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)

dc.creatorMarinho, MAT
dc.creatorJunqueira, ACM
dc.creatorAzeredo-Espin, AML
dc.date2011
dc.dateSEP
dc.date2014-07-30T17:29:37Z
dc.date2015-11-26T16:46:47Z
dc.date2014-07-30T17:29:37Z
dc.date2015-11-26T16:46:47Z
dc.date.accessioned2018-03-28T23:32:43Z
dc.date.available2018-03-28T23:32:43Z
dc.identifierGenetica. Springer, v. 139, n. 9, n. 1189, n. 1207, 2011.
dc.identifier0016-6707
dc.identifier1573-6857
dc.identifierWOS:000298607800011
dc.identifier10.1007/s10709-011-9621-x
dc.identifierhttp://www.repositorio.unicamp.br/jspui/handle/REPOSIP/65988
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/65988
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1274638
dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.descriptionThe 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.
dc.description139
dc.description9
dc.description1189
dc.description1207
dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.descriptionFAPESP [09/51723, 05/50100-5, 06/61217-3, 08/56769-2]
dc.languageen
dc.publisherSpringer
dc.publisherDordrecht
dc.publisherHolanda
dc.relationGenetica
dc.relationGenetica
dc.rightsfechado
dc.rightshttp://www.springer.com/open+access/authors+rights?SGWID=0-176704-12-683201-0
dc.sourceWeb of Science
dc.subjectITS2
dc.subjectInternal transcribed spacer 2
dc.subjectSecondary structure
dc.subjectCalliphoridae
dc.subjectRibosomal-rna Genes
dc.subjectGenus Lucilia Diptera
dc.subjectDna-sequences
dc.subjectMitochondrial Genome
dc.subjectConcerted Evolution
dc.subjectMaximum-likelihood
dc.subjectSaccharomyces-cerevisiae
dc.subjectBlowflies Calliphoridae
dc.subjectSpecies Identification
dc.subjectBayesian Phylogenetics
dc.titleEvaluation 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)
dc.typeArtículos de revistas


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