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Jordão LSB, Morim MP, Baumgratz JFA, Simon MF, Eppinghaus ALC, Calfo VA. TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research. Biol Methods Protoc 2024; 9:bpae017. [PMID: 38566774 PMCID: PMC10984730 DOI: 10.1093/biomethods/bpae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.
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Affiliation(s)
- Lucas Sá Barreto Jordão
- Centro Nacional de Conservação da Flora—CNCFlora, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Marli Pires Morim
- Diretoria de Pesquisa Científica—DIPEQ, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - José Fernando A Baumgratz
- Diretoria de Pesquisa Científica—DIPEQ, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Marcelo Fragomeni Simon
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica–PqEB, Brasília, 70770-901, Brazil
| | - André L C Eppinghaus
- Centro Nacional de Conservação da Flora—CNCFlora, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Vicente A Calfo
- Centro Nacional de Conservação da Flora—CNCFlora, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
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Ascendino S, Maia VC. Insect galls of Atlantic Forest areas of Serra da Bodoquena (MS, Midwestern Brazil). AN ACAD BRAS CIENC 2023; 95:e20191091. [PMID: 38088695 DOI: 10.1590/0001-3765202320191091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2023] Open
Abstract
An inventory of insect galls of Serra da Bodoquena (MS, Midwestern Brazil) was carried out in an area of semideciduous seasonal forest situated in the Califórnia Farm. Three field works were done in August/2011, December/2011 and April/2012, when the local vegetation was examined during 40 hours per expedition. Fifty-eight gall morphotypes were found on 40 host plants, 38 of them native. The host plants are distributed in 18 families. The native plants include eight endemic species in Brazil, which together totaled 14 gall morphotypes. Zanthoxylum L. sp. (Rutaceae), an endemic genus in Brazil, hosts one gall morphotype. The non endemic native plants totaled 26 gall morphotypes. Ten new host plants are recorded for the first time in Brazil. The medium number of gall morphotypes per plant species was 1.45. Salicaceae, Bignoniaceae, and Asteraceae presented the highest number of galled species and the greatest gall richness. Leaves were the most frequent galled plant organ and there was a predominance of globoid galls. Diptera (Cecidomyiidae) were the most frequent gallers, but Hemipteran and Thysanopteran galls were also found. The associated fauna was composed of inquilines (Diptera: Muscomorpha and Cecidomyiidae - Trotteria sp., and Thysanoptera), successors (Psocoptera), and parasitoids (Hymenoptera).
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Affiliation(s)
- Sharlene Ascendino
- Museu Nacional, Depto. De Entomologia, Quinta da Boa Vista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Valéria Cid Maia
- Museu Nacional, Depto. De Entomologia, Quinta da Boa Vista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
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Campos GBD, Costa EC, Santos DLS, Carvalho-Fernandes SP, Santos-Silva J. Insect galls and associated fauna in two areas of Cerrado sensu stricto in the State of Bahia, Brazil. AN ACAD BRAS CIENC 2021; 93:e20201442. [PMID: 34586179 DOI: 10.1590/0001-3765202120201442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/16/2021] [Indexed: 11/21/2022] Open
Abstract
This study inventoried and characterized the richness of galling insects based on gall morphotypes and their host plants in two Cerrado sensu stricto areas of Caetité municipality in Bahia State, Brazil, to aid the identification of galling insects and their host plants, as well as to contribute to the knowledge and conservation of local biodiversity. The survey was conducted in the Moita dos Porcos archaeological site and João Barroca Farm site, adopting the random walking methodology for sampling, during 12 months. We recorded 98 gall morphotypes on 42 plant species belonging to 36 genera and 22 families. Leguminosae, Malpighiaceae and Myrtaceae demonstrated the greatest richness of galls, and the Copaifera langsdorffii was the super-host species, with 16 gall morphotypes. Most galls occur on leaves, and may be globoid, glabrous, grouped, and are usually unilocular, and brown. The galling insects identified belonged to Coleoptera, Diptera, Lepidoptera, and Thysanoptera. Eight plant host species and eight gall morphotypes were recorded for the first time in Cerrado areas in Brazil. The areas surveyed demonstrated high richness of gall morphotypes and host plants, evidencing the importance of studying and preserving different areas of the same biome.
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Affiliation(s)
- Gabriela B D Campos
- Universidade do Estado da Bahia, Programa de Pós-graduação em Biodiversidade Vegetal, Departamento de Educação-DEDC, Rua da Gangorra, 503, CHESF, 48608-240 Paulo Afonso, BA, Brazil
| | - Elaine C Costa
- Universidade Federal de Minas Gerais, Programa de Pós-graduação em Biologia Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Avenida Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Débora L S Santos
- Universidade do Estado da Bahia, Departamento de Ciências Humanas - DCH, Avenida Contorno, s/n, Centro, 46400-000 Caetité, BA, Brazil
| | - Sheila P Carvalho-Fernandes
- Universidade Federal do Rio de Janeiro/UFRJ, Departamento de Entomologia, Museu Nacional, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Juliana Santos-Silva
- Universidade do Estado da Bahia, Programa de Pós-graduação em Biodiversidade Vegetal, Departamento de Educação-DEDC, Rua da Gangorra, 503, CHESF, 48608-240 Paulo Afonso, BA, Brazil
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Maia VC. Review of the inquilinous fauna associated with insect galls in Brazilian restingas. BRAZ J BIOL 2021; 82:e235395. [PMID: 34105660 DOI: 10.1590/1519-6984.235395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
Several records of associated fauna, including parasitoids, inquilines, predators, and successors, have been reported by insect gall inventories in Brazilian restingas. Although most guilds are well established, inquilines have frequently been misinterpreted. In this paper, the inquilinous fauna of insect galls is revised based on five criteria: food habit; coexistence with the inducer; modification of gall tissues or production of new tissues; phylogenetic relationship with the inducer; and mobility. Gall inventories dated from 1988 to 2019 were examined, totaling 16 publications, eight of them with inquiline records. This guild was reported in 53 gall morphotypes in 44 plant species and four morphospecies distributed among 36 genera of 24 host families for a total of 65 records. Most inquilines were repositioned into the cecidophage guild and others into the kleptoparasite guild, resulting in a large reduction in the frequency of inquilines (from 65 to five records), and in first reports of cecidophages and kleptoparasites, with 46 and 13 records, respectively. Cecidophage was the most diverse guild with insects of five orders (Diptera, Coleoptera, Lepidoptera, Hemiptera, and Thysanoptera) while kleptoparasites were represented only by two orders (Diptera and Hymenoptera) and inquiline solely by Hymenoptera. Other results indicate that Leptothorax sp. (Formicidae) could be a successor and not an inquiline.
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Affiliation(s)
- V C Maia
- Universidade Federal do Rio de Janeiro - UFRJ, Museu Nacional, Departamento de Entomologia, Rio de Janeiro, RJ, Brasil
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Gätjens-Boniche O, Sánchez-Valverde M, Trejos-Araya C, Espinoza-Obando R, Pinto-Tomás AA, Hanson PE. Plant galls recorded from Guanacaste Conservation Area-Costa Rica as an integrated concept of a biological database. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2020-1153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Galling insects are specialist herbivorous that have the ability of manipulating plant tissue to form complex biological structures called galls. Even though different organisms have the ability to induce galls in plants, insect galls have the highest degree of structural complexity. The main goal of this study was to obtain a preliminary systematic record of plant gall morphotypes from the Guanacaste Conservation Area in Costa Rica and integrate the information into a biological database. Plant gall morphotypes were recorded, characterized and deposited into a specialized herbarium established as a reference for the inventory. Moreover, organisms associated with gall morphotypes were included in the inventory when it was possible to obtain and identify them. Galls were collected in the rainy season over a period of three years. In total, we recorded forty-four families, seventy genera, and eighty-seven host plant species. One hundred thirty-one morphotypes of plant galls were identified in the Guanacaste Conservation Area. The family with the highest number of gall morphotypes was Fabaceae (8.4%). Leaves were the organ with the largest number of galls (71%), followed by stems (17.6%), and apical buds (6.9%). The predominant gall shape was globular (25.2%), followed by discoid (18.3%). Fifty-nine percent of the galls had a glabrous texture, which was most common on leaves, with 77%. One hundred twenty of our field records (91.6%) of plant galls were new morphotypes not only for Costa Rica but also the world. As a consequence of this research and considering the prospect of future increases in new gall records (and associated organisms), we proposed having the biological entities resulting from the inventory placed in a cecidiarium. This repository represents a standardized and comprehensive way to manage the data and biological materials associated with the plant galls. We also suggest a nomenclature for standardizing gall morphotype registries and identifications. This work is the first and most detailed inventory of plant galls carried out thus far in the Guanacaste Conservation Area.
