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bioRxiv2018

Trends and perspectives on the use of social network analysis in behavioural ecology: a bibliometric approach

The increased popularity and improved accessibility of social network analysis has improved our ability to test hypotheses about the complexity of animal social structure. To gain a deeper understanding of the use and application of social network analysis, we systematically surveyed the literature and extracted information on publication trends from articles using social network analysis. We synthesize trends in social network research over time and highlight variation in the use of different aspects of social network analysis. Our primary finding highlights the increase in use of social network analysis over time and from this finding, we observed an increase in the number of review and methods of social network analysis. We also found that most studies included a relatively small number (median = 15, range = 4-1406) of individuals to generate social networks, while the number and type of social network metrics calculated in a given study varied zero to nine (median = 2, range 0-9). The type of data collection or the software programs used to analyze social network data have changed; SOCPROG and UCINET have been replaced by various R packages over time. Finally, we found strong taxonomic and conservation bias in the species studied using social network analysis. Most species studied using social networks are mammals (111/201, 55%) or birds (47/201, 23%) and the majority tend to be species of least concern (119/201, 59%). We highlight emerging trends in social network research that may be valuable for distinct groups of social network researchers: students new to social network analysis, experienced behavioural ecologists interested in using social network analysis, and advanced social network users interested in trends of social network research. In summary we address the temporal trends in social network publication practices, highlight potential bias in some of the ways we employ social network analysis, and provide recommendations for future research based on our findings.

animal behavior and cognition↗
bioRxiv2018

Evolution of phenotypic plasticity in response to ethanol between sister species with different ecological histories (Drosophila melanogaster and D. simulans)

The contribution of phenotypic plasticity to adaptation is contentious, with contradictory empirical support for its role in evolution. Here I investigate the possibility that phenotype plasticity has contributed to adaptation to a novel resource. If phenotype plasticity contributes to adaptation, it is thought to evolve in a process termed genetic accommodation. Under this model, the initial response to the environment is widely variable due to cryptic genetic variation, which is then refined by selection to a single adaptive response. I examine the role of phenotypic plasticity in adaptation here by comparing two species of Drosophila that differ in their adaptation to ethanol (Drosophila melanogaster and D. simulans). Both species are human commensals with a recent cosmopolitan expansion, but only D. melanogaster is adapted to ethanol exposure. I measure phenotype plasticity in response to ethanol with gene expression and an approach that combines information about expression and alternative splicing. I find evidence for adaptation to ethanol through genetic accommodation, suggesting that the evolution of phenotype plasticity contributed to the ability of D. melanogaster to exploit a novel resource. I also find evidence that alternative splicing may be more important for the adaptive response to ethanol than overall changes in exon expression.

evolutionary biology↗
bioRxiv2018

Lessons learned when looking for non-neutral ecological processes in the built environment: the bacterial and fungal microbiota of shower tiles

With periodic pulses of water, bathroom showers represent a habitat in the built environment with a high potential for microbial growth. We set out to apply a neutral model of microbial community assembly and to identify deviations from the model that would indicate non-neutral dynamics, such as selective pressures for individual taxa, in this particular indoor habitat. Following a cleaning event, the bacterial and fungal microbiota of the shower stalls in two residences in the San Francisco Bay Area were observed over a four-week period. We observed strong differences in composition between houses, preventing us from combining samples and thus limiting our statistical power. We also identified different aspects of the sampling scheme that could be improved, including increasing the sampling area (to ensure sufficient biomass) and increasing the number of replicates within an individual shower. The data from this pilot study indicate that immigrants to the built environment arising from human shedding dominate the shower ecosystem and that growth conditions are relatively unfavorable despite the water availability. We offer suggestions on how to improve the studying and sampling of microbes in indoor environments.

microbiology↗
bioRxiv2018

Marine Fe-oxidizing Zetaproteobacteria: Historical, ecological, and genomic perspectives

The Zetaproteobacteria are a class of bacteria typically associated with marine Fe oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, as well as saline terrestrial aquifers and springs. Isolates from a range of environments all grow by Fe oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe oxidation at the low O2 concentrations common to Fe(II)-rich oxic/anoxic transition zones. Also, Zetaproteobacteria make a variety of biomineral morphologies as a repository for Fe(III) waste, and as attachment structures. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, various habitats enrich for different sets of Zetaproteobacteria. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2, and nitrate availability, based on genomic analyses. Also, a putative Fe oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as specialists in Fe oxidation. In all, culture, genomic, and environmental studies suggest that Zetaproteobacteria are widespread, and therefore have a broad influence on marine and saline terrestrial Fe cycling.

