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bioRxiv2018

Non-linear changes in modelled terrestrial ecosystems subjected to perturbations

When perturbed ecosystems undergo rapid and non-linear changes, this can result in regime shifts to an entirely different ecological state. The need to understand the extent, nature, magnitude and reversibility of these changes is urgent given the profound effects that humans are having on the natural world. It remains very challenging to empirically document non-linear changes and regime shifts within complex, real ecological communities, or even to demonstrate such shifts in simplified experimental systems. General ecosystem models, which simulate the dynamics of entire ecological communities based on a mechanistic representation of ecological processes, provide an alternative and novel way to project ecosystem changes across all scales and trophic levels and to forecast impact thresholds beyond which dramatic or irreversible changes may occur. We model non-linear changes in four terrestrial biomes subjected to human removal of plant biomass, such as occurs through agricultural land-use change. We find that irreversible and non-linear responses are predicted to be common where removal of vegetation exceeds 80% (a level that occurs across nearly 10% of the terrestrial surface), especially for organisms at higher trophic levels and in less productive ecosystems such as drylands. Very large, irreversible changes to the entire ecosystem structure are expected at levels of vegetation removal akin to those in the most intensively used real-world ecosystems. Our results suggest that the projected 21st century rapid increases in agricultural land conversion to feed an expanding human population, may lead to widespread trophic cascades and in some cases irreversible changes to the structure of ecological communities.

ecology↗

bioRxiv2014

Panpulmonate habitat transitions: tracing the evolution of Acochlidia (Heterobranchia,Gastropoda)

The evolution and diversification of euthyneuran slugs and snails was likely strongly influenced by habitat transitions from marine to terrestrial and limnic systems. Well-supported euthyneuran phylogenies with detailed morphological data can provide information on the historical, biological and ecological background in which these habitat shifts took place allowing for comparison across taxa. Acochlidian slugs are basal pulmonates with uncertain relationships to other major panpulmonate clades. They present a unique evolutionary history with representatives in the marine mesopsammon, but also benthic lineages in brackish water, limnic habitats and (semi-)terrestrial environments. We present the first comprehensive molecular phylogeny on Acochlidia, based on a global sampling that covers nearly 85 % of the described species diversity, and additionally, nearly doubles known diversity by undescribed taxa. Our phylogenetic hypotheses are highly congruent with previous morphological analyses and confirm all included recognized families and genera. We further establish an ancestral area chronogram for Acochlidia, document changes in diversification rates in their evolution via the birth-death-shift-model and reconstruct the ancestral states for major ecological traits. Based on our data, Acochlidia originated from a marine, mesopsammic ancestor adapted to tropical waters, in the mid Mesozoic Jurassic. We found that the two major subclades present a remarkably different evolutionary history. The Microhedylacea are morphologically highly-adapted to the marine mesopsammon. They show a circum-tropical distribution with several independent shifts to temperate and temperate cold-habitats, but remained in stunning morphological and ecological stasis since the late Mesozoic. Their evolutionary specialization, which includes a remarkable and potentially irreversible meiofaunal syndrome, guaranteed long-term survival and locally high species densities but also resembles a dead-end road to morphological and ecological diversity. In contrast, the Hedylopsacea are characterized by morphological flexibility and ecologically by independent habitat shifts out of the marine mesopsammon, conquering (semi-)terrestrial and limnic habitats. Originating from interstitial ancestors with moderate adaptations to the mesopsammic world, they reestablished a benthic lifestyle and secondary gigantism in body size. The major radiations and habitat shifts in hedylopsacean families occured in the central Indo-West Pacific in the Paleogene. In the Western Atlantic only one enigmatic representative is known probably presenting a relict of a former pan-Tethys distribution of the clade. This study on acochlidian phylogeny and biogeography adds another facet of the yet complex panpulmonate evolution and shows the various parallel pathways in which these snails and slugs invaded non-marine habitats. Given the complex evolutionary history of Acochlidia, which represent only a small group of Panpulmonata, this study highlights the need to generate comprehensively-sampled species-level phylogenies to understand euthyneuran evolution.

