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) |
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Authors: | M A T Marinho A C M Junqueira A M L Azeredo-Espin |
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Institution: | (1) Molecular Biology and Genetic Engineering Center (CBMEG), Campinas State University (UNICAMP), CP 6010, Campinas, SP, 13083-875, Brazil;(2) Department of Genetics and Evolution (DGE), Biology Institute (IB), Campinas State University (UNICAMP), CP 6010, Campinas, SP, 13083-875, Brazil |
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Abstract: | 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. |
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