microbiology↗
bioRxiv2017

The network structure of cancer ecosystems

Ever since Pagets seed-and-soil and Ewings connectivity hypotheses to explain tumor metastasis (1,2), it has become clear that cancer progression can be envisaged as an ecological phenomenon. This connection has flourished during the past two decades (3-7), giving rise to important insights into the ecology and evolution of cancer progression, with therapeutic implications (8-10). Here, we take a metapopulation view of metastasis (i.e. the migration to and colonization of, habitat patches) and represent it as a bipartite network, distinguishing source patches, or organs that host a primary tumor, and acceptor patches, or organs colonized ultimately from the source through metastasis. Using 20,326, biomedical records obtained from literature, we show that: (i) the network structure of cancer ecosystems is non-random, exhibiting a nested subset pattern as has been found both in the distribution of species across islands and island-like habitats (11-13), and in the distribution of among species interactions across different ecological networks (14-16); (ii) similar to ecological networks, there is a heterogeneous distribution of degree (i.e., number of connections associated with a source or acceptor organ); (iii) there is a significant correlation between metastatic incidence (or the frequency with which tumor cells from a source organ colonize an acceptor one) and arterial blood supply, suggesting that more irrigated organs have a higher probability of developing metastasis or being invaded; (iv) there is a positive correlation between metastatic incidence and acceptor organ degree (or number of different tumor-bearing source organs that generate metastasis in a given acceptor organ), and a negative one between acceptor organ degree and number of stem cell divisions, implying that there are preferred sink organs for metastasis and that this could be related to average acceptor organ cell longevity; (v) there is a negative association between organ cell turnover and source organ degree, implying that organs with rapid cell turnovers tend to generate more metastasis, a process akin to the phenomenon of propagule pressure in ecology (17); and (vi) the cancer ecosystem network exhibits a modular structure in both source and acceptor patches, suggesting that some of them share more connections among themselves than with the rest of the network. We show that both niche-related processes occurring at the organ level as well as spatial connectivity and propagule pressure contribute to metastaticspread and result in a non-random cancer network, which exhibits a truncated power law degree distribution, clustering and a nested subset structure. The similarity between the cancer network and ecological networks highlights the importance of ecological approaches in increasing our understanding of patterns in cancer incidence and dynamics, which may lead to new strategies to control tumor spread within the human ecosystem.

ecology↗
bioRxiv2018

The community and ecosystem consequences of intraspecific diversity: a meta-analysis

Understanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity-ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within-species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non-linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity-function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within-species biodiversity for understanding ecological dynamics.

ecology↗
bioRxiv2018

Pathogens, parasites, and parasitoids of ants: a synthesis of parasite biodiversity and epidemiological traits

1.Ants are among the most ecologically successful organisms on Earth, with a global distribution and diverse nesting and foraging ecologies. Ants are also social organisms, living in crowded, dense colonies that can range up to millions of individuals. Understanding the ecological success of the ants requires understanding how they have mitigated one of the major costs of social living-infection by parasitic organisms. Additionally, the ecological diversity of ants suggests that they may themselves harbor a diverse, and largely unknown, assemblage of parasites. As a first step, we need to know the taxonomic and functional diversity of the parasitic organisms infecting ants. To that end, we provide a comprehensive review of the parasitic organisms infecting ants by collecting all extant records. We synthesize major patterns in parasite ecology by categorizing how parasites encounter their ant hosts, whether they require host death as a developmental necessity, and how they transmit to future hosts.\n\nWe report 1,415 records of parasitic organisms infecting ants, the majority of which come from order Diptera (34.8%), phylum Fungi (25.6%), and order Hymenoptera (25.1%). Most parasitic organisms infecting ants are parasitoids (89.6%), requiring the death of their host as developmental necessity and most initially encounter their hosts in the extranidal environment (68.6%). Importantly, though most parasitic organisms infecting ants only need a single host to complete their life cycle (89.2%), the vast majority need to leave the nest before transmission to the next ant host can occur (88.3%), precluding ant-to-ant transmission within the nest. With respect to the host, we only found records for 9 out of 17 extant ant sub-families, and for 82 out of the currently recognized 334 ant genera. Though there is likely bias in the records reported, both host and parasite ecological traits and evolutionary histories underlie the pattern of ant-parasite association reported here. This work provides a foundation for future work that will begin to untangle the ecological drivers of ant-parasite relationships and the evolutionary implications thereof.

ecology↗
bioRxiv2017

Rapid evolution slows extinctions in food webs

Historically, evolutionary changes have been thought to act on much longer time scales than ecological dynamics. However, a recent body of research has demonstrated that evolution that is rapid enough to dramatically affect ecological dynamics can lead to feedbacks between ecological and evolutionary processes. Thus, to understand the stability of ecological communities, we must also consider evolutionary change in the component species. Here, we use individual-based simulations of a quantitative genetic eco-evolutionary model to describe how trait evolution influences the stability of ecological communities. On short time scales, faster evolutionary rates decreased the probability of species extinctions as populations at low densities were rescued via trait evolution. However, on longer time scales, evolutionary had little effect on the number of extinctions. The extent of short-term evolutionary rescue depended on the source of trait variation; populations with variation generated through mutation experienced more rescue events and were less prone to extinction, relative to populations with only standing trait variation. Trait evolution leading to more rescued populations increased the stability of the community on timescales relevant to conservation. Our work highlights the importance of intraspecific trait variation and the evolutionary mechanisms maintaining this variation for community ecology, as well as management of declining populations in a community context.

ecology↗
bioRxiv2018

Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

The smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts that selection, dispersal and drift are main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.\n\nSIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmental selection, dispersal and random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

ecology↗
bioRxiv2026

A strong-to-weak interaction shift during microbiome succession is coupled to colonizer-dependent antimicrobial resistance

The outcome of ecological succession is often attributed to the characteristics of the invader or the resident community, but rarely to how the community's interaction network reorganizes during assembly. Here, we track intraspecific lineage dynamics and infer time-resolved community interaction networks using Dynamic Covariance Mapping during ecological invasion of the mouse gut by a chromosomally barcoded, spectinomycin-resistant Escherichia coli K12 colonizer. The network is initially dominated by strong, predominantly inhibitory interactions, but as community diversity recovers, the distribution of interaction strengths contracts toward zero, producing a community increasingly dominated by weak and near-neutral interactions. The dominant eigenvalue of the DCM-inferred interaction matrix moves toward marginal stability predicted for dynamically assembling ecological networks. This pattern replicates across eight independent mice in two experimental cohorts, at both inter- and intra-species resolution. The ecological transition coincides with the reproducible resurgence of Paenibacillaceae to high relative abundance and persistent coexistence with E. coli under continued spectinomycin pressure. Whole-genome sequencing of recovered Paenibacillus macerans isolates identifies recurrent mutations in ribosomal protein S5 region associated with spectinomycin binding and strongly implicating this variant in resistance. Strikingly, under antibiotic pressure but without E. coli K12 invasion, resident Paenibacillaceae never blooms, indicating that expansion of the resistant population depends on the ecological context established by the colonizer. These findings show that gut microbiome succession is accompanied by a reproducible transition from strong toward weak interactions and link this network reorganization to the colonizer-dependent ecological benefit of antimicrobial resistance.

ecology↗
bioRxiv2016

Immunoecology of species with alternative reproductive tactics and strategies

Alternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecological, developmental, behavioural, life-history, and physiological profile that shifts the balance between reproduction and self-maintenance, one aspect being immunity. Immunoecological work on species with ARTS, which is the topic of this review, is particularly interesting because the alternative morphs make it possible to separate the effects of sex, per se, from other factors that in other species are inextricably linked with sex. We first summarize the evolution, development and maintenance of ARTS. We then review immunoecological hypotheses relevant to species with ARTS, dividing them into physiological, life-history, and ecological hypotheses. In context of these hypotheses, we critically review in detail all immunoecological studies we could find on species with ARTS. Several interesting patterns emerge. Oddly, there is a paucity of studies on insects, despite the many benefits that arise from working with insects: larger sample sizes, simple immune systems, and countless forms of alternative reproductive strategies and tactics. Of all the hypotheses considered, the immunocompetence handicap hypothesis has generated the greatest amount of work, but not necessarily the greatest level of understanding. Unfortunately, it is often used as a general guiding principle rather than a source of explicitly articulated predictions. Other hypotheses are usually considered a posteriori, but it is perhaps time that they take centre stage. Whereas blanket concepts such as "immunocompetence" and "androgens" might useful to develop a rationale, predictions need to be far more explicitly articulated. Integration so far has been a one-way street, with ecologists delving deeper into physiology, seemingly at the cost of ignoring their organisms evolutionary history and ecology. One possible useful framework is to divide ecological and evolutionary factors affecting immunity into those that stimulate the immune system, and those that depress it. Finally, the contributions of genomics to ecology are being increasingly recognized, including in species with ARTS, but we must ensure that evolutionary and ecological hypotheses drive the effort, as there is no grandeur in the strict reductionist view of life.

Evolutionary Biology↗
bioRxiv2015

Reticulate evolution is favoured in influenza niche switching.

Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.\n\nSignificance StatementAre the processes that result in the exchange of genes between microbes quantitatively advantageous for those microbes when switching between ecological niches? To address this question, we consider the influenza A virus as a model microbe, with its ability to infect multiple host species (ecological niches) and undergo reassortment (exchange genes) with one another. Through our analysis of sequence data from the Influenza Research Database and the Barcode of Life Database, we find that the greater the quantitative difference between influenza hosts, the greater the proportion of reassortment events were found. More broadly, for microbes, we infer that reticulate evolutionary processes should be quantitatively favoured when switching between ecological niches.

Ecology↗
bioRxiv2016

Using null models to infer microbial co-occurrence networks

Although microbial communities are ubiquitous in nature, relatively little is known about the structural and functional roles of their constituent organisms underlying interactions. A common approach to study such questions begins with extracting a network of statistically significant pairwise co-occurrences from a matrix of observed operational taxonomic unit (OTU) abundances across sites. The structure of this network is assumed to encode information about ecological interactions and processes, resistance to perturbation, and the identity of keystone species. However, common methods for identifying these pairwise interactions can contaminate the network with spurious patterns that obscure true ecological signals. Here, we describe this problem in detail and develop a solution that incorporates null models to distinguish ecological signals from statistical noise. We apply these methods to the initial OTU abundance matrix and to the extracted network. We demonstrate this approach by applying it to a large soil microbiome data set and show that many previously reported patterns for these data are statistical artifacts. In contrast, we find the frequency of three-way interactions among microbial OTUs to be highly statistically significant. These results demonstrate the importance of using appropriate null models when studying observational microbiome data, and suggest that extracting and characterizing three-way interactions among OTUs is a promising direction for unraveling the structure and function of microbial ecosystems.\n\nAuthor SummaryMicrobes are ubiquitous in the environment. We know that microbial communities - the groups of microbes that live together, interact, and depend on one another - vary across environments. Multiple processes, ranging from competition between microbes to environmental stress, are believed to alter microbial community composition. Here, we describe a set of statistical techniques that can more accurately identify the underlying taxa relationships that structure the observed abundances of microbes across habitats. Using a large data set of soil samples collected across North and South America, we both illustrate the statistical artifacts that incorrect methods can introduce and describe proper techniques based on appropriate null models for studying how the abundances of taxa vary across soil samples. These tools improve our ability to distinguish ecologically meaningful interactions from simple statistical noise in such observational data. Our application of these tools suggests some previous claims about the network structure of microbial communities may be statistical artifacts. Furthermore, we find that three-way interactions among microbial taxa are significantly more common than we would expect at random, and thus may provide a novel means for identifying ecologically meaningful interactions.

Ecology↗
bioRxiv2017

Foresight Is Required To Enforce Sustainability Under Time-Delayed Biodiversity Loss

Natural habitat loss and fragmentation generate a time-delayed loss of species and associated ecosystem services. Since social-ecological systems (SESs) depend on a range of ecosystem services, lagged ecological dynamics may affect their long-term sustainability. Here, we investigate the role of consumption changes in sustainability enforcement, under a time-delayed ecological feedback on agricultural production. We use a stylized model that couples the dynamics of biodiversity, technology, human demography and compliance to a social norm prescribing sustainable consumption. Compliance to the sustainable norm reduces both the consumption footprint and the vulnerability of SESs to transient overshoot-and-collapse population crises. We show that the timing and interaction between social, demographic and ecological feedbacks govern the transient and long-term dynamics of the system. A sufficient level of social pressure (e.g. disapproval) applied on the unsustainable consumers leads to the stable coexistence of unsustainable and sustainable or mixed equilibria, where both defectors and conformers coexist. Under bistability conditions, increasing time delays reduces the basin of attraction of the mixed equilibrium, thus resulting in abrupt regime shifts towards unsustainable pathways. Given recent evidence of large ecological relaxation rates, such results call for farsightedness and a better understanding of lag effects when studying the sustainability of coupled SESs.

ecology↗
bioRxiv2017

Environmental engineering is an emergent feature of diverse ecosystems and drives community structure

A central question in ecology is to understand the ecological processes that shape community structure. Niche-based theories have emphasized the important role played by competition for maintaining species diversity. Many of these insights have been derived using MacArthurs consumer resource model (MCRM) or its generalizations. Most theoretical work on the MCRM has focused on small ecosystems with a few species and resources. However theoretical insights derived from small ecosystems many not scale up large ecosystems with many resources and species because large systems with many interacting components often display new emergent behaviors that cannot be understood or deduced from analyzing smaller systems. To address this shortcoming, we develop a sophisticated statistical physics inspired cavity method to analyze MCRM when both the number of species and the number of resources is large. We find that in this limit, species generically and consistently perturb their environments and significantly modify available ecological niches. We show how our cavity approach naturally generalizes niche theory to large ecosystems by accounting for the effect of this emergent environmental engineering on species invasion and ecological stability. Our work suggests that environmental engineering is a generic feature of large, natural ecosystems and must be taken into account when analyzing and interpreting community structure. It also highlights the important role that statistical-physics inspired approaches can play in furthering our understanding of ecology.

ecology↗
bioRxiv2017

Improved management facilitates return of an iconic fish species

Species declines and losses of biota are often associated with shifting baselines in perceived historical abundances, and/or neglect or abandonment of recovery actions aimed at ecological restoration. Such declines are frequently accompanied by contractions in the geographical distribution of the species, with associated negative ecological impacts and diminishing socio-economic benefits. Here we show using citizen science and other data that after 50-60 years of near total absence, the iconic top predator and highly migratory species bluefin tuna, Thunnus thynnus, returned by the hundreds if not thousands in waters near Denmark, Norway and Sweden during August-October 2015-2017. The re-utilisation of this former habitat is part of a geographically more widespread expansion of the summer foraging area to the northern part of the northeast Atlantic Ocean, encompassing waters from east Greenland to west Sweden. The remarkable return to the Skagerrak, Kattegat and North Sea has been facilitated by improved fishery management for bluefin tuna and its prey. Bluefin tuna biomass in the northeast Atlantic and Mediterranean has been increasing since a recovery plan was implemented in the late 2000s, and biomasses of two key prey species (herring, Clupea harengus; mackerel, Scomber scombrus) recovered during the late 1980s-1990s. The reappearance of bluefin tuna in the Skagerrak-Kattegat and other waters of northern Europe, despite a recent history of mismanagement and illegal fishing in the northeast Atlantic and Mediterranean which led to a critical population decline, offers hope that other marine ecological recoveries are possible under improved management of fisheries and ecosystems. One Sentence SummaryImproved management promotes the return of an ocean icon to northern Europe. Significance StatementCommercial fisheries are often perceived being in a state of decline and collapse, putting food and economic security at risk. Such declines are frequently accompanied by contractions in stock distribution, negative ecological impacts and diminishing socio-economic benefits. Here we present an example based on one of the worlds most valuable and iconic fish species, bluefin tuna, which demonstrates that effective management of both bluefin tuna and its prey has been a key factor leading to a remarkable reoccupation of formerly lost habitat. This reappearance, following decades of absence, occurred despite the bluefin tuna stock having had a recent, long history of unsustainable and illegal exploitation. Marine ecological recovery actions can be successful, even in situations which may initially appear intractable.

