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Results for “Ecology”

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bioRxiv2019

Low marine food levels mitigate high migration costs in anadromous populations

Migratory fish populations, like salmon, have dramatically declined for decades. Because of their extensive and energetically costly breeding travel anadromous fish are sensitive to a variety of environmental threats, in particular infrastructure building in freshwater streams and food declines in the ocean. Here, we analyze the effects of these two threats combined. Unexpectedly, we find that low marine food availabilities favor, as opposed to threaten, the ecological success of endangered populations. This counterintuitive effect results from an aspect of individual energetics that individuals switching to higher food levels reach larger sizes with concomitant larger migration costs but have lower energy densities. Surprisingly, the decline of food levels in the ocean after the completion of dams may thus mitigate the risk of extinction of migratory fish populations. This highlights the need of a mechanistic understanding integrating individual energetics, life history, and population dynamics to accurately assess biological consequences of environmental change.

ecology↗

bioRxiv2019

The distinct phenotypic signatures of dispersal and stress in an arthropod model: from physiology to life history

Dispersing individuals are expected to encounter costs during transfer and in the novel environment, and may also have experienced stress in their natal patch. Given this, a non-random subset of the population should engage in dispersal and eventually show divergent stress-related responses towards new conditions. Dispersal allows escape from stress, but is equally subjecting individuals to it.\n\nPhysiological shifts expressed in the metabolome form a major part of responses to stress exposure and are expected to be associated with the dispersal phenotype, thereby shaping physiological dispersal syndromes. We analyzed how metabolic profiles and life-history traits varied between dispersers and residents of the model two-spotted spider mite Tetranychus urticae, and whether and how these syndromes varied with exposure to a stressful new host plant (tomato). Regardless of the effect of host plant, we found a physiological dispersal syndrome where, relative to philopatric individuals, dispersers were characterized by lower leaf consumption rates and a lower concentration of several amino acids, indicating a potential dispersal-foraging trade-off. As a possible consequence of this lower food intake, dispersers also showed a lower reproductive performance. Responses to tomato exposure were consistent with this plant being a stressor for Tetranychus urticae, including reduced fecundity and reduced feeding by mites. Tomato-exposed mites laid larger eggs, which can be interpreted as a plastic response to food stress, increasing the likelihood of survival to maturity. Contrary to what could be expected from the costs of dispersal and stress resistance and from previous meta-population level studies, there was no interaction between dispersal status and host plant for any of the examined traits, indicating that the impacts of a new stressful host plant are equally incurred by residents and dispersers.\n\nWe thus provide novel insights in the processes that shape dispersal and the putative feedbacks on ecological dynamics in spatially structured populations.

ecology↗

bioRxiv2019

The planktonic protist interactome: emerging trends after a century of research

Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts, parasites, predators and/or prey. Symbiosis was the most common interaction (43% of all records), followed by predation (39%) and parasitism (18%). Using bipartite networks, we found that protistan predators seem to be \"multivorous\", while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e. Stramenopiles, Alveolata and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the compiled interactions. All in all, despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.

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bioRxiv2019

Segregation of floricolous ants along latitudinal and urbanization gradients

Recent call has been made to study the biogeography of species interactions in order to better understand ecosystems states and processes, as well as their response to global anthropogenic disturbances. Ants (Formicidae) are a dominant group of arthropods with a central role in ecosystem functioning. Many ant species, those feeding on liquids, are floricolous and consume nectar. The biogeography of ant-flower interactions is still poorly studied and especially in temperate area. Here we quantify variations in ant-flower interaction frequency in response to latitudinal and urbanization gradients at a country scale.\n\nWe used data from a flower-visitor monitoring program that includes pictures on 2511 flower plants across Continental France (Mainland) and over 4 years. We analysed the occurrence of the ant-flower interactions along two gradients: latitude and urbanization, this for 10 ant taxa corresponding to different taxonomical level (from family to species).\n\nAnts visited 26 % of the sampled plants. Most of the observed ant-flower interaction involved the subfamily Formicinae (82.1 %), followed by Myrmicinae and Dolichoderinae (6.9 % and 4.6 % respectively). Globally, (i) the probability of occurrence was negatively related to latitudes (ii) and to urbanization at lower latitude. (iii) Responses to latitude among sub families, genus and species level responses were segregated and taxonomically aggregated.\n\nAt lower taxonomic levels we found clear latitudinal niche partitioning among ant taxa suggesting that competition, on both evolutionary and ecological time scales, is a major process structuring ant communities. Finally, our results highlight that the effects of large scale perturbation like urbanization can vary and affect latitudinal gradient.

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bioRxiv2019

A test of the evolution of increased competitive ability in two invaded regions

O_LIFinding patterns that predict and explain the success of non-native species has been an important focus in invasion ecology. The evolution of increased competitive ability (EICA) hypothesis has been a frequently used framework to understand invasion success. Evolution of increased competitive ability predicts that 1. Non-native populations will escape from coevolved specialist herbivores and this release from specialist herbivores should result in relaxed selection pressure on specialist-related defense traits, 2. There will be a trade-off between allocation of resources for resistance against specialist herbivores and allocation to traits related to competitive ability and 3. This shift will allow more allocation to competitive ability traits.\nC_LIO_LIWe tested the predictions of EICA in the model plant Mimulus guttatus, a native of western North America (WNA). We compared how well the predictions of EICA fit patterns in two non-native regions, the United Kingdom (UK) and eastern North America (ENA). Coupled with extensive herbivore surveys we quantified genetic variation for herbivore resistance traits and fitness/ competitive ability traits to test adherence to the predictions of EICA in a common greenhouse environment.\nC_LIO_LIHerbivore communities differed significantly between WNA, UK, and ENA populations with evidence of specialist herbivore escape in the UK, but not necessarily the ENA plants. Compared to native plants, resistance traits were lower in non-native UK plants with the exception of trichome density, while the non-native ENA plants had equivalent or higher levels of herbivore resistance traits. The UK plants had increased competitive traits than native plants while the ENA plants had equivalent competitive traits to native plants. The UK plants, but not the ENA plants, showed some signs of tradeoffs between resistance traits and fitness/ competitive ability.\nC_LIO_LISynthesis. Plants from the UK conformed to predictions of EICA more closely than those from ENA. The UK invasion is an older, more successful invasion, suggesting that support for EICA may be highest in more successful invasions. The lack of comprehensive conformity of either non-native region to the predictions of EICA also leaves room for other hypotheses that may add to our mechanistic understanding of the success of non-native plant invasions.\nC_LI

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bioRxiv2019

Predicting primary production in the southern California Current Ecosystem from chlorophyll, nutrient concentrations, and irradiance

We investigated the processes driving variability in primary productivity in the California Current Ecosystem (CCE) in order to develop an algorithm for predicting primary productivity from in situ irradiance, nutrient, and chlorophyll (chl) measurements. Primary productivity data from seven process cruises of the CCE Long-Term Ecological Research (CCE LTER) program were used to parameterize the algorithm. An initial algorithm was developed using only irradiance to predict chl-specific productivity was found to have model-data misfit that was correlated with NH4+ concentrations. We thus found that the best estimates of primary productivity were obtained using an equation including NH4+ and irradiance: PP/Chl = V0mx(1-exp(-xPAR/V0m)xNH4/(NH4+KS), where PP/Chl is chlorophyll-specific primary production in units of mg C d-1 / mg Chl, PAR is photosynthetically active radiation (units of Ei m-2 s-1), NH4+ is in units of mol L-1, V0m = 66.5 mg C d-1 / mg Chl, = 1.5, and KS = 0.025 mol L-1. We then used this algorithm to compute primary productivity rates for the CCE-P1706 cruise on which in situ primary productivity samples were not available. We compared these estimates to independent productivity estimates derived from protistan grazing dilution experiments and found excellent agreement.

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bioRxiv2019

Compounding the disturbance: Family forest owner reactions to invasive forest insects

Invasive forest insect and pathogens (FIP) are having significant, direct, adverse impacts. Interactions between FIPs and forest owners have the potential to create ecosystem impacts that compound direct impacts. We assessed family forest owners responses to numerous contingent behavior, FIP-outbreak scenarios in the northeastern U.S. based on FIP outbreak attributes. Sixty-two percent of scenario responses (n=2,752) reflected a harvest intent as a result of FIPs; 84% of respondents (n=688) would consider harvesting in at least one of the four hypothetical scenarios presented to them. Harvest intention increased with greater FIP-related tree mortality and decreased with delayed total tree mortality. Owners with larger holdings, who had previously harvested forest products, and live on their forestland had greater intentions to harvest in response to FIPs. Results suggest that FIPs could transform the regional harvest regime with socio-ecological impacts that are distinct from those caused by FIPs or harvesting alone.