Evolutionary Biology↗

bioRxiv2015

Fecundity selection theory: concepts and evidence

Fitness results from the optimal balance between survival, mating success and fecundity. The interactions between these three components of fitness vary importantly depending on the selective context, from positive covariation between them, to antagonistic pleiotropic relationships when fitness increases in one reduce fitness of others. Therefore, elucidating the routes through which selection shapes life history and phenotypic adaptations via these fitness components is of primary significance to understand ecological and evolutionary dynamics. However, while the fitness components mediated by natural (survival) and sexual (mating success) selection have extensively been debated from most possible perspectives, fecundity selection remains considerably less studied. Here, we review the theory, evidence and implications of fecundity selection as a driver of sex-specific adaptive evolution. Based on accumulating literature on the life-history, phenotypic and ecological aspects of fecundity, we (i) suggest that fecundity is restricted to refer to brood size per reproductive episode, while annual and lifetime fecundity should not be used interchangeably with fecundity as they represent different life history parameters; (ii) provide a generalized redefinition of fecundity selection that encompasses any traits that influence fecundity in any direction (from high to low) and in either sex; (iii) review the (macro)ecological basis of fecundity selection (e.g., ecological pressures that influence predictable spatial variation in fecundity); (iv) suggest that most ecological theories of fecundity selection should be tested in organisms other than birds; (v) argue that the longstanding fecundity selection hypothesis of female-biased sexual size dimorphism (SSD) has gained inconsistent support, that strong fecundity selection does not necessarily drive female-biased SSD, and that this form of SSD can be driven by other selective pressures; and (vi) discuss cases in which fecundity selection operates on males.

Evolutionary Biology↗

bioRxiv2015

Interactions retain the co-phylogenetic matching that communities lost

Both species and their interactions are affected by changes that occur at evolutionary time-scales, and these changes shape both ecological communities and their phylogenetic structure. That said, extant ecological community structure is contingent upon random chance, environmental filters, and local effects. It is therefore unclear how much ecological signal local communities should retain. Here we show that, in a host-parasite system where species interactions vary substantially over a continental gradient, the ecological significance of individual interactions is maintained across different scales. Notably, this occurs despite the fact that observed community variation at the local scale frequently tends to weaken or remove community-wide phylogenetic signal. When considered in terms of the interplay between community ecology and coevolutionary theory, our results demonstrate that individual interactions are capable and indeed likely to show a consistent signature of past evolutionary history even when woven into communities that do not.

Evolutionary Biology↗

bioRxiv2016

Testing for local adaptation and evolutionary potential along altitudinal gradients in rainforest Drosophila: limitations of laboratory estimates.

Predicting how species will respond to the rapid climatic changes predicted this century is an urgent task. Species Distribution Models (SDMs) use the current relationship between environmental variation and species abundances to predict the effect of future environmental change on their distributions. However, two common assumptions of SDMs are likely to be violated in many cases: (1) that the relationship of environment with abundance or fitness is constant throughout a species range and will remain so in future, and (2) that abiotic factors (e.g. temperature, humidity) determine species distributions. We test these assumptions by relating field abundance of the rainforest fruit fly Drosophila birchii to ecological change across gradients that include its low and high altitudinal limits. We then test how such ecological variation affects the fitness of 35 D. birchii families transplanted in 591 cages to sites along two altitudinal gradients, to determine whether genetic variation in fitness responses could facilitate future adaptation to environmental change. Overall, field abundance was highest at cooler, high altitude sites, and declined towards warmer, low altitude sites. By contrast, cage fitness (productivity) increased towards warmer, lower altitude sites, suggesting that biotic interactions (absent from cages) drive ecological limits at warmer margins. In addition, the relationship between environmental variation and abundance varied significantly among gradients, indicating divergence in ecological niche across the species range. However, there was no evidence for local adaptation within gradients, despite greater productivity of high altitude than low altitude populations when families were reared under laboratory conditions. Families also responded similarly to transplantation along gradients, providing no evidence for fitness trade-offs that would favour local adaptation. These findings highlight the importance of (1) measuring genetic variation of key traits under ecologically relevant conditions, and (2) considering the effect of biotic interactions when predicting species responses to environmental change.

