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      Disruption of the odorant coreceptor Orco impairs foraging and host finding behaviors in the New World screwworm fly

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          Abstract

          The evolution of obligate ectoparasitism in blowflies (Diptera: Calliphoridae) has intrigued scientists for over a century, and surprisingly, the genetics underlying this lifestyle remain largely unknown. Blowflies use odors to locate food and oviposition sites; therefore, olfaction might have played a central role in niche specialization within the group. In insects, the coreceptor Orco is a required partner for all odorant receptors (ORs), a major gene family involved in olfactory-evoked behaviors. Hence, we characterized the Orco gene in the New World screwworm, Cochliomyia hominivorax, a blowfly that is an obligate ectoparasite of warm-blooded animals. In contrast, most of the closely related blowflies are scavengers that lay their eggs on dead animals. We show that the screwworm Orco orthologue ( ChomOrco) is highly conserved within Diptera, showing signals of strong purifying selection. Expression of ChomOrco is broadly detectable in chemosensory appendages, and is related to morphological, developmental, and behavioral aspects of the screwworm biology. We used CRISPR/Cas9 to disrupt ChomOrco and evaluate the consequences of losing the OR function on screwworm behavior. In two-choice assays, Orco mutants displayed an impaired response to floral-like and animal host-associated odors, suggesting that OR-mediated olfaction is involved in foraging and host-seeking behaviors in C. hominivorax. These results broaden our understanding of the chemoreception basis of niche occupancy by blowflies.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              PAML 4: phylogenetic analysis by maximum likelihood.

               Ziheng Yang (2007)
              PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
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                Author and article information

                Contributors
                conchamc@si.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                31 May 2021
                31 May 2021
                2021
                : 11
                Affiliations
                [1 ]GRID grid.411087.b, ISNI 0000 0001 0723 2494, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, , University of Campinas (UNICAMP), ; Campinas, SP 13083-875 Brazil
                [2 ]GRID grid.8536.8, ISNI 0000 0001 2294 473X, Department of Genetics, Institute of Biology, , Federal University of Rio de Janeiro (UFRJ), ; Rio de Janeiro, RJ 21941-902 Brazil
                [3 ]GRID grid.508981.d, USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, ; Kerrville, TX 78028 USA
                [4 ]GRID grid.411087.b, ISNI 0000 0001 0723 2494, Department of Structural and Functional Biology, Institute of Biology, , University of Campinas (UNICAMP), ; Campinas, SP 13083-862 Brazil
                [5 ]GRID grid.438006.9, ISNI 0000 0001 2296 9689, Microscopy Laboratory, , Smithsonian Tropical Research Institute (STRI), ; Tupper Building, Panama city, 0843-03092 Panama
                [6 ]USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Screwworm Research Site, Pacora, Panama
                [7 ]USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648 USA
                [8 ]GRID grid.438006.9, ISNI 0000 0001 2296 9689, Laboratory of Ecological and Evolutionary Genomics, , Smithsonian Tropical Research Institute (STRI), ; Gamboa, Panama
                [9 ]GRID grid.40803.3f, ISNI 0000 0001 2173 6074, Department of Entomology and Plant Pathology, , North Carolina State University, ; Campus Box 7613, Raleigh, NC 27695 USA
                Article
                90649
                10.1038/s41598-021-90649-x
                8167109
                34059738
                db10115c-40aa-4cff-8224-bfe31785c0cf
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: ARS-COPEG
                Award ID: 58-6205-4-002-F
                Award ID: 58-6205-4-002-F
                Award Recipient :
                Funded by: FASEP
                Award ID: 2015/02079-9
                Award ID: 2015/02079-9
                Award Recipient :
                Funded by: USDA-ARS
                Award ID: 58-3094-7-015-FN
                Award ID: 58-3094-7-015-FN
                Award ID: 58-3094-7-015-FN
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000014, Smithsonian Institution;
                Award ID: Pell Grant
                Award Recipient :
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                © The Author(s) 2021

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                agricultural genetics, functional genomics

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