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bioRxiv2018

Towards a unification of niche and neutral models of community ecology

Ecological models of community dynamics fall into two main categories. The neutral theory of biodiversity correctly predicts various large-scale ecosystem characteristics such as the species abundance distributions. On a smaller scale, the niche theory of species competition explains population dynamics and interactions between two to a dozen species. Despite the successes of the two theories, they rely on two contradictory assumptions. In the neutral theory each species is competitively equivalent while in the niche theory every species is specialized to exploit a specific part of its environment. Here we propose a resolution to this contradiction using a game theory model of competition with an attractor hyperplane as its equilibrium solution. When the population dynamics shifts within the hyperplane, it is selectively neutral. However, any movement perpendicular to the hyperplane is subject to restoring forces similar to what is predicted by the niche theory. We show that this model correctly reproduces empirical species abundance distributions and is also compatible with species removal experiments.

ecology↗

bioRxiv2018

Interaction modifications lead to greater robustness than pairwise non-trophic effects in ecological networks

O_LIConsiderable emphasis has been placed recently on the importance of incorporating non-trophic effects in to our understanding of ecological networks. Interaction modifications are well established as generating strong non-trophic impacts by modulating the strength of inter-specific interactions.\nC_LIO_LIFor simplicity and comparison with direct interactions within a network context, the consequences of interaction modifications have often been described as direct pairwise interactions. The consequences of this assumption have not been examined in non-equilibrium settings where unexpected consequences of interaction modifications are most likely.\nC_LIO_LITo test the distinct dynamic nature of these higher-order effects we directly compare, using dynamic simulations, the robustness to extinctions under perturbation of systems where interaction modifications are either explicitly modelled or represented by corresponding equivalent pairwise non-trophic interactions.\nC_LIO_LIFull, multi-species representations of interaction modifications resulted in a greater robustness to extinctions compared to equivalent pairwise effects. Explanations for this increased stability despite apparent greater dynamic complexity can be found in additional routes for dynamic feedbacks. Furthermore, interaction modifications changed the relative vulnerability of species to extinction from those trophically connected close to the perturbed species towards those receiving a large number of modifications.\nC_LIO_LIFuture empirical and theoretical research into non-trophic effects should distinguish interaction modifications from direct pairwise effects in order to maximise information about the system dynamics. Interaction modifications have the potential to shift expectations of species vulnerability based exclusively on trophic networks.\nC_LI

ecology↗

bioRxiv2018

Inferring macro-ecological patterns from local species’ occurrences

O_LIBiodiversity provides support for life, vital provisions, regulating services and has positive cultural impacts. It is therefore important to have accurate methods to measure biodiversity, in order to safeguard it when we discover it to be threatened. For practical reasons, biodiversity is usually measured at fine scales whereas diversity issues (e.g. conservation) interest regional or global scales. Moreover, biodiversity may change across spatial scales. It is therefore a key challenge to be able to translate local information on biodiversity into global patterns.\nC_LIO_LIMany databases give no information about the abundances of a species within an area, but only its occurrence in each of the surveyed plots. In this paper, we introduce an analytical framework to infer species richness and abundances at large spatial scales in biodiversity-rich ecosystems when species presence/absence information is available on various scattered samples (i.e. upscaling).\nC_LIO_LIThis framework is based on the scale-invariance property of the negative binomial. Our approach allows to infer and link within a unique framework important and well-known biodiversity patterns of ecological theory, such as the Species Accumulation Curve (SAC) and the Relative Species Abundance (RSA) as well as a new emergent pattern, which is the Relative Species Occupancy (RSO).\nC_LIO_LIOur estimates are robust and accurate, as confirmed by tests performed on both in silico-generated and real forests. We demonstrate the accuracy of our predictions using data from two well-studied forest stands. Moreover, we compared our results with other popular methods proposed in the literature to infer species richness from presence-absence data and we showed that our framework gives better estimates. It has thus important applications to biodiversity research and conservation practice.\nC_LI

ecology↗

bioRxiv2018

Detection of a novel insect specific flavivirus across ecologically diverse populations of Aedes aegypti on the Caribbean Island of Saint Lucia

Outbreaks of mosquito-borne arboviral diseases including dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV) and chikungunya virus (CHIKV) have recently occurred in the Caribbean. The geographical range of the principle vectors responsible for transmission, Aedes (Ae.) aegypti and Ae. albopictus is increasing and greater mosquito surveillance is needed in the Caribbean given international tourism is so prominent. The island of Saint Lucia has seen outbreaks of DENV and CHIKV in the past five years but vector surveillance has been limited with the last studies dating back to the late 1970s. Natural disasters have changed the landscape of Saint Lucia and the island has gone through significant urbanisation. In this study, we conducted an entomological survey of Ae. aegypti and Ae. albopictus distribution across the island and analysed environmental parameters associated with the presence of these species. Although we collected Ae. aegypti across a range of sites across the island, no Ae. albopictus were collected despite traps being placed in diverse ecological settings. The number of Ae. aegypti collected was significantly associated with higher elevation and semi-urban settings yielded female mosquito counts per trap-day that were 5-fold lower than urban settings. Screening for arboviruses revealed a high prevalence of a novel insect-specific flavivirus closely related to cell fusing agent virus (CFAV). We discuss the implications that natural disasters, water storage and lack of mosquito surveillance have on arboviral outbreaks in Saint Lucia and implications for insect only flaviviruses on surveillance and detection of pathogenic flaviviruses.

ecology↗

bioRxiv2026

Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates

Understanding the processes that shape microbial biodiversity and community structure is a key objective of the field of microbial ecology. The processes driving assembly of benthic biofilm bacteria on functionally important reef substrates, such as crustose coralline algae (CCA) and calcium carbonate, are not well understood, despite their critical contributions to the maintenance of biodiversity and ecosystem function on reefs. To characterize the patterns of community assembly and biogeography on these substrates, climax biofilm bacterial communities from 11 reef sites were collected, and full 16S small subunit rRNA genes were sequenced. Though CCA- and carbonate-associated communities demonstrated different diversity, composition, and correlations with environmental conditions, communities on both substrates were assembled according to similar processes. Stochastic processes dominated assembly on both substrates, primarily drift with moderate influence from dispersal limitation and selection. Sub-communities of habitat generalists and specialists, as well as rare and abundant taxa, experienced disparate patterns of assembly that remained consistent between substrates, highlighting the importance of individual taxa traits in shaping community assembly. These results provide insight into the factors shaping benthic biofilm bacterial assembly and biogeography in a tropical reef ecosystem and contribute to understanding of reef resilience in the face of environmental change.

ecology↗

bioRxiv2015

Unearthing the microbial ecology of soil carbon cycling with DNA-SIP

Introductory ParagraphWe explored the microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes. We show that microbial life history traits are likely to constrain the diversity of microorganisms that participate in the soil C-cycle.

Microbiology↗

bioRxiv2015

speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution

1. Large-scale species occurrence data from geo-referenced observations and collected specimens are crucial for analyses in ecology, evolution and biogeography. Despite the rapidly growing availability of such data, their use in evolutionary analyses is often hampered by tedious manual classification of point occurrences into operational areas, leading to a lack of reproducibility and concerns regarding data quality.\n\n2. Here we present speciesgeocodeR, a user-friendly R-package for data cleaning, data exploration and data visualization of species point occurrences using discrete operational areas, and linking them to analyses invoking phylogenetic trees.\n\n3. The three core functions of the package are 1) automated and reproducible data cleaning, 2) rapid and reproducible classification of point occurrences into discrete operational areas in an adequate format for subsequent biogeographic analyses, and 3) a comprehensive summary and visualization of species distributions to explore large datasets and ensure data quality. In addition, speciesgeocodeR facilitates the access and analysis of publicly available species occurrence data, widely used operational areas and elevation ranges. Other functionalities include the implementation of minimum occurrence thresholds and the visualization of coexistence patterns and range sizes. SpeciesgeocodeR accompanies a richly illustrated and easy-to-follow tutorial and help functions.

Evolutionary Biology↗

bioRxiv2016

Fine-scale human population structure in southern Africa reflects ecological boundaries

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about population history within southern Africa. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the =Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking =Khomani (formerly hunter-gatherers) share recent ancestry with other Khoe-speaking forager populations that forms a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited impact from eastern African genetic diffusion.

Genetics↗

bioRxiv2016

iVirus: facilitating new insights in viral ecology with software and community datasets imbedded in a cyberinfrastructure

Microbes impact nutrient and energy transformations throughout the worlds ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. While some bottlenecks, e.g., few reference genomes and non-quantitative viromics, have been overcome, the void of centralized datasets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and datasets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these datasets using existing analytical tools (software applications known as \"Apps\") for assembly, ORF prediction, and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web-based and powered by CyVerse super-computing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances towards new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

Bioinformatics↗

bioRxiv2016

Going down the rabbit hole: a review on how to link genome-wide data with ecology and evolution in natural populations

O_LICharacterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species.\nC_LIO_LIThe study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a burst of analytical tools that can confuse users.\nC_LIO_LISuch confusion can limit the amount of information effectively retrieved from complex genomic datasets. In addition, the lack of a unified analytical pipeline impairs the diffusion of the most recent analytical tools into fields like conservation biology.\nC_LIO_LITo address this need, we describe possible analytical protocols and link these with more than 70 methods dealing with genome-scale datasets. We summarise the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.\nC_LI

Evolutionary Biology↗

bioRxiv2016

Bottom-up ecology of the human microbiome: from metagenomes to metabolomes

The environmental metabolome is a dominant and essential factor shaping microbial communities. Thus, we hypothesized that metagenomic datasets could reveal the quantitative metabolic status of a given sample. Using a newly developed bottom-up ecology algorithm, we predicted high-resolution metabolomes of hundreds of metagenomic datasets from the human microbiome, revealing body-site specific metabolomes consistent with known metabolomics data, and suggesting that common cosmetics ingredients are some of the major metabolites shaping the human skin microbiome.

Bioinformatics↗

bioRxiv2016

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Microbiology↗

bioRxiv2016

Tempo and timing of ecological trait divergence associated with transitions to coexistence in birds

Summary paragraphOrganismal traits may evolve either gradually or in rapid pulses followed by periods of stasis, but the relative importance of these evolutionary models in generating biodiversity has proven difficult to resolve1,2. In addition, while it is often assumed that pulses of trait evolution are associated with speciation events, few studies have explicitly examined how the tempo of trait divergence varies with respect to different geographical phases of speciation. Thus, we still know little about the trajectories of trait divergence over timescales relevant to speciation, or the extent to which these trajectories are shaped by variation in geographical isolation and overlap (sympatry) among incipient species. Here, we combine divergence time estimates, trait measurements, and geographic range data for avian sister species pairs worldwide to examine the tempo and timing of trait divergence during allopatric speciation. We show that divergence in two important ecological traits--?body mass and beak morphology--is best explained by a model including pulses of divergence and periods of relative stasis. We also infer that trait divergence pulses often precede sympatry, and that pulses leading to greater trait disparity are associated with earlier transitions to sympatry. These findings suggest that early pulses of trait divergence promote subsequent transitions to sympatry, rather than such pulses occurring after sympatry has been established, for example via character displacement3. Incorporating pulsed divergence models into allopatric speciation theory helps to resolve some apparently contradictory observations, including widespread instances of both rapid sympatry and prolonged geographical exclusion4-6.

evolutionary biology↗

bioRxiv2017

Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology

Oysters naturally harbor the human gastric pathogen Vibrio parahaemolyticus, but the nature of this association is unknown. Because microbial interactions could influence the accumulation of V. parahaemolyticus in oysters, we investigated the composition of the microbiome in water and oysters at two ecologically unique sites in the Great Bay Estuary, New Hampshire using 16s rRNA profiling. We then evaluated correlations between bacteria inhabiting the oyster with V. parahaemolyticus abundance quantified using a most probable number (MPN) analysis. Even though oysters filter-feed, their microbiomes were not a direct snapshot of the bacterial community in overlaying water, suggesting they selectively accumulate some bacterial phyla. The microbiome of individual oysters harvested more centrally in the bay were relatively more similar to each other and had fewer unique phylotypes, but overall more taxonomic and metabolic diversity, than the microbiomes from tributary-harvested oysters that were individually more variable with lower taxonomic and metabolic diversity. Oysters harvested from the same location varied in V. parahaemolyticus abundance, with the highest abundance oysters collected from one location. This study, which to our knowledge is the first of its kind to evaluate associations of V. parahaemolyticus abundance with members of individual oyster microbiomes, implies that sufficient sampling and depth of sequencing may reveal microbiome members that could impact V. parahaemolyticus abundance.

microbiology↗

bioRxiv2017

The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)

Interactions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, can contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and P.flexilis. Utilizing ecological niche modeling, demographic modeling, and genomic cline analyses, we illustrated a history of divergence with continuous gene flow between these species. We found an abundance of advanced generation hybrids and a lack of loci exhibiting large allele frequency differences across the hybrid zone. Additionally, we found evidence for climate-associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. Our results are consistent with extrinsic factors, such as climate, being an important isolating mechanism for these species. A buildup of intrinsic incompatibilities and of co-adapted gene complexes is also apparent in our results, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in creating and enforcing species boundaries. Overall, we lend support to the hypothesis that varying strengths and directions of selection pressures across the long lifespans of conifers, in combination with their life history strategies, delay the evolution of strong intrinsic incompatibilities.

evolutionary biology↗

bioRxiv2017

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

Mycobacterium africanum (Maf) causes up to half of human tuberculosis in West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including both L5 and L6. We found that the genomic diversity of L6 was higher than in L5, and the selection pressures differed between both groups. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Conversely, human T cell epitopes were under purifying selection in L5, but under positive selection in L6. Although only 10% of the T cell epitopes were variable, mutations were mostly lineage-specific. Our findings indicate that Maf L5 and L6 are genomically distinct, possibly reflecting different ecological niches.

genomics↗

bioRxiv2017

Correlated disasters and need-based transfers: The limits of risk pooling systems in simulated ecologies

Throughout their evolutionary history, humans have faced risks including drought, disease, natural disasters and other unexpected negative events. To deal with these risks, humans use a variety of risk management strategies, some of which involve relying on others in times of need in order to pool risk. However, the effectiveness of risk pooling strategies can be limited when there is high synchronicity of need. Here we investigate the limits of two resource transfer systems for pooling risk (need-based transfers, NBT, and debt-based transfers, DBT) in simulated ecologies with different degrees of correlated disasters using an agent-based model of the need-based transfer system of the Maasai. Overall, we find that survival is higher when shocks are less correlated among partners, when groups are larger, and when network structure is characterized by preferential attachment networks, which have a more modular structure than regular or small world networks. We also find that NBT strategies consistently outperform DBT strategies across a wide variety of parameter values and that the advantage of NBT over DBT is greatest when shocks are less correlated and group size is small. Our results also suggest that systems of sharing that are based on recipient need are less vulnerable than systems that are based on debt and credit, especially in small world and regular networks.

animal behavior and cognition↗

bioRxiv2018

Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities

The degradation of particulate organic matter in the ocean is a central process in the global carbon cycle, the mode and tempo of which is determined by the bacterial communities that assemble on particle surfaces. Although recent studies have shed light on the dynamics of community assembly on particles -which serve as hotspots of microbial activity in the ocean, the mapping from community composition to function, i.e. particle degradation, remains completely unexplored. Using a collection of marine bacteria cultured from different stages of succession on chitin micro-particles we found that the hydrolytic power of communities is highly dependent on community composition. Different particle degrading taxa -all of which were early successional species during colonization- displayed characteristic particle half-lives that differed by ~170 hours, comparable to the residence time of particles in the oceans mixed layer1. These half-lives were in general longer in multispecies communities, where the growth of obligate cross-feeders limited the ability of degraders to colonize and consume particles. Remarkably, above a certain critical initial ratio of cross-feeder to degrader cells, particle degradation was completely blocked along with the growth of all members of the community. We showed that this interaction occurred between a variety of strains of different taxonomic origins and that it only appears when bacteria interact with particles, suggesting a mechanism by which non-degrading secondary consumers occlude access to the particle resource. Overall, our results show that micro-scale community ecology on particle surfaces can have significant impact on carbon turnover in the ocean.

microbiology↗