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Results 1 through 20 out of 2738

in category ecology


1: Model-based projections of Zika virus infections in childbearing women in the Americas

T. Alex Perkins, Amir S. Siraj et al.

12,833 downloads (posted 12 Feb 2016)

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.


2: Flowers respond to pollinator sound within minutes by increasing nectar sugar concentration.

Marine Veits, Itzhak Khait et al.

9,543 downloads (posted 28 Dec 2018)

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 ...


3: Distance Sampling in R

David L Miller, Eric Rexstad et al.

9,519 downloads (posted 14 Jul 2016)

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-e...


4: Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens

Greg Boyce, Emile Gluck-Thaler et al.

9,049 downloads (posted 24 Jul 2018)

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-ass...


5: Behavioural effects of temperature on ectothermic animals: unifying thermal physiology and behavioural plasticity

Paul K. Abram, Guy Boivin et al.

8,363 downloads (posted 09 Jun 2016)

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...


6: Modeling Zero-Inflated Count Data With glmmTMB

Mollie E. Brooks, Kasper Kristensen et al.

7,443 downloads (posted 01 May 2017)

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 presen...


7: Analyzing ecological networks of species interactions

Eva Delmas, Mathilde Besson et al.

5,150 downloads (posted 28 Feb 2017)

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 highli...


8: Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Paul Carini, Patrick J Marsden et al.

4,809 downloads (posted 16 Mar 2016)

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 i...


9: Transmission dynamics of Zika virus in island populations: a modelling analysis of the 2013-14 French Polynesia outbreak

Adam Kucharski, Sebastian Funk et al.

3,741 downloads (posted 07 Feb 2016)

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...


10: Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus

Sebastian Funk, Adam J. Kucharski et al.

3,427 downloads (posted 11 Mar 2016)

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 islan...


11: Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

Søren M. Karst, Morten S Dueholm et al.

3,335 downloads (posted 22 Aug 2016)

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 presen...


12: Applications for deep learning in ecology

Sylvain Christin, Éric Hervet et al.

3,313 downloads (posted 30 May 2018)

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 i...


13: pcadapt: an R package to perform genome scans for selection based on principal component analysis

Keurcien Luu, Eric Bazin et al.

3,237 downloads (posted 30 May 2016)

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 indivi...


14: ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms

William E Peterman

3,236 downloads (posted 29 Jul 2014)

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....


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

João P. M. Araújo, David P. Hughes

3,186 downloads (posted 04 Apr 2014)

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 ...


16: LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately

Zoe L Getman-Pickering, Adam Campbell et al.

3,149 downloads (posted 23 Sep 2019)

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 ...


17: The Paradox Of Constant Oceanic Plastic Debris: Evidence For Evolved Microbial Biodegradation?

Ricard Solé, Ernest Fontich et al.

3,133 downloads (posted 09 May 2017)

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 ...


18: The dynamic core microbiome: Structure, dynamics and stability

Johannes R. Björk, Robert B. O’Hara et al.

3,131 downloads (posted 14 May 2017)

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 stud...


19: Caterpillars lack a resident gut microbiome

Tobin J Hammer, Daniel H Janzen et al.

3,124 downloads (posted 30 Apr 2017)

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 ...


20: Beyond species: why ecological interaction networks vary through space and time

T. Poisot, D.B. Stouffer et al.

3,018 downloads (posted 03 Jan 2014)

Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological mechanisms act locally on the existence of inter-specific interactions. Here we argue that the current conceptualization of species interaction networks is ill-suited for this task. Instead, we propose tha...