Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,903 bioRxiv papers from 309,378 authors.
Most downloaded bioRxiv papers, all time
in category ecology
2,981 results found. For more information, click each entry to expand.
12,862 downloads ecology
Zika virus is a mosquito-borne pathogen that is rapidly spreading across the Americas. Due to associations between Zika virus infection and a range of fetal maladies, the epidemic trajectory of this viral infection poses a significant concern for the nearly 15 million children born in the Americas each year. Ascertaining the portion of this population that is truly at risk is an important priority. One recent estimate suggested that 5.42 million childbearing women live in areas of the Americas that are suitable for Zika occurrence. To improve on that estimate, which did not take into account the protective effects of herd immunity, we developed a new approach that combines classic results from epidemiological theory with seroprevalence data and highly spatially resolved data about drivers of transmission to make location-specific projections of epidemic attack rates. Our results suggest that 1.65 (1.45-2.06) million childbearing women and 93.4 (81.6-117.1) million people in total could become infected before the first wave of the epidemic concludes. Based on current estimates of rates of adverse fetal outcomes among infected women, these results suggest that tens of thousands of pregnancies could be negatively impacted by the first wave of the epidemic. These projections constitute a revised upper limit of populations at risk in the current Zika epidemic, and our approach offers a new way to make rapid assessments of the threat posed by emerging infectious diseases more generally.
9,974 downloads ecology
Marine Veits, Itzhak Khait, Uri Obolski, Eyal Zinger, Arjan Boonman, Aya Goldshtein, Kfir Saban, Udi Ben-Dor, Paz Estlein, Areej Kabat, Dor Peretz, Ittai Ratzersdorfer, Slava Krylov, Daniel Chamovitz, Yuval Sapir, Yossi Yovel, Lilach Hadany
Can plants hear? That is, can they sense airborne sounds and respond to them? Here we show that Oenothera drummondii flowers, exposed to the playback sound of a flying bee or to synthetic sound-signals at similar frequencies, produced sweeter nectar within 3 minutes, potentially increasing the chances of cross pollination. We found that the flowers vibrated mechanically in response to these sounds, suggesting a plausible mechanism where the flower serves as the plant's auditory sensory organ. Both the vibration and the nectar response were frequency-specific: the flowers responded to pollinator sounds, but not to higher frequency sound. Our results document for the first time that plants can rapidly respond to pollinator sounds in an ecologically relevant way. Sensitivity of plants to pollinator sound can affect plant-pollinator interactions in a wide range of ways: Plants could allocate their resources more adequately, focusing on the time of pollinator activity; pollinators would then be better rewarded per time unit; flower shape may be selected for its effect on hearing ability, and not only on signaling; and pollinators may evolve to make sounds that the flowers can hear. Finally, our results suggest that plants may be affected by other sounds as well, including antropogenic ones.
9,858 downloads ecology
Estimating the abundance and spatial distribution of animal and plant populations is essential for conservation and management. We introduce the R package Distance that implements distance sampling methods to estimate abundance. We describe how users can obtain estimates of abundance (and density) using the package as well documenting the links it provides with other more specialized R packages. We also demonstrate how Distance provides a migration pathway from previous software, thereby allowing us to deliver cutting-edge methods to the users more quickly.
9,595 downloads ecology
Greg R. Boyce, Emile Gluck-Thaler, Jason C. Slot, Jason E. Stajich, William J. Davis, Tim Y. James, John R. Cooley, Daniel G. Panaccione, Jørgen Eilenberg, Henrik H. De Fine Licht, Angie M. Macias, Matthew C. Berger, Kristen L. Wickert, Cameron M. Stauder, Ellie J. Spahr, Matthew D. Maust, Amy M. Metheny, Chris Simon, Gene Kritsky, Kathie T. Hodge, Richard A. Humber, Terry Gullion, Dylan P. G. Short, Teiya Kijimoto, Dan Mozgai, Nidia Arguedas, Matt T. Kasson
Entomopathogenic fungi routinely kill their hosts before releasing infectious spores, but select species keep insects alive while sporulating, which enhances dispersal. Transcriptomics and metabolomics studies of entomopathogens with post-mortem dissemination from their parasitized hosts have unraveled infection processes and host responses, yet mechanisms underlying active spore transmission by Entomophthoralean fungi in living insects remain elusive. Here we report the discovery, through metabolomics, of the plant-associated amphetamine, cathinone, in four Massospora cicadina-infected periodical cicada populations, and the mushroom-associated tryptamine, psilocybin, in annual cicadas infected with Massospora platypediae or Massospora levispora, which appear to represent a single fungal species. The absence of some fungal enzymes necessary for cathinone and psilocybin biosynthesis along with the inability to detect intermediate metabolites or gene orthologs are consistent with possibly novel biosynthesis pathways in Massospora. The neurogenic activities of these compounds suggest the extended phenotype of Massospora that modifies cicada behavior to maximize dissemination is chemically-induced.