Evolutionary Biology↗

bioRxiv2016

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single cell genomes and a 5-year metagenomic time series. The single cell genomes grouped into 15 monophyletic clusters (termed \"tribes\") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

Evolutionary Biology↗

bioRxiv2016

Habitat preference predicts genetic diversity and population divergence in Amazonian birds

The ecological traits of organisms may predict important evolutionary parameters such as genetic diversity, population genetic structure, and demographic history. Making these ecological-evolutionary links is difficult because robust, comparable genetic estimates are required from many species with differing ecologies. In Amazonian birds, differences in habitat preference are an important component of ecological diversity. A subset of Amazonian birds is restricted to forest edge and open forest along floodplains, whereas another subset occurs only in the interior of tall, upland forest. Here, we examine the link between habitat and evolutionary metrics using 20 pairs of closely related and co-distributed bird species in which one member of the pair occurs primarily in forest edge and floodplains, and the other occurs in upland forest interior. We use standardized geographic sampling and genomic data from the same set of 2,416 independent markers to estimate genetic diversity, population structure, and demographic history in each species. We find that species of upland forest have higher genetic diversity, greater divergence across the landscape, more genetically distinct populations, and deeper gene histories than floodplain species. Our results reveal that species ecology in the form of habitat preference is an important predictor of genetic diversity and divergence and suggest that floodplain and upland avifaunas in the Amazon may be on separate evolutionary trajectories and require different conservation strategies.

evolutionary biology↗

bioRxiv2017

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic radiation of trophic specialist pupfishes

Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of the fixed variants between the specialist species lie in regions with discordant topologies. These regions include signatures of selective sweeps and adaptive introgression from neighboring islands into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador contributed 10-fold more to divergence between specialist species within the radiation than adaptive introgression of Caribbean genetic variation; however, some of these introgressed regions from distant islands were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador specialist from an island 300 km away. The complex emerging picture of the origins of adaptive radiation on San Salvador indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may also be required to trigger adaptive radiation in the presence of ecological opportunity.\n\nAuthor summaryGroups of closely related species can rapidly evolve to occupy diverse ecological roles, but the ecological and genetic conditions that trigger this diversification are still highly debated. We examine patterns of molecular evolution across the genomes of a rapid radiation of pupfishes that includes two trophic specialists. Despite apparently widespread ecological opportunities and gene flow across the Caribbean, this radiation is endemic to a single Bahamian Island. Using the whole genomes of 42 pupfish we find evidence of extensive and previously unexpected variation in evolutionary relatedness among Caribbean pupfish. Two sources of genetic variation have contributed to the adaptive diversification of complex phenotypes in this system: selective sweeps of genetic variation from across the Caribbean that was brought into San Salvador through hybridization and genetic variation found on San Salvador. While genetic variation from San Salvador appears to be relatively more common in the divergence observed among specialists, hybridization probably played an important role in the evolution of the complex phenotypes as well. Our findings that multiple sources of genetic variation contribute to the San Salvador radiation suggest that a complex suite of factors, including hybridization with other species, may be required to trigger adaptive radiation in the presence of ecological opportunity.

evolutionary biology↗

bioRxiv2017

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

evolutionary biology↗

bioRxiv2014

Diversity of entomopathogens Fungi: Which groups conquered the insect body?

