Previous phylogenetic analyses of the auraria species complex have led to conflicting hypotheses concerning their relationship;therefore the addition of new sequence data is necessary to discover the phylogeny of this...Previous phylogenetic analyses of the auraria species complex have led to conflicting hypotheses concerning their relationship;therefore the addition of new sequence data is necessary to discover the phylogeny of this species complex. Here we present new data derived from 22 genes to reconstruct the phylogeny of the auraria species complex. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny. Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (21,882 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships. Phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset show that D. subauraria was well supported as the first species by separated analysis, concatenated dataset analysis, and some previous analysis, then followed by D. auraria and D. biauraria, D. quadraria and D. triauraria. The close relationships of D. quadraria and D. triauraria were consistent with most previous studies. The phylogenetic position of the D. auraria and D. biauraria will be resolved by more data sets.展开更多
从NCBI数据库在线网站搜集了赤霉素受体基因核苷酸序列,分析了所获基因的进化关系。结果表明,植物的98个GID1基因拥有共同的根系,进化为Group A、Group B、Group C和Group D 4组。Group A GID1基因在单子叶植物纲中没有GID1a、GID1b、GI...从NCBI数据库在线网站搜集了赤霉素受体基因核苷酸序列,分析了所获基因的进化关系。结果表明,植物的98个GID1基因拥有共同的根系,进化为Group A、Group B、Group C和Group D 4组。Group A GID1基因在单子叶植物纲中没有GID1a、GID1b、GID1c分类现象,在双子叶植物纲中基因有简单的Group B GID1b,Group C GID1a,且GID1c聚类现象;Group D由被子植物门单子叶植物和双子叶植物及苔藓植物门小立苔藓植物的基因组成;GID1基因组在进化过程中可能出现复制突变,所有GID1基因具有相同的保守区域,可利用基因之间的保守性来克隆未知基因;102条序列归属于91种植物,尚有更多单子叶植物、裸子植物和蕨类植物的GID1基因有待克隆。展开更多
DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA seque...DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.展开更多
文摘Previous phylogenetic analyses of the auraria species complex have led to conflicting hypotheses concerning their relationship;therefore the addition of new sequence data is necessary to discover the phylogeny of this species complex. Here we present new data derived from 22 genes to reconstruct the phylogeny of the auraria species complex. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny. Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (21,882 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships. Phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset show that D. subauraria was well supported as the first species by separated analysis, concatenated dataset analysis, and some previous analysis, then followed by D. auraria and D. biauraria, D. quadraria and D. triauraria. The close relationships of D. quadraria and D. triauraria were consistent with most previous studies. The phylogenetic position of the D. auraria and D. biauraria will be resolved by more data sets.
文摘从NCBI数据库在线网站搜集了赤霉素受体基因核苷酸序列,分析了所获基因的进化关系。结果表明,植物的98个GID1基因拥有共同的根系,进化为Group A、Group B、Group C和Group D 4组。Group A GID1基因在单子叶植物纲中没有GID1a、GID1b、GID1c分类现象,在双子叶植物纲中基因有简单的Group B GID1b,Group C GID1a,且GID1c聚类现象;Group D由被子植物门单子叶植物和双子叶植物及苔藓植物门小立苔藓植物的基因组成;GID1基因组在进化过程中可能出现复制突变,所有GID1基因具有相同的保守区域,可利用基因之间的保守性来克隆未知基因;102条序列归属于91种植物,尚有更多单子叶植物、裸子植物和蕨类植物的GID1基因有待克隆。
基金supported by the National Natural Science Foundation of China(No.60371046).
文摘DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.