ecology↗

bioRxiv2019

Catching the big picture of the Mediterranean Sea biodiversity with an end-to-end model of climate and fishing impacts

The Mediterranean Sea is among the main hotspots of marine biodiversity in the world. Under combined pressures of fishing activities and climate change it has also become a hotspot of global change, with increased concern about the worsening status of marine exploited species. More integrated modelling approaches are needed to anticipate global change impacts in the Mediterranean Sea, in order to help decision makers prioritizing management actions and strategies, mitigating impacts and adapting to changes. Our challenge was to develop a holistic model of the marine biodiversity in the Mediterranean Sea with an explicit representation of the spatial multispecies dynamics of exploited resources under the combined influence of climate variability and fishing pressure. An individual-based ecosystem model OSMOSE (Object-oriented Simulator of Marine ecOSystEms), including 100 marine species (fish, cephalopods and crustaceans) and representing about 95 % of the total declared catches, has been implemented for the first time at a high spatial resolution (400 km2) and at a large spatial scale (whole Mediterranean basin). The coupling of OSMOSE to the NEMOMED 12 physical model, and to the Eco3M-S biogeochemical and low trophic level model has been achieved to build the OSMOSE-MED end-to-end model. We fitted OSMOSE-MED to observed and estimated data of biomass and commercial catches using a likelihood approach and an evolutionary optimization algorithm. The outputs of OSMOSE-MED were then verified against observed biomass and catches, and confronted to independent datasets (MEDITS data, diet compositions and trophic levels). Although some improvements are suggested for future developments, the model results at different hierarchical levels, from individuals up to the ecosystem scale, were consistent with current knowledge and observations on the structure, the functioning and the dynamics of the ecosystems in the Mediterranean Sea. All the modelling steps, from the comprehensive representation of key ecological processes and feedbacks, the careful parameterization of the model, the confrontation to observed data, and the positive outcome from the validation process, allowed to strengthen the degree of realism of OSMOSE-MED and its relevance as an impact model to explore the futures of marine biodiversity under scenarios of global change, and as a tool to support the implementation of ecosystem-based fisheries management in the Mediterranean Sea.

ecology↗

bioRxiv2019

Functional diversity plays a role in driving β-diversity: Or does it?

Patrick and Brown (2018) suggest that functional diversity of the species pool has an important role in generating {beta}-diversity. Using a combination of path analysis and model selection, they ostensibly provide support for this hypothesis; however, they neglected to put theory and modeling into proper ecological and statistical context. Here, I present a re-analysis of their data. I conclude that the drivers of {beta}-diversity are variable, with functional diversity typically having a reduced, if any, role compared to consistently stronger roles played by {gamma}-diversity or environmental variation on structuring {beta}-diversity.

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bioRxiv2019

Associated organisms inhabiting the calcareous sponge Clathrina lutea in La Parguera Natural Reserve, Puerto Rico

Sponges provide an array of ecological services and benefits for Caribbean coral reefs. They function as habitats for a bewildering variety of species, however limited attention has been paid in the systematics and distribution of sponge-associated fauna in the class Calcarea or for that matter of sponges in the Caribbean. The goal of this study was to characterize infaunal assemblages from a calcareous sponge, Clathrina lutea, across multiple reefs from the La Parguera Natural Reserve, Puerto Rico. The associated fauna from 43 C. lutea specimens yielded a total of 2,249 associated infauna distributed in seven invertebrate phyla. Arthropoda was the most abundant phylum accounting for 62.5% of total abundance, followed by Annelida (21.0%) and Nematoda (5.5%). Limited patterns of temporal or spatial variability were surmised due to the opportunistic sampling effort afforded to this investigation from the cryptic nature of this species. A concordance between our data set and those for the class Demospongiae were observed, with the most abundant associated fauna being copepods and polychaetes. However, when compared to other Calcarea, the present study found considerably more associated fauna.

ecology↗

bioRxiv2019

Confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations

BackgroundThe discovery of CRISPR-based gene editing and its application to homing-based gene drive systems has been greeted with excitement, for its potential to control mosquito-borne diseases on a wide scale, and concern, for the invasiveness and potential irreversibility of a release. Gene drive systems that display threshold-dependent behavior could potentially be used during the trial phase of this technology, or when localized control is otherwise desired, as simple models predict them to spread into partially isolated populations in a confineable manner, and to be reversible through releases of wild-type organisms. Here, we model hypothetical releases of two recently-engineered threshold-dependent gene drive systems - reciprocal chromosomal translocations and a form of toxin-antidote-based underdominance known as UDMEL - to explore their ability to be confined and remediated. ResultsWe simulate releases of Aedes aegypti, the mosquito vector of dengue, Zika and other arboviruses, in Yorkeys Knob, a suburb of Cairns, Australia, where previous biological control interventions have been undertaken on this species. We monitor spread to the neighboring suburb of Trinity Park to assess confinement. Results suggest that translocations could be introduced on a suburban scale, and remediated through releases of non-disease-transmitting male mosquitoes with release sizes on the scale of what has been previously implemented. UDMEL requires fewer releases to introduce, but more releases to remediate, including of females capable of disease transmission. Both systems are expected to be confineable to the release site; however, spillover of translocations into neighboring populations is less likely. ConclusionsOur analysis supports the use of translocations as a threshold-dependent drive system capable of spreading disease-refractory genes into Ae. aegypti populations in a confineable and reversible manner. It also highlights increased release requirements when incorporating life history and population structure into models. As the technology nears implementation, further ecological work will be essential to enhance model predictions in preparation for field trials.

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bioRxiv2019

Targeted expansion of Protected Areas to maximise the persistence of terrestrial mammals

Over a quarter of species assessed by the IUCN Red List are threatened with extinction. A global commitment to protect 17% of land and 10% of the oceans by 2020 is close to being achieved, but with limited ecological impacts due to its inadequacy and poor enforcement. Here, we reverse-engineer IUCN Red List criteria to generate area-based conservation targets and spatial conservation priorities to minimize the extinction risk of the world terrestrial mammals. We find that approximately 60% of the Earths non-Antarctic land surface would require some form of protection. Our results suggest that global conservation priority schemes, among which the Aichi targets, will be inadequate to secure the persistence of terrestrial mammals. To achieve this goal, international cooperation is required to implement a connected and comprehensive conservation area network, guided by high priority regions outlined in this study.

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bioRxiv2019

Fitness effects of host-bacterial interactions - the microbial perspective

Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germ free hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial structure of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the fractions of both species on the host do not match the fractions reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that the rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems. ImportanceThis work studies microbial interactions within the microbiome of the simple cnidarian, Hydra, and investigates whether microbial species coexistence and community stability depends on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydras microbiome differs depending on the environment and only results in a stable coexistence in the host context. The interactive ecology between the host, the two most dominant microbes, but also the less abundant members of the microbiome, are critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

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bioRxiv2019

Niche differentiation is spatially and temporally regulated in the rhizosphere

The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial function in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Population transcripts were binned with a unique reference database generated from soil isolate and single amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition gene expression, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were high in the combined rhizosphere-detritusphere--suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.

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bioRxiv2019

On the efficacy of restoration in stream networks: comment and critique

Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, meta-community, and restoration ecology. Swan and Brown (2017, 2018) evaluated the effect of restoration on sites receiving various combinations of in-channel manipulation and riparian reforestation treatments. Given the difference in the relative importance of environmental filtering and dispersal between headwaters and mainstems and the structure of river networks, I contend that different restoration treatments have differential effects between headwaters and mainstems. I hypothesized in-channel manipulations would have more consistent effects between headwaters and mainstems compared to riparian reforestation, and I used this hypothesis to guide site selection in the re-analysis. I then compared results from the re-analysis to those presented by Swan and Brown (2017, 2018). I did not find any effects of restoration on local diversity, spatial dissimilarity, or temporal variability, let alone differential effects of restoration between headwaters and mainstems; these results are contrary Swan and Brown (2017, 2018), who reported that restoration increased taxonomic richness, increased spatial dissimilarity, and decreased temporal variability in restored headwater streams. I demonstrate further that the statistical tests conducted by Swan and Brown (2017, 2018) were invalid and, therefore, recommend the use of the results presented here. More broadly, I suggest, in agreement with Swan and Brown (2017, 2018) and a growing body of research, that river and stream restoration will likely have greater success if a regional approach is taken to designing and implementing restoration projects.

ecology↗

bioRxiv2019

Predicting the conservation status of Europe’s Data Deficient sharks and rays

Shark and ray biodiversity is threatened primarily by overfishing and the globalisation of trade, and Europe has been one of the most documented heavily fished regions for a relatively long time. Yet, we have little idea of the conservation status of the hundreds of Data Deficient shark and ray species. It is important to derive some insight into the status of these species, both to understand global extinction rates and also to ensure that any threatened Data Deficient species are not overlooked in conservation planning. Here, we developed a biological and ecological trait model to predict the categorical conservation status of 26 Northeast Atlantic and 15 Mediterranean Sea Data Deficient sharks and rays. We first developed an explanatory model based on all species evaluated on the International Union for Conservation of Nature (IUCN) Red List of Threatened SpeciesTM, using maximum body size, median depth (as a proxy for fisheries exposure), and reproductive mode, and then predicted the status of all Data Deficient species. Almost half of Northeast Atlantic (46%, n=12 of 26), and two-thirds of Mediterranean (67%, n=10 of 15) Data Deficient species are predicted to be in one of the three IUCN threatened categories. Northeast Atlantic Data Deficient species are predicted to be 1.2 times more threatened than evaluated species (38%, n=36 of 94), whereas threat levels in the Mediterranean Sea are relative for each (66%, n=38 of 58). This case study is intended for extrapolation to the global shark and ray dataset upon completion of the global IUCN Red List assessment. Trait-based, categorical prediction of conservation status is a cost-effective approach towards incorporating Data Deficient species into (i) estimates of lineage-wide extinction rates, (ii) revised protected species lists, and (iii) Red List Indices, thus preventing poorly known species from reaching extinction unnoticed.

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bioRxiv2019

Monitoring soil microorganisms with community-level physiological profiles using Biolog EcoPlatesTM in Chaohu lakeside wetland, east China

Under the circumstance of wetland degradation, we used Biolog EcoPlates method to investigate the impact of ecological restoration on the function of topsoil microbial communities by monitoring their metabolic diversity around Chaohu lakeside wetland. Four restoration patterns including reed shoaly land (RL), poplar plantation land (PL), abandoned shoaly grassland (GL) and cultivated flower land (FL) were selected. The result showed a rapid growth trend at the initial stage of incubation, following the fastest change rate at 72 h in both dormant and growing seasons, and the AWCD values of RL pattern was the highest at the detection points of each culture time, while the GL were the lowest. The calculation of diversity indicators also displayed significant lower McIntosh index in dormant season and Shannon-Wiener index in growing season in GL than in the others (P < 0.05). Carbohydrates and carboxylic acids were found to be the dominant substrates used in dormant season, whereas amino acids, polymers and phenolic acids were increasingly utilized by the microbial communities in growing season. We observed soil total potassium as the key factor that significantly affected the utilization efficiency of different carbon sources in both seasons (P < 0.05).

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bioRxiv2019

Freshwater invasive clams grow faster and reproduce earlier in recently introduced populations with reduced growth rates

Many species are shifting their ranges being forced to rapidly respond to novel stressful environmental conditions. Colonizing individuals experience strong selective forces that favor the expression of life history traits notably affecting dispersal and reproductive rates in newly invaded habitats. Limited information is currently available on trait variation within the invasive range despite being critical for understanding ecological and evolutionary factors that drive the process of range expansion of invasive species. Here we evaluated life history shifts of the widely introduced Asian clam Corbicula, within its invaded range. Through an exhaustive literature search, we obtained data for 17 invasive Corbicula populations from different ecosystems worldwide. We tested the relationship between population and individual parameters relevant to the process of range expansion. Our main results are that recently introduced Corbicula populations were characterized by (i) low density and low rate of population increase, (ii) clams reproduced earlier in slow-growing populations, and (iii) density had no effect on population increase. All Corbicula populations analyzed in this study, which are fixed for one genotype (lineage Form A/R), experienced different selective environments in the introduced range. These findings support the perspective that adaptive phenotypic plasticity favored the expression of traits that maximize fitness in recently established populations, which faced stronger r-selective forces relative to long-established ones. We discuss the role of plasticity in facilitating rapid adaptation and increasing the likelihood of populations to overcome difficulties associated with low densities and low population increase in newly invaded areas.

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