The entomopathogenic Fungi comprise a wide range of ecologically diverse species. This group of parasites can be found distributed among all fungal phyla and as well as among the ecologically similar but phylogenetically distinct Oomycetes or water molds, that belong to a different kingdom (Stramenopila). As a group, the entomopathogenic fungi and water molds parasitize a wide range of insect hosts from aquatic larvae in streams to adult insects of high canopy tropical forests. Their hosts are spread among 18 orders of insects, in all developmental stages such as: eggs, larvae, pupae, nymphs and adults exhibiting completely different ecologies. Such assortment of niches has resulted in these parasites evolving a considerable morphological diversity, resulting in enormous biodiversity, much of which remains unknown. Here we gather together a huge amount of records of these entomopathogens to comparing and describe both their morphologies and ecological traits. These findings highlight a wide range of adaptations that evolved following the evolutionary transition to infecting the most diverse and widespread animals on Earth, the insects.

Ecology↗

bioRxiv2016

Stochastic competitive exclusion leads to a cascade of species extinctions

Community ecology has traditionally relied on the competitive exclusion principle, a piece of common wisdom in conceptual frameworks developed to describe species assemblages. Key concepts in community ecology, such as limiting similarity and niche partitioning, are based on competitive exclusion. However, this classical paradigm in ecology relies on implications derived from simple, deterministic models. Here we show how the predictions of a symmetric, deterministic model about the way extinctions proceed can be utterly different from the results derived from the same model when ecological drift (demographic stochasticity) is explicitly considered. Using analytical approximations to the steady-state conditional probabilities for assemblages with two and three species, we demonstrate that stochastic competitive exclusion leads to a cascade of extinctions, whereas the symmetric, deterministic model predicts a multiple collapse of species. To test the robustness of our results, we have studied the effect of environmental stochasticity and relaxed the species symmetry assumption. Our conclusions highlight the crucial role of stochasticity when deriving reliable theoretical predictions for species community assembly.

Ecology↗

bioRxiv2016

A roadmap for a quantitative ecosystem-based environmental impact assessment

A new roadmap for quantitative methodologies of Environmental Impact Assessment (EIA) is proposed, using an ecosystem-based approach. EIA recommendations are currently based on case-by-case rankings, distant from statistical methodologies, and based on ecological ideas that lack proof of generality or predictive capacities. These qualitative approaches ignore process dynamics, scales of variations and interdependencies and are unable to address societal demands to link socio-economic and ecological processes (e.g. population dynamics). We propose to re-focus EIA around the systemic formulation of interactions between organisms (organized in populations and communities) and their environments but inserted within a strict statistical framework. A systemic formulation allows scenarios to be built that simulate impacts on chosen receptors. To illustrate the approach, we design a minimum ecosystem model that demonstrates non-trivial effects and complex responses to environmental changes. We suggest further that an Ecosystem-Based EIA - in which the socio-economic system is an evolving driver of the ecological one - is more promising than a socio-economic-ecological system where all variables are treated as equal. This refocuses the debate on cause-and-effect, processes, identification of essential portable variables, and a potential for quantitative comparisons between projects, which is important in cumulative effects determinations.

Ecology↗

bioRxiv2016

Deterministic assembly processes govern seasonal and spatial variation in microbiomes across hydrologically-connected hyporheic zones

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic, and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function.\n\nOriginality-Significance StatementSubsurface zones of groundwater and surface water mixing (hyporheic zones) are hotspots of biogeochemical activity and strongly influence carbon, nutrient and contaminant dynamics within riverine ecosystems. Hyporheic zone microbiomes are responsible for up to 95% of riverine ecosystem respiration, yet the ecology of these microbiomes remains poorly understood. While significant progress is being made in the development of microbially-explicit ecosystem models, poor understanding of hyporheic zone microbial ecology impedes development of such models in this critical zone. To fill the knowledge gap, we present a comprehensive analysis of biogeographical patterns in hyporheic microbiomes as well as the ecological processes that govern their composition and function through space and time. Despite pronounced hydrologic connectivity throughout the hyporheic zone--and thus a strong potential for dispersal--we find that ecological selection deterministically governs microbiome composition within local environments, and we identify specific groups of organisms that correspond to seasonal changes in hydrology. Based on our results, we propose a conceptual model for hyporheic zone metabolism in which comparatively high-organic C conditions during surface water intrusion into the hyporheic zone support heterotrophic metabolisms that succumb to autotrophy during time periods of groundwater discharge. These results provide new opportunities to develop microbially-explicit ecosystem models that incorporate the hyporheic zone and its influence over riverine ecosystem function.

ecology↗

bioRxiv2017

Partitioning the effects of eco-evolutionary feedbacks on community stability

AO_SCPCAPBSTRACTC_SCPCAPA fundamental challenge in ecology continues to be identifying mechanisms that stabilize community dynamics. By altering the interactions within a community, eco-evolutionary feedbacks may play a role in community stability. Indeed, recent empirical and theoretical studies demonstrate that these feedbacks can stabilize or destabilize communities, and moreover, that this sometimes depends on the relative rate of ecological to evolutionary processes. So far, theory on how eco-evolutionary feedbacks impact stability exists for only for a few special cases. In our work, we develop a general theory for determining the effects of eco-evolutionary feedbacks on stability in communities with an arbitrary number of interacting species and evolving traits for when evolution is slow and fast. We characterize how eco-evolutionary feedbacks lead to stable communities that would otherwise be unstable, and vice versa. We show how this characterization provides a partitioning of the roles of direct and indirect feedbacks between ecological and evolutionary processes on stability, and how this partitioning depends on the rate of evolution relative to the ecological time scales. Applying our methods to models of competing species and food chains, we demonstrate how the functional form of trade offs, genetic correlations between traits, and the rate of evolution determine whether eco-evolutionary feedbacks stabilize or destabilize communities.

ecology↗

bioRxiv2017

Unifying concepts of biological function from molecules to ecosystems.

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity theory to create a precise definition of biological function which spans scales of biological organisation and can be quantified in the unifying currency of biomass, enabling comparisons of functional effectiveness (irrespective of the specific function) across the field of ecology. We give precise definitions of ecological and ecosystem function that bring clarity and precision to studies of biodiversity-ecosystem function relationships and questions of ecological redundancy. To illustrate the new concepts and their unifying power, we construct a simple community-level model with nutrient cycling and animal-plant mutualism, emphasising the importance of its network structure in determining overall functioning. This type of network structure is that of an autocatalytic set of functional relationships, which also appears at biochemical, cellular and organism levels of organisation, creating a nested hierarchy. This enables a common and unifying concept of function to apply from molecular interaction networks up to the global ecosystem.

ecology↗

bioRxiv2017

Niche characteristics and potential distribution of Thelocactus species, a Mexican genus of globular cacti.

AimAlthough Mexican Cactaceae are a significative component of Mexican flora and have a relevant economic and ornamental value, the knowledge of the environmental factors characterising their niche is still quite incomplete. This study was aimed at defining the potential distribution and ecological niche of Thelocactus species.\n\nMethodsClimatic and environmental variables constraining the distribution of Thelocactus species were identified by means of environmental niche models (ENM) and ordination techniques, and used to generate potential distribution maps. The constructed ENMs were compared to assess the similarities of the ecological niche of Thelocactus species and to know if they share the same ecological niche space.\n\nResultsThe distribution of Thelocactus species was mostly limited by a combination of two environmental factors, isothermality and precipitation of wettest quarter. The null hypothesis of the niche equivalency test was rejected for all paired comparisons between all Thelocactus species except between the pair Thelocactus leucacanthus-Thelocactus hastifer. The results of the niche similarity tests were quite varied, for some species pairs the niche similarities were higher than expected by chance, for others the null hypothesis was rejected, while in other species pairs niches were more similar than expected by chance, but only in one direction.\n\nMain conclusionsThe differences in habitat requirements were well documented by the significative differences in the niche ecological space as shown by the equivalency test, while the high percentage of niches that were more similar than expected by chance suggest a high degree of niche conservatism among Thelocactus species. The spatial predictions could serve to improve field design sampling to discover new populations, while niche characteristics could be relevant for improving preservation actions and guiding reintroduction programs for a better conservation of Thelocactus species.

ecology↗

bioRxiv2017

Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)

