Dataset Information

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies.

ABSTRACT: Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.

SUBMITTER: Matos-Maravi P

PROVIDER: S-EPMC6499058 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies.

Matos-Maraví Pável P Duarte Ritter Camila C Barnes Christopher J CJ Nielsen Martin M Olsson Urban U Wahlberg Niklas N Marquina Daniel D Sääksjärvi Ilari I Antonelli Alexandre A

PeerJ 20190430

Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succi ...[more]

PMID: 31106048

Similar Datasets

Project description:Worldwide, crop production is intrinsically intertwined with biological, environmental and economic systems, all of which involve complex, inter-related and spatially-sensitive phenomena. Thus knowing the location of agriculture matters much for a host of reasons. There are several widely cited attempts to model the spatial pattern of crop production worldwide, not least by pixilating crop production statistics originally reported on an areal (administrative boundary) basis. However, these modeled measures have had little scrutiny regarding the robustness of their results to alternative data and modeling choices. Our research casts a critical eye over the nature and empirical plausibility of these types of datasets. To do so, we determine the sensitivity of the 2005 variant of the spatial production allocation model data series (SPAM2005) to eight methodological-cum-data choices in nine agriculturally-large and developmentally-variable countries: Brazil, China, Ethiopia, France, India, Indonesia, Nigeria, Turkey and the United States. We compare the original published estimates with those obtained from a series of robustness tests using various aggregations of the pixelized spatial production indicators (specifically, commodity-specific harvested area, production quantity and yield). Spatial similarity is empirically assessed using a pixel-level spatial similarity index (SSI). We find that the SPAM2005 estimates are most dependent on the degree of disaggregation of the underlying national and subnational production statistics. The results are also somewhat sensitive to the use of a simple spatial allocation method based solely on cropland proportions versus a cross-entropy allocation method, as well as the set of crops or crop aggregates being modeled, and are least sensitive to the inclusion of crude economic elements. Finally, we assess the spatial concordance between the SPAM2005 estimates of the area harvested of major crops in the United States and pixelated measures derived from remote-sensed data.

Project description:Clinical evidence available for the assessment of medical devices (MDs) is frequently insufficient. New MDs should be subjected to high quality clinical studies to demonstrate their benefit to patients. The randomized controlled trial (RCT) is the study design reaching the highest level of evidence in order to demonstrate the efficacy of a new MD. However, the clinical context of some MDs makes it difficult to carry out a conventional RCT. The objectives of this review are to present problems related to conducting conventional RCTs and to identify other experimental designs, their limitations, and their applications. A systematic literature search was conducted for the period January 2000 to July 2012 by searching medical bibliographic databases. Problems related to conducting conventional RCTs of MDs were identified: timing the assessment, eligible population and recruitment, acceptability, blinding, choice of comparator group, and learning curve. Other types of experimental designs have been described. Zelen's design trials and randomized consent design trials facilitate the recruitment of patients, but can cause ethical problems to arise. Expertise-based RCTs involve randomization to a team that specializes in a given intervention. Sometimes, the feasibility of an expertise-based randomized trial may be greater than that of a conventional trial. Cross-over trials reduce the number of patients, but are not applicable when a learning curve is required. Sequential trials have the advantage of allowing a trial to be stopped early depending on the results of first inclusions, but they require an independent committee. Bayesian methods combine existing information with information from the ongoing trial. These methods are particularly useful in situations where the number of subjects is small. The disadvantage is the risk of including erroneous prior information. Other types of experimental designs exist when conventional trials cannot always be applied to the clinical development of MDs.

Project description:BackgroundFoodborne and zoonotic diseases such as brucellosis present many challenges to public health and economic welfare. Increasingly, researchers and public health institutes use disability-adjusted life years (DALYs) to generate a comprehensive comparison of the population health impact of these conditions. DALYs calculations, however, entail a number of methodological choices and assumptions, with data gaps and uncertainties to accommodate. Thisreview identifies existing brucellosis burden of disease studies and analyzes their methodological choices, assumptions, and uncertainties. It supports the Global Burden of Animal Diseases programme in the development of a systematic methodology to describe the impact of animal diseases on society, including human health.Methods/principal findingsA systematic search for brucellosis burden of disease calculations was conducted in pre-selected international and grey literature databases. Using a standardized reporting framework, we evaluated each estimate on a variety of key methodological assumptions necessary to compute a DALY. Fourteen studies satisfied the inclusion criteria (human brucellosis and quantification of DALYs). One study reported estimates at the global level, the rest were national or subnational assessments. Data regarding different methodological choices were extracted, including detailed assessments of the adopted disease models. Most studies retrieved brucellosis epidemiological data from administrative registries. Incidence data were often estimated on the basis of laboratory-confirmed tests. Not all studies included mortality estimates (Years of Life Lost) in their assessments due to lack of data or the assumption that brucellosis is not a fatal disease. Only two studies used a model with variable health states and corresponding disability weights. The rest used a simplified singular health state approach. Wide variation was seen in the duration chosen for brucellosis, ranging from 2 weeks to 4.5 years, irrespective of the whether a chronic state was included.ConclusionAvailable brucellosis burden of disease assessments vary widely in their methodology and assumptions. Further research is needed to better characterize the clinical course of brucellosis and to estimate case-fatality rates. Additionally, reporting of methodological choices should be improved to enhance transparency and comparability of estimates. These steps will increase the value of these estimates for policy makers.

Dataset Information

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies.

Publications

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets