbiotic bacteria in their uropygial gland that are expected to colonize eggshells where they protect embryos from pathogens. Bacterial communities were characterized by ARISA (Automated rRNA Intergenetic Spacer Region) and studied the nestedness characteristics of bacterial communities living in the uropygial secretion, bill, belly and eggshells of each sampled female hoopoes. We detected a consistent nested pattern of bacterial communities of hoopoes; from the uropygial gland to the eggshell. We also found evidence of study year and reproductive events influencing the level of nestedness of bacterial communities of hoopoes. These results indicate that bacterial communities of eggshells and body parts of female hoopoes are at least partially conditioned by the symbiotic community in the uropygial gland. We discuss the importance of these results for understanding this host–microbial mutualism functioning and evolution.     

Spatial structure,host heterogeneity and parasite virulence: implications for vaccine‐driven evolution

Natural host‐parasite interactions exhibit considerable variation in host quality, with profound consequences for disease ecology and evolution. For instance, treatments (such as vaccination) may select for more transmissible or virulent strains. Previous theory has addressed the ecological and evolutionary impact of host heterogeneity under the assumption that hosts and parasites disperse globally. Here, we investigate the joint effects of host heterogeneity and local dispersal on the evolution of parasite life‐history traits. We first formalise a general theoretical framework combining variation in host quality and spatial structure. We then apply this model to the specific problem of parasite evolution following vaccination. We show that, depending on the type of vaccine, spatial structure may select for higher or lower virulence compared to the predictions of non‐spatial theory. We discuss the implications of our results for disease management, and their broader fundamental relevance for other causes of host heterogeneity in nature.     

Incorporating the process of vertical transmission into understanding of host–symbiont dynamics

Variation exists in the frequency of obligate, vertically transmitted symbiotic organisms within and among host populations; however, these patterns have not been adequately explained by variable fitness effects of symbionts on their hosts. In this forum, we call attention to another equally important, but overlooked mechanism to maintain variation in the frequency of symbioses in nature: the rate of vertical transmission. On ecological time scales, vertical transmission can affect the equilibrium frequencies of symbionts in host populations, with potential consequences for population and community dynamics. In addition, vertical transmission has the potential to influence the evolution of symbiosis, by affecting the probability of fixation of symbiosis (and therefore the evolution of complexity) and by allowing hosts to sanction against costly symbionts. Here we use grass–epichloae symbioses as a model system to explore the causes and consequences of variation in vertical transmission rates. We identify critical points for symbiont transmission that emerge from considering the host growth cycle devoted to reproduction (asexual vs sexual) and the host capability to maintain homeostasis. We also use information on the process of transmission to predict the environmental factors that would most likely affect transmission rates. Altogether, we aim to highlight the vertical transmission rate as an important process for understanding the ecology and evolution of symbiosis, using grass–epichloae interactions as a case study.