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Crustacea: Isopoda) De Portugal E Da Macaronésia Universidade do Minho Escola de Ciências Nuno Miguel Araújo Gomes Construção de uma biblioteca de referência de DNA barcodes para Isópodes marinhos (Crustacea: Isopoda) de Portugal e da Macaronésia Tese de Mestrado Mestrado de Ecologia Trabalho efetuado sob a orientação do Professor Doutor Filipe Costa Outubro de 2014 Agradecimentos Gostaria agradecer ao meu orientador, Doutor Filipe Costa pela oportunidade de trabalho nas áreas da taxonomia e DNA barcoding e pelo auxilio na elaboração desta tese. Um agradecimento à Doutora Luísa Borges e à Mestre Sara Ferreira pelo ensino e iniciação no trabalho laboratorial. Gostaria também de agradecer aos colegas Marcos Teixeira, Jorge Lobo e Cláudia Hollatz pela ajuda, companheirismo e pelo bom ambiente de trabalho. Um agradecimento ao Pedro Vieira e ao Doutor Henrique Queiroga pela disponibilização de espécimes e sequências de DNA, e aos Doutores Ronaldo Sousa, Marina Cunha e Susana Carvalho pela disponibilização de material bibliográfico importantes para a realização desta tese. Este trabalho foi financiado por Fundos FEDER através do Programa Operacional de Factores de Competitividade - COMPETE e por Fundos Nacionais através da FCT "Fundação para a Ciência e a Tecnologia (FCT)” / MEC no âmbito dos projetos FCOMP-01-0124-FEDER-015429 (ref. FCT: PTDC/MAR/113435/2009) e PEst-OE/BIA/UI4050/2014. iii Construção de uma biblioteca de referência de DNA barcodes para Isópodes marinhos (Crustacea Isopoda) de Portugal e da Macaronésia Resumo Apesar de a ordem Isopoda constituir um dos mais diversos grupos de crustáceos presentes em vários habitats marinhos, o conhecimento sobre a sua biodiversidade ainda é insuficiente, comprometendo o planeamento de estratégias de gestão de meios marinhos. A utilização de bibliotecas de referência de DNA barcodes (sequências de DNA obtidas a partir da extremidade 5’ do gene mitocondrial da sub-unidade I do citocromo oxidase, COI-5P) para auxiliar a identificação e a catalogação de macro invertebrados bentónicos marinhos tem contribuído para a melhoria do conhecimento sobre a composição e distribuição espacial destas comunidades, possibilitando o recurso a técnicas de sequenciação de segunda geração para agilização de métodos de monitorização. Este estudo teve como objetivos: 1) a compilação e elaboração de uma lista atualizada (“checklist”) de espécies de isópodes marinhos registados em Portugal continental e nos arquipélagos dos Açores e Madeira; 2) contribuir para a construção de uma biblioteca de DNA barcodes de isópodes marinhos das mesmas regiões. A elaboração da lista resultou na compilação de 146 espécies registadas desde zonas de mar profundo a zonas costeiras e estuarinas. Para a construção de uma biblioteca de referência de DNA barcodes de isópodes foram identificados 250 espécimes e geradas 105 sequências, resultantes de sequenciação bidirecional englobando 26 morfoespécies, distribuídas por 32 MOTU´s, recolhidas em vários pontos do Atlântico Nordeste, maioritariamente ao longo da costa de Portugal e da Galiza e nos arquipélagos dos Açores, Canárias e Madeira. Todos os espécimes foram catalogados na base de dados BOLD, incluindo dados sobre identificação taxonómica, dados de colheita e respetivas sequências e cromatogramas. De modo a garantir a qualidade dos resultados foram compiladas 60 sequências publicadas para comparação e classificação das sequências obtidas. As divergências intraespecíficas para os espécimes analisados variaram entre os 0 e os 2,8%, com uma divergência interespecífica média de 29%, variando entre 12% e 59%, comprovando-se a capacidade de descriminação do fragmento COI-5P para as espécies de isópodes em estudo. Foram encontradas 2 linhagens alopátricas de Campecopea lusitanica com 22% de divergência, e 3 linhagens de Dynamene edwardsi separadas entre a costa de Portugal e os arquipélagos da Madeira e Canárias com divergências entre os 18% e 21%. iv Construction of a DNA barcode reference library for marine Isopods (Crustacea: Isopoda) from Portugal and Macaronésia Abstract Although the order Isopoda constitutes one of the most diverse groups of crustaceans, ocurring in a wide range of marine habitats and transition ecosystems, a rigorous and extensive knowldege of its biodiversity has not been reached yet, which may compromise the informed planning and management of the marine environment. The use of DNA barcodes (DNA sequences from the 5´end of the mitochondrial gene cytochrome oxydase I, or COI-5P) reference libraries to aid species identification and inventories of marine macroinvertebrates, has contributed to an improved knowledge of the composition and distribution of these communities, and enabled possible uses of second generation sequencing in in high-throughput monitoring methods. The objectives of this study were: 1) the compilation of an updated checklist for marine isopod species registed in Portuguese continental waters, and the archipelagos of Azores and Madeira; 2) contribute to the construction of a reference library of DNA barcodes for marine isopods from the same regions. The checklist compiles 146 species recorded in a variety of habitats, from deep-sea to coastal, estuarine and lagunar systems. As for the construction of the DNA barcode reference library we obtained 105 DNA sequences, resulting from bidirecional sequencing, assigned to 26 morphospecies and distributed in 32 MOTU´s, from specimens collected along the Northeast Atlantic, mostly along the coast of Portugal and Galiza and in the archipelagos of Azores, Canary and Madeira. Specimens were cataloged in the BOLD database with taxonomic information, collection data, and respective sequence and cromatograms. To assure the quality of the obtained data, 60 published COI-5 sequences were mined to compare and classify the sequences here generated. Intraspecific divergences ranged from 0 to 2,8% for the analysed specimens, and mean interspecific divergence was 29%, (ranging from 12% to 59%), globally confirming the species diagnosis ability of COI-5P barcodes for these isopod species. In addition, we detected two alopatric lineages of Campecopea lusitanica with a divergence of 22%, as well as three divergent lineages of Dynamene edwardsi which split among the west coast of Portugal and the archipelagos of Madeira and Canaries with a divergence ranging between 18 and 21%. The analises of partial sequences from the nuclear gene 18s rRNA of lineage- representative specimens of D. edwardsi confirmed the patterns observed with COI-5P. v Índice Agradecimentos ………………………………………………………………………………………………………iii Resumo …………………………………………………………………………………………………………………iv Abstract ………………………………………………………………………………………………………………….v Índice …………………………………………………………………………………………………………………….vi Índice de figuras ………………………………………………………………………………………………………vii Índice de tabelas ………………………………………………………………………………………………………iv Capítulo 1 Introdução geral 1.1 Diversidade, distribuição e ecologia de Isópodes marinhos (Crustacea: Isopoda)….. 2 1.2 Registo fóssil e classificação da ordem Isopoda…………………………………….…………3 1.3 Importância ecológica e impacto ambiental e económico……………………………….….4 1.4 Impedimento taxonómico e o uso de metodologias moleculares …………………………5 1.5 Objetivos gerais………………………………………………………………………………………....6 Referências……………………………………………………………………………………………….7 Capítulo 2 Checklist de Isópodes marinhos (Crustacea: Isopoda) para a costa de Portugal continental, Açores e Madeira 2.1 Introdução………………………………………………………………………………………..…….15 2.2 Metodologia……………………………………………………………………………………….…..15 2.3 Resultados………………………………………………………………………………………….….16 2.4 Discussão………………………………………………………………………………………………37 Referências…………………………………………………………………………………………………..39 vi Capítulo 3 Construção de uma biblioteca de referência de DNA barcodes para Isópodes marinhos (Crustacea: Isopoda) de Portugal e da Macaronêsia 3.1 Introdução………………………………………………………………………………………………52 3.2 Metodologia……………………………………………………………………………………………53 3.2.1 Material de estudo……………………………………………………………………..53 3.2.2 Inventariação e processamento de amostras…………………………………..54 3.2.3 Extração, amplificação e sequenciação de DNA……………………………….54 3.2.4 Tratamento e análise de dados…………………………………………………….56 Alinhamento e construção de árvores filogenéticas…………………………56 Delimitação de MOTUs……………………………………………………………..57 Classificação dos DNA barcodes da biblioteca de referência…………….57 Teste de saturação de substituição nucleotídica e reconstrução de filogenias profundas……………………………………………………………..58 3.3 Resultados……………………………………………………………………………………………..59 3.3.1 Construção e classificação da biblioteca de referência………………………59 3.3.2 Linhagens divergentes de Dynamene edwardsi………………………………..62 3.3.3 Saturação de substituição nucleotídica…………………………………………..63 3.3.4 Reconstrução filogenética……………………………………………………………64 3.4 Discussão………………………………………………………………………………………………65 3.4.1 Construção da biblioteca de referência…………………………………………..65 3.4.2 Classificação da biblioteca de referência………………………………………..65 3.4.3 Possíveis complexos de linhagens crípticas…………………………………….66 3.4.4 Reconstrução filogenética……………………………………………………………67 Referências…………………………………………………………………………………………………..67 Capítulo 4 Considerações finais…………………………………………………………………………………………..74 Anexos……………………………………………………………………………………………………………….75 vii Índice de figuras Figura 1.1- Locais de amostragem dos espécimes de Isópodes usados para a construção da biblioteca de referência…………………………………………………………………….………………………..53 Figura 1.2- Árvore Neighbour-Joining compactada calculada com o modelo de substituição nucleotídica K2P……………………………………………………………………………………..………………..60
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