The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths
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DOI：
10.1016/j.gene.2005.01.008
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发表时间：
2005-04-11
期刊：
影响因子：
3.5
通讯作者：
Nishida, M
中科院分区：
文献类型：
--
作者：
Inoue, JG;Miya, M;Nishida, M
我们测定了印尼腔棘鱼Latimeria menadosis的线粒体基因组全序列。基因组内容和组织结构与典型脊椎动物包括科摩罗腔棘鱼、文昌鱼等完全相同。两个物种之间的核苷酸总差异(不包括对照区域)为4.28%。这两个物种之间的分化时间是使用来自两个腔棘鱼和26个放线蕨类的完整线粒体基因组数据估计的，这些放线蕨类代表了主要的放线蕨类谱系和一个外群。对来自12个蛋白质编码基因(不包括ND6基因)的串联氨基酸序列和来自12个蛋白质编码基因(没有第三密码子位置)、22个转移RNA基因和两个核糖体RNA基因的串联核苷酸序列进行了分割贝叶斯分析。在去除进化较快或较慢的序列后，还对12个蛋白质编码基因的串联氨基酸序列进行了分子时钟分析。以石棺-光化蕨裂解体为校准点(450Mya)，估算出的Menadoensis和Chalumnae的分歧时间为40-30Mya，比前人的研究结果(<；6.3Mya)要早得多。假设Latimeria的最新祖先沿着穿越欧亚大陆的非洲深海岸连续分布，我们的估计与印度与欧亚大陆(50 Mya)的碰撞以及随后主要河流的形成造成的淤积导致腔棘鱼栖息地分离导致印度两侧种群分化的假设是一致的。(C)2005 Elsevier B.V.保留所有权利。
We determined the whole mitochondrial genome sequence for Indonesian coelacanth Latimeria menadoensis. The genome content and organization were identical to that of typical vertebrates including Comoran coelacanth, Latimeria chalumnae. The overall nucleotide differences between the two species (excluding the control region) was 4.28%. The divergence time between the two species was estimated using whole mitochondrial genome data from the two coelacanths and 26 actinopterygians that represent major actinopterygian lineages plus an outgroup. Partitioned Bayesian analyses were conducted with the two data sets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding ND6 gene) and concatenated nucleotide sequences from 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The molecular clock analysis was also conducted with the concatenated amino acid sequences from the 12 protein-coding genes after removing faster or more slowly evolving sequences. Using the sarcopterygian-actinopterygian split as a calibration point (450 Mya), divergence time estimation between L. menadoensis and L. chalumnae fell in the range of 40-30 Mya, which is much older than those of the previous studies (< 6.3 Mya). Assuming that the most recent ancestor of Latimeria was distributed continuously along the deep coasts of Africa through Eurasia, our estimate is in agreement with the hypothesis that the collision of India with Eurasia (50 Mya) and the subsequent siltation caused by the formation of major rivers resulted in a coelacanth habitat disjunction that allowed populations on either side of India to diverge. (c) 2005 Elsevier B.V. All rights reserved.