caa a22 4500 44584499X CHVBK 20180317145356.0 cr unu---uuuuu 170323e20110901xx s 000 0 eng 10.1007/s10709-011-9621-x doi (NATIONALLICENCE)springer-10.1007/s10709-011-9621-x 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) [Elektronische Daten] [M. Marinho, A. Junqueira, A. Azeredo-Espin] 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. Springer Science+Business Media B.V., 2011 ITS2 nationallicence Internal transcribed spacer 2 nationallicence Secondary structure nationallicence Calliphoridae nationallicence Marinho M. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut Junqueira A. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut Azeredo-Espin A. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut Genetica Springer Netherlands 139/9(2011-09-01), 1189-1207 0016-6707 139:9<1189 2011 139 10709 https://doi.org/10.1007/s10709-011-9621-x text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10709-011-9621-x text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Marinho M. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut NATIONALLICENCE 700 1- Junqueira A. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut NATIONALLICENCE 700 1- Azeredo-Espin A. Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, 13083-875, Campinas, SP, Brazil aut NATIONALLICENCE 773 0- Genetica Springer Netherlands 139/9(2011-09-01), 1189-1207 0016-6707 139:9<1189 2011 139 10709 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer