Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 94,912 bioRxiv papers from 404,161 authors.

Most downloaded bioRxiv papers, all time

in category ecology

4,114 results found. For more information, click each entry to expand.

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
more details view paper

Posted to bioRxiv 24 Jan 2020

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
21,936 downloads ecology

Shi Zhao, Qianyin Lin, Jinjun Ran, Salihu S. Musa, Guangpu Yang, Weiming Wang, Yijun Lou, Daozhou Gao, Lin Yang, Daihai He, Maggie H Wang

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.

2: Model-based projections of Zika virus infections in childbearing women in the Americas
more details view paper

Posted to bioRxiv 12 Feb 2016

Model-based projections of Zika virus infections in childbearing women in the Americas
12,985 downloads ecology

T. Alex Perkins, Amir S. Siraj, Corrine Warren Ruktanonchai, Moritz UG Kraemer, Andrew J. Tatem

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.

3: Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens
more details view paper

Posted to bioRxiv 24 Jul 2018

Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens
12,786 downloads ecology

Greg 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.

4: Flowers respond to pollinator sound within minutes by increasing nectar sugar concentration.
more details view paper

Posted to bioRxiv 28 Dec 2018

Flowers respond to pollinator sound within minutes by increasing nectar sugar concentration.
10,961 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.

5: Distance Sampling in R
more details view paper

Posted to bioRxiv 14 Jul 2016

Distance Sampling in R
10,867 downloads ecology

David L Miller, Eric Rexstad, Len Thomas, Laura Marshall, Jeffrey L Laake

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.

6: Behavioural effects of temperature on ectothermic animals: unifying thermal physiology and behavioural plasticity
more details view paper

Posted to bioRxiv 09 Jun 2016

Behavioural effects of temperature on ectothermic animals: unifying thermal physiology and behavioural plasticity
10,525 downloads ecology

Paul K. Abram, Guy Boivin, Joffrey Moiroux, Jacques Brodeur

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: Modeling Zero-Inflated Count Data With glmmTMB
more details view paper

Posted to bioRxiv 01 May 2017

Modeling Zero-Inflated Count Data With glmmTMB
10,170 downloads ecology

Mollie E. Brooks, Kasper Kristensen, Koen J. van Benthem, Arni Magnusson, Casper W. Berg, Anders Nielsen, Hans J. Skaug, Martin Mächler, Ben Bolker

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.

8: Glacier ice archives fifteen-thousand-year-old viruses
more details view paper

Posted to bioRxiv 07 Jan 2020

Glacier ice archives fifteen-thousand-year-old viruses
9,164 downloads ecology

Zhi-Ping Zhong, Natalie E. Solonenko, Yueh-Fen Li, Maria C. Gazitúa, Simon Roux, Mary E. Davis, James L Van Etten, Ellen Mosley-Thompson, Virginia I. Rich, Matthew B. Sullivan, Lonnie G. Thompson

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 artificial-ice-core control experiments, and was then applied to two authentic ice cores to profile their microbes and viruses. The microbes differed significantly across the two ice cores, presumably representing the very different climate conditions at the time of deposition that is similar to findings in other cores. Separately, viral particle enrichment and ultra-low-input quantitative viral metagenomic sequencing from ~520 and ~15,000 years old ice revealed 33 viral populations (i.e., species-level designations) that represented four known genera and likely 28 novel viral genera (assessed by gene-sharing networks). In silico host predictions linked 18 of the 33 viral populations to co-occurring abundant bacteria, including Methylobacterium, Sphingomonas, and Janthinobacterium, indicating that viruses infected several abundant microbial groups. Depth-specific viral communities were observed, presumably reflecting differences in the environmental conditions among the ice samples at the time of deposition. Together, these experiments establish a clean procedure for studying microbial and viral communities in low-biomass glacier ice and provide baseline information for glacier viruses, some of which appear to be associated with the dominant microbes in these ecosystems.

9: Analyzing ecological networks of species interactions
more details view paper

Posted to bioRxiv 28 Feb 2017

Analyzing ecological networks of species interactions
5,795 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.

10: Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
more details view paper

Posted to bioRxiv 16 Mar 2016

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
5,232 downloads ecology

Paul Carini, Patrick J Marsden, Jonathan W Leff, Emily E Morgan, Michael S Strickland, Noah Fierer

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.

11: Mapping migration in a songbird using high-resolution genetic markers
more details view paper

Posted to bioRxiv 08 Aug 2014

Mapping migration in a songbird using high-resolution genetic markers
5,064 downloads ecology

Kristen Ruegg, Eric C. Anderson, Kristina L Paxton, Vanessa Apkenas, Sirena Lao, Rodney B. Siegel, David F. DeSante, Frank Moore, Thomas B Smith

Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited–the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for connecting populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify populations of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 single nucleotide polymorphisms (SNPs) selected from a large pool of candidates (~450,000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, accurate, and amenable to high throughput screening than previously described tracking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms.

12: 2019-20 Wuhan coronavirus outbreak: Intense surveillance is vital for preventing sustained transmission in new locations
more details view paper

Posted to bioRxiv 25 Jan 2020

2019-20 Wuhan coronavirus outbreak: Intense surveillance is vital for preventing sustained transmission in new locations
4,885 downloads ecology

R.N. Thompson

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 hospitalisation for 47 patients infected in the current outbreak are used to generate an estimate for the probability that an imported case is followed by sustained human-to-human transmission. Under the assumptions that the imported case is representative of the patients in China, and that the 2019-nCoV is similarly transmissible to the SARS coronavirus, the probability that an imported case is followed by sustained human-to-human transmission is 0.37. However, if the mean time from symptom onset to hospitalisation can be halved by intense surveillance, then the probability that an imported case leads to sustained transmission is only 0.005. This emphasises the importance of current surveillance efforts in countries around the world, to ensure that the ongoing outbreak will not become a large global epidemic.

13: A systematic review and meta-analysis of the human blood index of the major African malaria vectors
more details view paper

Posted to bioRxiv 23 Sep 2018

A systematic review and meta-analysis of the human blood index of the major African malaria vectors
4,284 downloads ecology

James Orsborne, Luis Furuya-Kanamori, Claire L Jeffries, Mojca Kristan, Abdul Rahim Mohammed, Yaw A Afrane, Kathleen O’Reilly, Eduardo Massad, Chris Drakeley, Thomas Walker, Laith Yakob

The proportion of mosquito blood-meals that are of human origin, referred to as the 'human blood index' or HBI, is a key determinant of malaria transmission. We conducted a systematic review of the HBI for the major African malaria vectors. Evidence is presented for higher HBI among Anopheles gambiae (M/S forms and An. coluzzii/An. gambiae s.s. are not distinguished for most studies and therefore combined) as well as An. funestus when compared with An. arabiensis (prevalence odds ratio adjusted for whether mosquitoes were caught indoors and outdoors: 1.61 95%CI 1.08-2.39; 1.84 95%CI 1.35-2.52, respectively). This finding is in keeping with the entomological literature which describes An. arabiensis to be more zoophagic than the other major African vectors. However, meta-analysis also revealed that HBI was more associated with location of mosquito captures (indoors versus outdoors, R2=0.3) than with mosquito (sibling/) species (R2=0.11), and that this difference was significant (p<0.01). Some of the more important consequences of mosquito biting behaviour are discussed in the context of new theoretical and empirical developments that may improve both HBI assessment and how this metric can inform malaria control optimisation.

14: Applications for deep learning in ecology
more details view paper

Posted to bioRxiv 30 May 2018

Applications for deep learning in ecology
4,280 downloads ecology

Sylvain Christin, Éric Hervet, Nicolas Lecomte

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.

15: The dynamic core microbiome: Structure, dynamics and stability
more details view paper

Posted to bioRxiv 14 May 2017

The dynamic core microbiome: Structure, dynamics and stability
3,898 downloads ecology

Johannes R. Björk, Robert B. O’Hara, Marta Ribes, Rafel Coma, José M. Montoya

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.

16: Transmission dynamics of Zika virus in island populations: a modelling analysis of the 2013-14 French Polynesia outbreak
more details view paper

Posted to bioRxiv 07 Feb 2016

Transmission dynamics of Zika virus in island populations: a modelling analysis of the 2013-14 French Polynesia outbreak
3,848 downloads ecology

Adam J. Kucharski, Sebastian Funk, Rosalind M. Eggo, Henri-Pierre Mallet, W. John Edmunds, Eric J Nilles

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.

17: pcadapt: an R package to perform genome scans for selection based on principal component analysis
more details view paper

Posted to bioRxiv 30 May 2016

pcadapt: an R package to perform genome scans for selection based on principal component analysis
3,806 downloads ecology

Keurcien Luu, Eric Bazin, Michael G.B. Blum

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.

18: LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately
more details view paper

Posted to bioRxiv 23 Sep 2019

LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately
3,586 downloads ecology

Zoe L. Getman-Pickering, Adam T. Campbell, Nicholas Aflitto, Todd A. Ugine, Ari Grele, Julie Davis

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.

19: Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus
more details view paper

Posted to bioRxiv 11 Mar 2016

Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus
3,581 downloads ecology

Sebastian Funk, Adam J. Kucharski, Anton Camacho, Rosalind M. Eggo, Laith Yakob, Lawrence M. Murray, W. John Edmunds

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.

20: ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms
more details view paper

Posted to bioRxiv 29 Jul 2014

ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms
3,540 downloads ecology

William E Peterman

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.

Previous page 1 2 3 4 5 . . . 206 Next page


Sign up for the Rxivist weekly newsletter! (Click here for more details.)