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Urso-Guimarães MV, Koch I, Castello ACD. Diversity of insect galls from Mato Grosso State, Brazil: Cerrado. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2021-1189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract: The Midwest region of Brazil possesses large areas dominated by the Cerrado that is poorly known concerning insect gall and their interactions. In this study, we inventory the gall morphology, host plants, and the gall makers from Parque Nacional da Chapada dos Guimarães, Mato Grosso State, in areas of natural vegetation from Cerrado, for the first time. Samplings occurred in two expeditions, July 2012 and January 2013. We characterized 295 morphotypes of insect galls in 140 host plant species, with 89 gall makers; the richest family in host plants was Fabaceae (16.7%), and the species was Protium heptaphyllum (Aubl.) Marchand (Burseraceae, 3.7%). Parque Nacional da Chapada dos Guimarães is the richest Brazilian cerrado area in gall morphotypes (295) and the second in average morphotypes/host plant species (2.1). Additionally, six genera and 38 species are new records as host plants; two of them, Bernardia similis Pax and K.Hoffm and Ormosia macrophylla Benth., are new occurrences for Mato Grosso State, and other two, Vochysia petraea Warm. and Talisia subalbens (Mart.) Radlk. are listed in the Red List of Threatened Species IUCN. This inventory data represents a testimony of insect-plant interactions in a Brazilian Cerrado area that was consumed by an unprecedented fire in the dry season of 2020.
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Maia VC, Silva BGD. Insect galls of the Brazilian Cerrado: associated fauna. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2021-1202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Insect galls host a rich and diverse fauna of secondary dwellers, which compose the associated fauna. In Brazil, many inventories of insect galls in Cerrado areas have recorded secondary dwellers. These records were scattered in several papers. This study gathered literature data to provide an overview of the arthropod fauna associated with insect galls in the Brazilian Cerrado. We searched for scientific publications in online academic databases and retrieved 16 papers with data on the secondary dwellers. We limited our search to the period from 1988 to 2020. We updated the name of plant species and verified endemism and geographic distribution in Flora do Brasil 2020. We provided plant species uses based on the Tropical Useful Plants 2014. We found 163 gall morphotypes with secondary dwellers (16.8% of the total of gall morphotypes of the Brazilian Cerrado) on 94 plant species in 37 families. Asteraceae, Fabaceae, Myrtaceae, and Malpighiaceae exhibited the greatest number of records. These are the richest families in insect galls in the Brazilian Cerrado. Most arthropod fauna were recorded in galls of Cecidomyiidae (Diptera). Most records were in leaf galls, the predominant galled organ. Parasitoids were more frequent than successors, inquilines, and predators. Eulophidae and Eurytomidae were the most frequent parasitoid families. Inquilines were represented by Coleoptera, Diplopoda, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Psocoptera, and Thysanoptera; successors by Acari, Araneae, Cecidomyiidae (Diptera), Coleoptera, Collembola, and Formicidae (Hymenoptera), whereas predators by Pseudoscorpiones and Diptera. Most records were presented in suprageneric categories, showing that the taxonomic knowledge is very deficient. 29 plant species are endemic to Brazil and totaled 45 gall morphotypes with secondary dwellers; 46 plant species are useful and host secondary dwellers in 62 gall morphotypes. These data add ecological and economic importance to these arthropods.
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Santos-Silva J, AraÚjo TJ. Are Fabaceae the principal super-hosts of galls in Brazil? AN ACAD BRAS CIENC 2020; 92:e20181115. [PMID: 32785425 DOI: 10.1590/0001-3765202020181115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/11/2019] [Indexed: 11/21/2022] Open
Abstract
We surveyed 58 scientific articles published between 1987 and 2018 to evaluate the representative nature of the Fabaceae as hosts of insect galls in Brazil, and to gain a better understanding of the interactions between gall-inducing insects and plants and the evolutionary ecology of those insects and their plant hosts. A total of 438 gall morphotypes were reported as being generated by gall-inducing insects on 178 Fabaceae host species belonging to five subfamilies Caesalpinioideae (22 genera and 79 spp.), Cercidoideae (1 genus and 11 spp.), Detarioideae (6 genera and 17 spp.), Dialioideae (2 genera and 2 spp.), and Papilionoideae (26 genera and 69 spp.). The plant host genera demonstrating the greatest richness of gall-inducing insects were Inga, Bauhinia, and Copaifera; the super-host species were Copaifera langsdorffii, Bauhinia brevipes, and Copaifera sabulicola. Most of the galls were observed on leaves; they were mostly globoid, green, glabrous, isolated, and unilocular. The principal gall inducers belonged to Cecidomyiidae; the associated fauna was represented by Collembola, Coleoptera, Diptera, Formicidae, Hemiptera, Hymenoptera, Lepidoptera, Pseudoscorpionida, and Thysanoptera. Fabaceae are the principal super-hosts of galls and one of the most diverse families of angiosperms in Brazil, aggregating evidences for the hypotheses of floristic richness and taxon size.
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Affiliation(s)
- Juliana Santos-Silva
- Programa de Pós-graduação em Biodiversidade Vegetal, Universidade do Estado da Bahia, Paulo Afonso, BA, Brazil
| | - Tainar J AraÚjo
- Programa de Pós-graduação em Biodiversidade Vegetal, Universidade do Estado da Bahia, Paulo Afonso, BA, Brazil
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