Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera: Calliphoridae)

Autor(es)

Marinho, M. A. T. ^[1] ; Junqueira, A. C. M. ^[1] ; Azeredo-Espin, A. M. L. ^{[1, 2]}

Afiliação do(s) autor(es)

^[1] Campinas State Univ UNICAMP, Mol Biol & Genet Engn Ctr CBMEG, BR-13083875 Campinas, SP - Brazil

^[2] Campinas State Univ UNICAMP, Dept Genet & Evolut DGE, Biol Inst IB, BR-13083875 Campinas, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: Genetica; v. 139, n. 9, p. 1189-1207, 2011.
• Citações Web of Science: 11

Resumo

The internal transcribed spacer 2 (ITS2) is a small non-coding region located inside the nuclear ribosomal DNA cluster. ITS2 sequence variability is thought to be appropriate to differentiate species and for phylogenetic reconstructions analyses, which can be further improved if structural information is considered. We evaluated the potential of ITS2 as a molecular marker for phylogenetic inference in Calliphoridae (Diptera: Brachycera) using a broad range of inference methods and different substitution models, accounting or not for structural information. Sequence analyses revealed a hierarchically organized pattern of sequence variation and a small level of nucleotide substitution saturation. Intragenomic variation due to small sequence repeats was found mainly in the most variable domain (IV), but it has no significant impact on the phylogenetic signal at the species level. Inferred secondary structures revealed that GC pairs are more frequently found flanking bulges and loops regions in more conserved domains, thus ensuring structure stability. In the phylogenetic analyses, the use of substitution models accounting for structural information significantly improves phylogenetic inference in both neighbour-joining and Bayesian analyses, although the former provides limited resolution for dealing with highly divergent sequences. For Bayesian analyses, a significant improvement in likelihood was observed when considering structure information, although with small changes in topology and overall support, probably reflecting better evolutionary rates estimates. Based on these findings, ITS2 is a suitable molecular marker for phylogenetic analyses in Calliphoridae, at both species and generic level. (AU)

• Processo FAPESP: 08/56769-2 - Genômica mitocondrial e filogenia molecular do grupo Schizophora (Diptera: Brachycera) utilizando sequenciamento de nova geração
• Beneficiário: Ana Carolina Martins Junqueira
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 05/50100-5 - Caracterizacao do its2 do rdna como marcador molecular em moscas causadoras de miiases (diptera: calliphoridae).
• Beneficiário: Marco Antonio Tonus Marinho
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 06/61217-3 - Organização e estrutura do ITS2 em Calyptratae (Diptera: Brachycera) e sua implicação em estudos genético-evolutivos em moscas causadoras de miíases da família Calliphoridae
• Beneficiário: Marco Antonio Tonus Marinho
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto