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      Microsatellites for the Neotropical Ant, Odontomachus chelifer (Hymenoptera: Formicidae)

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          Abstract

          Odontomachus chelifer (Latreille) (Ponerinae) is a ground-dwelling, predominantly carnivorous ant whose colonies may contain multiple egg-laying queens and are potentially susceptible to border effects in the Brazilian savanna known as Cerrado. The ecology and natural history of O. chelifer is well studied, but very little is known about the genetic diversity of O. chelifer colonies. In this study, we developed microsatellite markers for the study of genetic variation in O. chelifer. We created a microsatellite-enriched library that resulted in the development and characterization of 22 markers, of which 18 were found to be polymorphic in the population studied. The mean expected heterozygosity was 0.59, whereas the mean rarified allelic richness was determined as 4.27 alleles per locus. The polymorphism level detected was similar to genetic diversity estimates found in other poneromorph ant species. The microsatellites developed here are likely to be useful for the investigation of colony structure, functional polygyny, breeding system, and population genetics in O. chelifer. Moreover, the description of O. chelifer’s genetic diversity is crucial for its conservation and maintenance of its ecological role in the Cerrado savanna.

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Primer3—new capabilities and interfaces

            Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
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              genepop'007: a complete re-implementation of the genepop software for Windows and Linux.

              This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls. © 2007 The Author.
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                Author and article information

                Contributors
                Role: Subject Editor
                Journal
                J Insect Sci
                J Insect Sci
                jis
                Journal of Insect Science
                Oxford University Press (US )
                1536-2442
                September 2020
                24 October 2020
                24 October 2020
                : 20
                : 5
                : 28
                Affiliations
                [1 ] Graduação em Ciências Biológicas, Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP, Brazil
                [2 ] Programa de Pós-Graduação em Ecologia, Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP, Brazil
                [3 ] Departamento de Biologia Vegetal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas , Campinas, SP, Brazil
                [4 ] Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP, Brazil
                Author notes
                Corresponding author, e-mail: pso@ 123456unicamp.br
                Author information
                http://orcid.org/0000-0002-4696-2999
                Article
                ieaa117
                10.1093/jisesa/ieaa117
                7585319
                33098430
                def4d46c-33a8-4a63-9d05-22f7f43c9794
                © The Author(s) 2020. Published by Oxford University Press on behalf of Entomological Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 July 2020
                : 10 September 2020
                Page count
                Pages: 6
                Funding
                Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, DOI 10.13039/501100002322;
                Award ID: 001
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico, DOI 10.13039/501100003593;
                Award ID: 116435/2019-4
                Award ID: 167161/2017-2
                Award ID: 306115/2013-1
                Award ID: 302219/2017-0
                Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo, DOI 10.13039/501100001807;
                Award ID: 2019/12683-1
                Award ID: 2017/18291-2
                Award ID: 2014/23141-1
                Award ID: 2017/16645-1
                Categories
                Short Communication
                AcademicSubjects/SCI01382

                Entomology
                molecular marker,simple sequence repeat,ponerinae,hymenoptera,social insect
                Entomology
                molecular marker, simple sequence repeat, ponerinae, hymenoptera, social insect

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