Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings
Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings
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DOI：
10.1016/j.gene.2007.10.001
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发表时间：
2008-01-15
期刊：
影响因子：
3.5
通讯作者：
Sumida, Masayuki
中科院分区：
文献类型：
--
作者：
Igawa, Takeshi;Kurabayashi, Atsushi;Sumida, Masayuki
本研究测定了日本林蛙、中华大蟾蜍和小口蟾蜍的线粒体全基因组序列。这些基因组的基因排列与基础无尾两栖动物(古无尾两栖动物亚目)的基因排列不同，但与衍生蛙类成员(新无尾无尾两栖亚目的Hyloidae和Ranoidae超科)的基因排列相同，表明在衍生无尾两栖动物的祖先谱系中发生了一次性的基因重排事件。此外，在日本血吸虫和日本血吸虫的控制区(CRS)中观察到了几个不同的重复基序，包括假定的终止相关序列(TASS)和保守序列块(CSB)，而在日本血吸虫的控制区中没有发现重复基序。利用mt基因的核苷酸和氨基酸数据进行的系统发育分析支持新臂尾类的单系分类。根据多个参考点的氨基酸数据估算的分化时间表明，这三个现存的两栖动物目可能起源于石炭纪，无尾两栖动物的分化发生在二叠纪和第三纪之间。我们还考察了数据类型和参考时间的设置对发散时间估计的影响。从几个数据集和参考时间设置估计的结果分歧时间表明，核苷酸数据的替代饱和可能导致高估(即较老的)分支时间，特别是对于早期分歧的分类群。我们还发现，新臂尾轮虫腐烂基因的替换率很高，快速替换可能会导致高估。为了纠正这种错误的估计，在新臂尾类中应用几个参考点是有效的。(C)2007爱思唯尔B.V保留所有权利。
We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian rot genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians. (c) 2007 Elsevier B.V All rights reserved.