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Currently indexing 83,433 bioRxiv papers from 359,611 authors.

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Results 1 through 20 out of 3572

in category ecology

 

1: Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak

Shi Zhao, Qianyin Lin et al.

21,231 downloads (posted 24 Jan 2020)

Backgrounds An ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number, R , of 2019-nCoV in the early phase of the outbreak. Methods Accounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate ( γ ), we estimated R by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI. Findings The early outbreak data largely follows the exponential growth. We estimated that the mean R ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R . Conclusion The mean estimate of R for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.

https://rxivist.org/papers/71805
https://doi.org/10.1101/2020.01.23.916395

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

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

12,948 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...

https://rxivist.org/papers/19270
https://doi.org/10.1101/039610

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

Greg Boyce, Emile Gluck-Thaler et al.

11,160 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...

https://rxivist.org/papers/18337
https://doi.org/10.1101/375105

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

Marine Veits, Itzhak Khait et al.

10,649 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 ...

https://rxivist.org/papers/40693
https://doi.org/10.1101/507319

5: Distance Sampling in R

David L Miller, Eric Rexstad et al.

10,561 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...

https://rxivist.org/papers/18864
https://doi.org/10.1101/063891

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

Paul K. Abram, Guy Boivin et al.

9,970 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...

https://rxivist.org/papers/19257
https://doi.org/10.1101/056051

7: Modeling Zero-Inflated Count Data With glmmTMB

Mollie E. Brooks, Kasper Kristensen et al.

9,186 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...

https://rxivist.org/papers/19040
https://doi.org/10.1101/132753

8: Glacier ice archives fifteen-thousand-year-old viruses

Zhi-Ping Zhong, Natalie E. Solonenko et al.

8,261 downloads (posted 07 Jan 2020)

While glacier ice cores provide climate information over tens to hundreds of thousands of years, study of microbes is challenged by ultra-low-biomass conditions, and virtually nothing is known about co-occurring viruses. Here we establish ultra-clean microbial and viral sampling procedures and apply them to two ice cores from the Guliya ice cap (northwestern Tibetan Plateau, China) to study these archived communities. This method reduced intentionally contaminating bacterial, viral, and free DNA to background levels in ...

https://rxivist.org/papers/70277
https://doi.org/10.1101/2020.01.03.894675

9: Analyzing ecological networks of species interactions

Eva Delmas, Mathilde Besson et al.

5,571 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...

https://rxivist.org/papers/18719
https://doi.org/10.1101/112540

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

Paul Carini, Patrick J Marsden et al.

5,085 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...

https://rxivist.org/papers/19304
https://doi.org/10.1101/043372

11: 2019-20 Wuhan coronavirus outbreak: Intense surveillance is vital for preventing sustained transmission in new locations

R.N. Thompson

4,672 downloads (posted 25 Jan 2020)

The outbreak of pneumonia originating in Wuhan, China, has generated 830 confirmed cases, including 26 deaths, as of 24 January 2020. The virus (2019-nCoV) has spread elsewhere in China and to other countries, including South Korea, Thailand, Japan and USA. Fortunately, there has not yet been evidence of sustained human-to-human transmission outside of China. Here we assess the risk of sustained transmission whenever the coronavirus arrives in other countries. Data describing the times from symptom onset to hospitalisat...

https://rxivist.org/papers/71943
https://doi.org/10.1101/2020.01.24.919159

12: Applications for deep learning in ecology

Sylvain Christin, Éric Hervet et al.

3,991 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...

https://rxivist.org/papers/18532
https://doi.org/10.1101/334854

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

Adam J. Kucharski, Sebastian Funk et al.

3,815 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...

https://rxivist.org/papers/19295
https://doi.org/10.1101/038588

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

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

3,642 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...

https://rxivist.org/papers/18776
https://doi.org/10.1101/137885

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

Keurcien Luu, Eric Bazin et al.

3,621 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...

https://rxivist.org/papers/19231
https://doi.org/10.1101/056135

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

Sebastian Funk, Adam J. Kucharski et al.

3,524 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...

https://rxivist.org/papers/19181
https://doi.org/10.1101/043265

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

Zoe L. Getman-Pickering, Adam T. Campbell et al.

3,471 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 ...

https://rxivist.org/papers/61478
https://doi.org/10.1101/777516

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

William E Peterman

3,458 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....

https://rxivist.org/papers/19435
https://doi.org/10.1101/007575

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

Søeren M. Karst, Morten S. Dueholm et al.

3,430 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...

https://rxivist.org/papers/19212
https://doi.org/10.1101/070771

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

João P. M. Araújo, David P. Hughes

3,394 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 ...

https://rxivist.org/papers/19446
https://doi.org/10.1101/003756