18S ribosomal RNA and tetrapod phylogeny

@article{Xia2003, abstract = {Previous phylogenetic analyses of tetrapod 18S ribosomal RNA ( rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms ( p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11: 152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by ( 1) the misalignment of the sequences, ( 2) the inappropriate use of the frequency parameters, and ( 3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species.}, author = {Xia, X. H. and Xie, Z. and Kjer, K. M. }, citeulike-article-id = {2345296}, journal = {Systematic Biology}, keywords = {alignment, animals, bibtex-import, birds, fossils, mammals, morphology, vertebrates}, number = {3}, pages = {283--295}, posted-at = {2008-02-06 23:58:30}, priority = {2}, title = {18S ribosomal RNA and tetrapod phylogeny}, volume = {52}, year = {2003} }

TY - JOUR ID - Xia2003 L3 - citeulike-article-id:2345296 TI - 18S ribosomal RNA and tetrapod phylogeny JF - Systematic Biology VL - 52 IS - 3 SP - 283 EP - 295 N2 - Previous phylogenetic analyses of tetrapod 18S ribosomal RNA ( rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms ( p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11: 152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by ( 1) the misalignment of the sequences, ( 2) the inappropriate use of the frequency parameters, and ( 3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species. KW - alignment KW - animals KW - bibtex-import KW - birds KW - fossils KW - mammals KW - morphology KW - vertebrates AU - Xia, XH AU - Xie, Z AU - Kjer, KM PY - 2003/// ER -