8,812 downloads ecology
Temperature imposes significant constraints on ectothermic animals, and these organisms have evolved numerous adaptations to respond to these constraints. While the impacts of temperature on the physiology of ectotherms have been extensively studied, there are currently no frameworks available that outline the multiple and often simultaneous pathways by which temperature can affect behaviour. Drawing from the literature on insects, we propose a unified framework that should apply to all ectothermic animals, generalizing temperature's behavioural effects into (1) Kinetic effects, resulting from temperature's bottom-up constraining influence on metabolism and neurophysiology over a range of timescales (from short- to long-term), and (2) Integrated effects, where the top-down integration of thermal information intentionally initiates or modifies a behaviour (behavioural thermoregulation, thermal orientation, thermosensory behavioural adjustments). We discuss the difficulty in distinguishing adaptive behavioural changes due to temperature from behavioural changes that are the products of constraints, and propose two complementary approaches to help make this distinction and class behaviours according to our framework: (i) behavioural kinetic null modeling and (ii) behavioural ecology experiments using temperature-insensitive mutants. Our framework should help to guide future research on the complex relationship between temperature and behaviour in ectothermic animals.
7,936 downloads ecology
Ecological phenomena are often measured in the form of count data. These data can be analyzed using generalized linear mixed models (GLMMs) when observations are correlated in ways that require random effects. However, count data are often zero-inflated, containing more zeros than would be expected from the standard error distributions used in GLMMs, e.g., parasite counts may be exactly zero for hosts with effective immune defenses but vary according to a negative binomial distribution for non-resistant hosts. We present a new R package, glmmTMB, that increases the range of models that can easily be fitted to count data using maximum likelihood estimation. The interface was developed to be familiar to users of the lme4 R package, a common tool for fitting GLMMs. To maximize speed and flexibility, estimation is done using Template Model Builder (TMB), utilizing automatic differentiation to estimate model gradients and the Laplace approximation for handling random effects. We demonstrate glmmTMB and compare it to other available methods using two ecological case studies. In general, glmmTMB is more flexible than other packages available for estimating zero-inflated models via maximum likelihood estimation and is faster than packages that use Markov chain Monte Carlo sampling for estimation; it is also more flexible for zero-inflated modelling than INLA, but speed comparisons vary with model and data structure. Our package can be used to fit GLMs and GLMMs with or without zero-inflation as well as hurdle models. By allowing ecologists to quickly estimate a wide variety of models using a single package, glmmTMB makes it easier to find appropriate models and test hypotheses to describe ecological processes.
5,309 downloads ecology
Eva Delmas, Mathilde Besson, Marie-Hélène Brice, Laura A. Burkle, Giulio V Dalla Riva, Marie-Josée Fortin, Dominique Gravel, Paulo R. Guimarães, David Hembry, Erica Newman, Jens M Olesen, Mathias M Pires, Justin D. Yeakel, Timothée Poisot
Networks provide one of the best representation for ecological communities, composed of many speecies with dense connections between them. Yet the methodological literature allowing one to analyse and extract meaning from ecological networks is dense, fragmented, and unwelcoming. We provide a general overview to the field, outlining both the intent of the different measures, their assumptions, and the contexts in which they can be used. We anchor this discussion in examples from empirical studies, and conclude by highlighting what we think should be the future developments in the field.
4,894 downloads ecology
It is implicitly assumed that the microbial DNA recovered from soil originates from living cells. However, because relic DNA (DNA from dead cells) can persist in soil for weeks to years, it could impact DNA-based analyses of microbial diversity. We examined a wide range of soils and found that, on average, 40% of prokaryotic and fungal DNA was derived from the relic DNA pool. Relic DNA inflated the observed prokaryotic and fungal diversity by as much as 55%, and caused misestimation of taxon abundances, including taxa integral to key ecosystem processes. These findings imply that relic DNA can obscure treatment effects, spatiotemporal patterns, and relationships between taxa and environmental conditions. Moreover, relic DNA may represent a historical record of microbes formerly living in soil.
3,768 downloads ecology
Between October 2013 and April 2014, more than 30,000 cases of Zika virus (ZIKV) disease were estimated to have attended healthcare facilities in French Polynesia. ZIKV has also been reported in Africa and Asia, and in 2015 the virus spread to South America and the Caribbean. Infection with ZIKV has been associated with neurological complications including Guillain-Barre Syndrome (GBS) and microcephaly, which led the World Health Organization to declare a Public Health Emergency of International Concern in February 2015. To better understand the transmission dynamics of ZIKV, we used a mathematical model to examine the 2013-14 outbreak on the six major archipelagos of French Polynesia. Our median estimates for the basic reproduction number ranged from 2.6-4.8, with an estimated 11.5% (95% CI: 7.32-17.9%) of total infections reported. As a result, we estimated that 94% (95% CI: 91-97%) of the total population of the six archipelagos were infected during the outbreak. Based on the demography of French Polynesia, our results imply that if ZIKV infection provides complete protection against future infection, it would take 12-20 years before there are a sufficient number of susceptible individuals for ZIKV to re-emerge, which is on the same timescale as the circulation of dengue virus serotypes in the region. Our analysis suggests that ZIKV may exhibit similar dynamics to dengue virus in island populations, with transmission characterized by large, sporadic outbreaks with a high proportion of asymptomatic or unreported cases.
3,551 downloads ecology
A lot of hype has recently been generated around deep learning, a group of artificial intelligence approaches able to break accuracy records in pattern recognition. Over the course of just a few years, deep learning revolutionized several research fields such as bioinformatics or medicine. Yet such a surge of tools and knowledge is still in its infancy in ecology despite the ever-growing size and the complexity of ecological datasets. Here we performed a literature review of deep learning implementations in ecology to identify its benefits in most ecological disciplines, even in applied ecology, up to decision makers and conservationists alike. We also provide guidelines on useful resources and recommendations for ecologists to start adding deep learning to their toolkit. At a time when automatic monitoring of populations and ecosystems generates a vast amount of data that cannot be processed by humans anymore, deep learning could become a necessity in ecology.
3,459 downloads ecology
The pacific islands of Micronesia have experienced several outbreaks of mosquito-borne diseases over the past decade. In outbreaks on small islands, the susceptible population is usually well defined, and there is no co-circulation of pathogens. Because of this, analysing such outbreaks can be useful for understanding the transmission dynamics of the pathogens involved, and particularly so for yet understudied pathogens such as Zika virus. Here, we compared three outbreaks of dengue and Zika virus in two different island settings in Micronesia, the Yap Main Islands and Fais, using a mathematical model of transmission dynamics, making full use of commonalities in disease and setting between the outbreaks. We found that the estimated reproduction numbers for Zika and dengue were similar when considered in the same setting, but that, conversely, reproduction number for the same disease can vary considerably by setting. On the Yap Main Islands, we estimated a reproduction number of 8.0-16 (95% Credible Interval (CI)) for the dengue outbreak and 4.8-14 (95% CI) for the Zika outbreak, whereas for the dengue outbreak on Fais our estimate was 28-102 (95% CI). We further found that the proportion of cases of Zika reported was smaller (95% CI 1.4%-1.9%) than that of dengue (95% CI 47%-61%). We confirmed these results in extensive sensitivity analysis. They suggest that models for dengue transmission can be useful for estimating the predicted dynamics of Zika transmission, but care must be taken when extrapolating findings from one setting to another.