ecology↗
bioRxiv2018

Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities

Because biodiversity is multidimensional and scale-dependent, it is challenging to estimate its change. However, it is unclear (1) how much scale-dependence matters for empirical studies, and (2) if it does matter, how exactly we should quantify biodiversity change. To address the first question, we analyzed studies with comparisons among multiple assemblages, and found that rarefaction curves frequently crossed, implying reversals in the ranking of species richness across spatial scales. Moreover, the most frequently measured aspect of diversity--species richness--was poorly correlated with other measures of diversity. Second, we collated studies that included spatial scale in their estimates of biodiversity change in response to ecological drivers and found frequent and strong scale-dependence, including nearly 10% of studies which showed that biodiversity changes switched directions across scales. Having established the complexity of empirical biodiversity comparisons, we describe a synthesis of methods based on rarefaction curves that allow more explicit analyses of spatial and sampling effects on biodiversity comparisons. We use a case study of nutrient additions in experimental ponds to illustrate how this multi-dimensional and multi-scale perspective informs the responses of biodiversity to ecological drivers.\n\nStatement of AuthorshipJC and BM conceived the study and the overall approach, and all authors participated in multiple working group meetings to develop and refine the approach. BM collected the data for the meta-analysis that led to Fig. 2,3; JC collected the data for the metaanalysis that led to Figure 4 and S1; SB and FM did the analyses for Figures 2-4; DM, FM and XX wrote the code for the analysis used for the recipe and case study in Figure 6. JC, BM and NG wrote first drafts of most sections, and all authors contributed substantially to revisions.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/275701_fig2.gif\" ALT=\"Figure 2\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@485725org.highwire.dtl.DTLVardef@151643corg.highwire.dtl.DTLVardef@8bc9e0org.highwire.dtl.DTLVardef@1729374_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Bivariate relationships between N, SPIE and S for 346 communities across the 37 datasets taken from McGill (2011b)(see Appendix 1). (A) S as a function of N; (B) S as a function of SPIE. (N vs SPIE not shown). Black lines depict the relationships across studies (and correspond to R2 fixed); colored points and lines show the relationships within studies. All axes are log-scale. Insets are histograms of the study-level slopes, with the solid line representing the slope across all studies. Gray bars indicate the study-level slope did not differ from zero, blue indicates a significant positive slope, and red indicates a significant negative slope.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC=\"FIGDIR/small/275701_fig3.gif\" ALT=\"Figure 3\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@12ee0e9org.highwire.dtl.DTLVardef@affc46org.highwire.dtl.DTLVardef@1db6453org.highwire.dtl.DTLVardef@97ab06_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Representative rarefaction curves, the proportion of curves that crossed, and counts of how often curves crossed. (A) Rarefaction curves for different local communities within two datasets: marine invertebrates (nematodes) along a gradient from a waste plant outlet (Lambshead 1986), and trees in a Ugandan rainforest (Eggeling 1947); axes are log-transformed. (B) Counts of how many times pairs of rarefaction curves (from the same community) crossed; y-axis is on a log-scale.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/275701_fig4.gif\" ALT=\"Figure 4\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@15d497borg.highwire.dtl.DTLVardef@18354fforg.highwire.dtl.DTLVardef@1413a54org.highwire.dtl.DTLVardef@15c8451_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Results of a meta-analysis of scale-dependent responses to a number of different ecological drivers (see Appendix 2). Points represent the log response ratio comparing species richness in control compared to treatments in a given comparison measured at the smallest (x-value) and largest (y-value) scale. The solid line indicates the 1: 1 line expected if effect sizes were not scale-dependent. Points above and below this line indicate effect sizes that are larger or smaller, respectively, as scale increases; points in the upper left and lower right quadrats represent cases where the direction of change shifted from positive to negative, or vice versa, with increasing scale. The dashed line indicates the best fit correlation, which is significantly different than the 1:1 line (P<0.01), indicating that overall, effect sizes tend to be larger at smaller scales than at larger scales. Colors for points indicate categorizations into different ecological drivers.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/275701_figS1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@f30150org.highwire.dtl.DTLVardef@1db2db9org.highwire.dtl.DTLVardef@970507org.highwire.dtl.DTLVardef@cb37e6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure S1.C_FLOATNO Results showing the ratio of log-response ratio effect sizes from experiments where species richness responses were measured at two spatial scales (small scale/large scale). The dashed line at 0 would indicate studies where the effect sizes were the same at the smaller and larger scale. For each category of ecological driver, the means are above 1, indicating that the measured effect size is larger at the smaller relative to larger size, and this difference is statistically significant for land use, invasive species, and grazing/predation.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC=\"FIGDIR/small/275701_fig6.gif\" ALT=\"Figure 6\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@1c313d0org.highwire.dtl.DTLVardef@49df71org.highwire.dtl.DTLVardef@1ec92a3org.highwire.dtl.DTLVardef@8f1693_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO Effect of nutrient additions on several measurements of biodiversity from Table 1 (see data in Appendix 3). Each biodiversity measure was calculated at the -scale (1 mesocosm) (Panels A,B), {gamma}-scale (15 mesocosms) (Panels C,D), as well as the -scale (i.e. turnover across scales, {gamma}/)(Panels D,E,F). See Chase (2010) for details on the experimental design and the mobr package (McGlinn et al. submitted, https://github.com/MoBiodiv/mobr) for details on the statistical methods\n\nC_FIG\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC=\"FIGDIR/small/275701_fig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@133d65org.highwire.dtl.DTLVardef@123b3faorg.highwire.dtl.DTLVardef@fce7ccorg.highwire.dtl.DTLVardef@1d62dab_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO A. Individual-based rarefaction curves of three hypothetical communities (labelled A,B, C) where ranked differences between communities are consistent across scales. B. Individual-based rarefaction curves of three hypothetical communities (labelled A,B, C) where rankings between communities switch because of differences in the total numbers of species, and their relative abundances. Dotted vertical lines illustrate sampling scales where rankings switch. These curves were generated using the sim_sad function from the mobsim R package (May et al. 2018).\n\nC_FIG\n\n\n\nData accessibility statementAll data for meta-analyses and case study will be deposited in a publically available repository with DOI upon acceptance (available in link for submission).

ecology↗
bioRxiv2018

White Spot Syndrome Virus and the Caribbean Spiny Lobster, Panulirus argus: Susceptibility and Behavioral Immunity

The Caribbean spiny lobster Panulirus argus is susceptible to infection by Panulirus argus Virus 1 (PaV1), the only virus known to naturally infect any lobster species. However, P. argus is able to mitigate PaV1 transmission risk by avoiding infected individuals. White Spot Syndrome Virus (WSSV) has a particularly wide host range. WSSV has not been documented in wild populations of spiny lobsters, but has been experimentally transmitted to six other lobster species from the genus Panulirus spp. While WSSV has been detected intermittently in wild populations of shrimp in the Caribbean region, the risk to P. argus has not been evaluated. Potential emergence of the disease could result in fisheries losses and ecological disruption. To assess the risk to P. argus, we tested its susceptibility to WSSV via injection and waterborne transmission. We also tested whether healthy lobsters can detect and avoid conspecifics with qPCR-quantifiable WSSV infections. We found P. argus to be highly susceptible to WSSV via intramuscular injection, with mortality reaching 88% four weeks post inoculation. Panulirus argus was also susceptible to WSSV via waterborne transmission, but WSSV burden was low after four weeks via qPCR. Behavioral assays indicated that P. argus can detect and avoid conspecifics infected with WSSV and the avoidance response was strongest for the most heavily infected individuals - a response comparable to PaV1-infected conspecifics. Panulirus argus is the first spiny lobster found to be susceptible to WSSV in the Americas, but it is possible that a generalized avoidance response by healthy lobsters against infected conspecifics provides a behavioral defense and may reduce WSSV infection potential and prevalence. Such avoidance may extend to other directly transmitted pathogens in spiny lobster populations preventing them from becoming common in their population.\n\nAuthor SummaryErica P. Ross is a PhD candidate at the University of Florida, studying the disease ecology of the Caribbean spiny lobster, with a focus on chemosensory ecology. Donald C. Behringer is an associate professor at the University of Florida and his research focuses on disease ecology, epidemiology, and fishery ecology, with a focus on crustaceans and other marine invertebrates. Jamie Bojko received his PhD from the University of Leeds and is currently a post-doctorate associate at the University of Florida studying experimental and systemic crustacean pathology.

ecology↗