Environmentally Transmitted Diseases Are Comparatively Poorly Understood And Managed, And Their Ecology Is Particularly Understudied. Here We Identify Challenges Of Studying Environmental Transmission And Persistence With A Six-Sided Interdisciplinary Review Of The Biology Of Anthrax (Bacillus Anthracis). Anthrax Is A Zoonotic Disease Capable Of Maintaining Infectious Spore Banks In Soil For Decades (Or Even Potentially Centuries), And The Mechanisms Of Its Environmental Persistence Have Been The Topic Of Significant Research And Controversy. Where Anthrax Is Endemic, It Plays An Important Ecological Role, Shaping The Dynamics Of Entire Herbivore Communities. The Complex Eco-Epidemiology Of Anthrax, And The Mysterious Biology Of Bacillus Anthracis During Its Environmental Stage, Have Necessitated An Interdisciplinary Approach To Pathogen Research. Here, We Illustrate Different Disciplinary Perspectives Through Key Advances Made By Researchers Working In Etosha National Park, A Long-Term Ecological Research Site In Namibia That Has Exemplified The Complexities Of AnthraxS Enzootic Process Over Decades Of Surveillance. In Etosha, The Role Of Scavengers And Alternate Routes (Waterborne Transmission And Flies) Has Proved Unimportant, Relative To The Long-Term Persistence Of Anthrax Spores In Soil And Their Infection Of Herbivore Hosts. Carcass Deposition Facilitates Green-Ups Of Vegetation To Attract Herbivores, Potentially Facilitated By Anthrax Spores Role In The Rhizosphere. The Underlying Seasonal Pattern Of Vegetation, And Herbivores Immune And Behavioral Responses To Anthrax Risk, Interact To Produce Regular \"Anthrax Seasons\" That Appear To Be A Stable Feature Of The Etosha Ecosystem. Through The Lens Of Microbiologists, Geneticists, Immunologists, Ecologists, Epidemiologists, And Clinicians, We Discuss How Anthrax Dynamics Are Shaped At The Smallest Scale By Population Genetics And Interactions Within The Bacterial Communities Up To The Broadest Scales Of Ecosystem Structure. We Illustrate The Benefits And Challenges Of This Interdisciplinary Approach To Disease Ecology, And Suggest Ways Anthrax Might Offer Insights Into The Biology Of Other Important Pathogens. Bacillus Anthracis, And The More Recently Emerged Bacillus Cereus Biovar Anthracis, Share Key Features With Other Environmentally-Transmitted Pathogens, Including Several Zoonoses And Panzootics Of Special Interest For Global Health And Conservation Efforts. Understanding The Dynamics Of Anthrax, And Developing Interdisciplinary Research Programs That Explore Environmental Persistence, Is A Critical Step Forward For Understanding These Emerging Threats.

ecology↗

bioRxiv2017

Modeling Marek’s disease virus transmission: a framework for evaluating the impact of farming practices and evolution on disease

Mareks disease virus (MDV) is a pathogen of chickens whose control has twice been un-dermined by pathogen evolution. Disease ecology is believed to be the main driver of this evolution, yet mathematical models of MDV disease ecology have never been confronted with data to test their reliability. Here, we develop a suite of MDV models that differ in the ecological mechanisms they include. We fit these models with maximum likelihood in pomp to data on MDV concentration in dust collected from two commercial broiler farms. Using AIC to compare the models, we find that virus dynamics are influenced by between-flock variation in host susceptibility to virus, shedding rate from infected birds, and cleanout efficiency. We also find evidence that virus is reintroduced to farms approximately once per month, but we do not find evidence that virus sanitization rates vary between flocks. Of the models that survive model selection, we find agreement between parameter estimates and previous experimental data, as well as agreement between field data and the predictions of these models, suggesting robustness of model predictions. Using the set of surviving models, we explore how changes to farming practices are predicted to influence MDV costs, should pathogen evolution undermine existing control measures. By quantitatively capturing the mechanisms of disease ecology, we have laid the groundwork to explore the future trajectory of virus evolution.

ecology↗