3,374 downloads ecology
Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies. However, the underlying reference databases of full-length rRNA gene sequences are underpopulated, ecosystem skewed, and subject to primer bias, which hamper our ability to study the true diversity of ecosystems. Here we present an approach that combines reverse transcription of full-length small subunit (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity). For the Eukaryotes, the novelty was even larger with 63% of all OTUs representing novel taxa. In addition, 15% of the 18S rRNA OTUs were highly novel sequences with less than 80% similarity to the databases. The generation of primer-free full-length SSU rRNA sequences enabled eco-system specific estimation of primer-bias and, especially for eukaryotes, showed a dramatic discrepancy between the in-silico evaluation and primer-free data generated in this study. The large amount of novel sequences obtained here reaffirms that there is still vast, untapped microbial diversity lacking representatives in the SSU rRNA databases and that there might be more than millions after all. With our new approach, it is possible to readily expand the rRNA databases by orders of magnitude within a short timeframe. This will, for the first time, enable a broad census of the tree of life.
3,357 downloads ecology
The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require grouping individuals into populations. Since its first release, pcadapt has evolved both in terms of statistical approach and software implementation. We present results obtained with robust Mahalanobis distance, which is a new statistic for genome scans available in the 2.0 and later versions of the package. When hierarchical population structure occurs, Mahalanobis distance is more powerful than the communality statistic that was implemented in the first version of the package. Using simulated data, we compare pcadapt to other software for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that the proportion of false discoveries is around a nominal false discovery rate set at 10% with the exception of BayeScan that generates 40% of false discoveries. We also find that the power of BayeScan is severely impacted by the presence of admixed individuals whereas pcadapt is not impacted. Last, we find that pcadapt and hapflk are the most powerful software in scenarios of population divergence and range expansion. Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.
3,317 downloads ecology
The long-term stability of microbiomes is crucial as the persistent occurrence of beneficial microbes and their associated functions ensure host health and well-being. Microbiomes are highly diverse and dynamic, making them challenging to understand. Because many natural systems work as temporal networks, we present an approach that allows identifying meaningful ecological patterns within complex microbiomes: the dynamic core microbiome. On the basis of six marine sponge species sampled monthly over three years, we study the structure, dynamics and stability of their microbiomes. What emerge for each microbiome is a negative relationship between temporal variability and mean abundance. The notion of the dynamic core microbiome allowed us to determine a relevant functional attribute of the microbiome: temporal stability is not determined by the diversity of a host's microbial assemblages, but rather by the density of those microbes that conform its core microbiome. The core microbial interaction network consisted of complementary members interacting weakly with dominance of comensal and amensal interactions that suggests self-regulation as a key determinant of the temporal stability of the microbiome. These interactions have likely coevolved to maintain host functionality and fitness over ecological, and even evolutionary time scales.
3,284 downloads ecology
1. Understanding how landscape features affect functional connectivity among populations is a cornerstone of landscape genetic analyses. However, parameterization of resistance surfaces that best describe connectivity is largely a subjective process that explores a limited parameter space. 2. ResistanceGA is a new R package that utilizes a genetic algorithm to optimize resistance surfaces based on pairwise genetic distances and either CIRCUITSCAPE resistance distances or cost distances calculated along least cost paths. Functions in this package allow for the optimization of both categorical and continuous resistance surfaces, as well as the simultaneous optimization of multiple resistance surfaces. 3. There is considerable controversy concerning the use of Mantel tests to accurately relate pairwise genetic distances with resistance distances. Optimization in ResistanceGA uses linear mixed effects models with the maximum likelihood population effects parameterization to determine AICc, which is the fitness function for the genetic algorithm. 4. ResistanceGA fills a void in the landscape genetic toolbox, allowing for unbiased optimization of resistance surfaces and for the simultaneous optimization of multiple resistance surfaces to create a novel composite resistance surface.
3,278 downloads ecology
1. In both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively. 2. We evaluate its accuracy and efficiency relative to existing herbivory assessment tools. 3. LeafByte has the same accuracy as ImageJ, the field standard, but is 50% faster. Other tools, such as BioLeaf and grid quantification, are quick and accurate, but limited in the information they can provide. Visual estimation is quickest, but it only provides a coarse measure of leaf damage and tends to overestimate herbivory. 4. LeafByte is a quick and accurate means of measuring leaf area and herbivory, making it a useful tool for research in fields such as ecology, entomology, agronomy, and plant science.
3,270 downloads ecology
The entomopathogenic Fungi comprise a wide range of ecologically diverse species. This group of parasites can be found distributed among all fungal phyla and as well as among the ecologically similar but phylogenetically distinct Oomycetes or water molds, that belong to a different kingdom (Stramenopila). As a group, the entomopathogenic fungi and water molds parasitize a wide range of insect hosts from aquatic larvae in streams to adult insects of high canopy tropical forests. Their hosts are spread among 18 orders of insects, in all developmental stages such as: eggs, larvae, pupae, nymphs and adults exhibiting completely different ecologies. Such assortment of niches has resulted in these parasites evolving a considerable morphological diversity, resulting in enormous biodiversity, much of which remains unknown. Here we gather together a huge amount of records of these entomopathogens to comparing and describe both their morphologies and ecological traits. These findings highlight a wide range of adaptations that evolved following the evolutionary transition to infecting the most diverse and widespread animals on Earth, the insects.
3,213 downloads ecology
Although the presence of vast amounts of plastic in the open ocean has generated great concern due to its potential ecological consequences, recent studies reveal that its measured abundance is much smaller than expected. Regional and global studies indicate that the difference between expected and actual estimates is enormous, suggesting that a large part of the plastic has been degraded by either physical and biotic processes. A paradoxical observation is the lack of a trend in plastic accumulation found in the North Atlantic Subtropical Gyre, despite the rapid increase in plastic production and disposal. In this paper we show, using mathematical and computer models, that this observation could be explained by the nonlinear coupling between plastic (as a resource) and an evolved set of organisms (the consumers) capable of degrading it. The result is derived using two different resource-consumer mathematical approaches as well as a spatially-dependent plastic-microbial model incorporating a minimal hydrodynamical coupling with a two-dimensional fluid. The potential consequences of the evolution of marine plastic garbage and its removal are outlined.
3,151 downloads ecology
Many animals are inhabited by microbial symbionts that influence their hosts' development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence and functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite the fact that these insects are enormously diverse, major agricultural pests, and dominant herbivores in many ecosystems. Using 16S rRNA gene sequencing and quantitative PCR, we characterized the gut microbiomes of wild leaf-feeding caterpillars in the United States and Costa Rica, representing 124 species from 16 families. Compared with other insects and vertebrates assayed using the same methods, the microbes we detected in caterpillar guts were unusually low-density and highly variable among individuals. Furthermore, the abundance and composition of leaf-associated microbes were reflected in the feces of caterpillars consuming the same plants. Thus, microbes ingested with food are present (though possibly dead or dormant) in the caterpillar gut, but host-specific, resident symbionts are largely absent. To test whether transient microbes might still contribute to feeding and development, we conducted an experiment on field-collected caterpillars of the model species Manduca sexta. Antibiotic suppression of gut bacterial activity did not significantly affect caterpillar weight gain, development, or survival. The high pH, simple gut structure, and fast transit times that typify caterpillar digestive physiology may prevent microbial colonization. Moreover, host-encoded digestive and detoxification mechanisms likely render microbes unnecessary for caterpillar herbivory. Caterpillars illustrate the potential ecological and evolutionary benefits of independence from symbionts, a lifestyle which may be widespread among animals.
3,113 downloads ecology
Fall armyworm, Spodoptera frugiperda, is a crop pest native to the Americas, which has invaded and spread throughout sub-Saharan Africa within two years. Recent estimates of 20-50% maize yield loss in Africa suggest severe damage to livelihoods. Fall armyworm is still infilling its potential range in Africa, and could spread to other continents. In order to understand fall armyworm year-round, global, potential distribution, we used evidence of the effects of temperature and precipitation on fall armyworm life-history, combined with data on native and African distributions to construct Species Distribution Models (SDMs). Fall armyworm has only invaded areas that have a climate similar to the native distribution, validating the use of climatic SDMs. The strongest climatic limits on fall armyworm year-round distribution are the coldest annual temperature and the amount of rain in the wet season. Much of sub-Saharan Africa can host year-round fall armyworm populations, but the likelihoods of colonising North Africa and seasonal migrations into Europe are hard to predict. South and Southeast Asia and Australia have climate that would permit fall armyworm to invade. Current trade and transportation routes reveal Australia, China, India, Indonesia, Malaysia, Philippines, and Thailand face high threat of fall armyworm invasions originating from Africa.
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