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      Do aphids in Dutch sweet pepper greenhouses carry heritable elements that protect them against biocontrol parasitoids?

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          Abstract

          Biological control (biocontrol) of crop pests is a sustainable alternative to the use of biodiversity and organismal health‐harming chemical pesticides. Aphids can be biologically controlled with parasitoid wasps; however, variable results of parasitoid‐based aphid biocontrol in greenhouses are reported. Aphids may display genetically encoded (endogenous) defences that increase aphid resistance against parasitoids as under high parasitoid pressure there will be selection for parasitoid‐resistant aphids, potentially affecting the success of parasitoid‐based aphid biocontrol in greenhouses. Additionally, aphids may carry secondary bacterial endosymbionts that protect them against parasitoids. We studied whether there is variation in either of these heritable elements in aphids in greenhouses of sweet pepper, an agro‐economically important crop in the Netherlands that is prone to aphid pests and where pest management heavily relies on biocontrol. We sampled aphid populations in organic (biocontrol only) and conventional (biocontrol and pesticides) sweet pepper greenhouses in the Netherlands during the 2019 crop growth season. We assessed the aphid microbiome through both diagnostic PCR and 16S rRNA sequencing and did not detect any secondary endosymbionts in the two most encountered aphid species, Myzus persicae and Aulacorthum solani. We also compared multiple aphid lines collected from different greenhouses for variation in levels of endogenous‐based resistance against the parasitoids commonly used as biocontrol agents. We found no differences in the levels of endogenous‐based resistance between different aphid lines. This study does not support the hypothesis that protective endosymbionts or the presence of endogenous resistant aphid lines affects the success of parasitoid‐based biocontrol of aphids in Dutch greenhouses. Future investigations will need to address what is causing the variable successes of aphid biocontrol and what (biological and management‐related) lessons can be learned for aphid control in other crops, and biocontrol in general.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Fitting Linear Mixed-Effects Models Usinglme4

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              phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

              Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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                Author and article information

                Contributors
                mariska.beekman@wur.nl
                Journal
                Evol Appl
                Evol Appl
                10.1111/(ISSN)1752-4571
                EVA
                Evolutionary Applications
                John Wiley and Sons Inc. (Hoboken )
                1752-4571
                15 February 2022
                October 2022
                : 15
                : 10 , Evolution in Agricultural Systems ( doiID: 10.1111/eva.v15.10 )
                : 1580-1593
                Affiliations
                [ 1 ] Laboratory of Genetics Wageningen University & Research Wageningen The Netherlands
                [ 2 ] Laboratory of Entomology Wageningen University & Research Wageningen The Netherlands
                Author notes
                [*] [* ] Correspondence

                Mariska M. Beekman, Laboratory of Genetics, Wageningen University & Research, PO Box 16, 6700 AA Wageningen, The Netherlands.

                Email: mariska.beekman@ 123456wur.nl

                Author information
                https://orcid.org/0000-0003-0498-5487
                https://orcid.org/0000-0003-1563-6282
                Article
                EVA13347
                10.1111/eva.13347
                9624084
                36330308
                d4a1b369-461d-4de8-b120-7fda70fcd237
                © 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 January 2022
                : 21 July 2021
                : 18 January 2022
                Page count
                Figures: 3, Tables: 0, Pages: 14, Words: 11585
                Funding
                Funded by: Koppert Biological Systems
                Funded by: Top Sector Horticultural and Starting materials (TKI T&U)
                Funded by: Nederlandse Organisatie voor Wetenschappelijk Onderzoek , doi 10.13039/501100003246;
                Award ID: ALWGR.2017.006
                Categories
                Special Issue Article
                Special Issue Article
                Custom metadata
                2.0
                October 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.0 mode:remove_FC converted:01.11.2022

                Evolutionary Biology
                aphidius parasitoids,aulacorthum solani,biocontrol,defensive symbiosis,endogenous resistance,myzus persicae

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