Robust time estimation reconciles views of the antiquity of placental mammals.
Robust time estimation reconciles views of the antiquity of placental mammals.
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稳健的时间估计可以核对胎盘哺乳动物上古的观点。
DOI：
10.1371/journal.pone.0000384
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发表时间：
2007-04-18
期刊：
影响因子：
3.7
通讯作者：
Okuhara, Yoshiyasu
中科院分区：
文献类型：
--
作者：
Kitazoe, Yasuhiro;Kishino, Hirohisa;Waddell, Peter J.;Nakajima, Noriaki;Okabayashi, Takahisa;Watabe, Teruaki;Okuhara, Yoshiyasu
分子研究报告的现代胎盘目分化时间早于白垩纪-第三纪界线，远早于古生物学数据。然而，这种差异可能不是真实的，而是因为在估计过程中违反了隐含的假设，例如进化速率的非渐进变化和未能对收敛进化进行校正。描述了对分子进化速率突变具有鲁棒性的散度时间估计的新方法。我们使用了一种多维向量空间（MVS）过程的变体来考虑可能的收敛进化。对突变速率变化和收敛演化的数值模拟表明，新方法比现有方法具有更好的性能。应用于完整的线粒体基因组鉴定了标记的速率加速和减速，这是目前的方法无法获得的。据估计，胎盘哺乳动物的根比假设对数布朗运动模型时要晚约1800万年。与使用标准最大似然树枝长度相比，使用MVS校正趋同进化的成对距离将树根的年龄降低了约2000万年。这两种方法结合起来，将胎盘哺乳动物的起源时间从大约1.22亿年前修正到接近8400万年前。因此，分子分化时间的估计分布与北美化石记录的定量分析和传统形态学观点大致一致。通过考虑突变速率变化的双重影响和在分子水平上直接考虑趋同进化，这些估计提供了分子结果、古生物分析和形态学预期之间的一致性。这里开发的程序与再现本研究结果的样本数据一起提供，特别适用于使用基因组规模序列长度的研究。
Molecular studies have reported divergence times of modern placental orders long before the Cretaceous–Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution. New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensional vector space (MVS) procedure to take account of possible convergent evolution. Numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods. Application to complete mitochondrial genomes identified marked rate accelerations and decelerations, which are not obtained with current methods. The root of placental mammals is estimated to be ∼18 million years more recent than when assuming a log Brownian motion model. Correcting the pairwise distances for convergent evolution using MVS lowers the age of the root about another 20 million years compared to using standard maximum likelihood tree branch lengths. These two procedures combined revise the root time of placental mammals from around 122 million years ago to close to 84 million years ago. As a result, the estimated distribution of molecular divergence times is broadly consistent with quantitative analysis of the North American fossil record and traditional morphological views. By including the dual effects of abrupt rate change and directly accounting for convergent evolution at the molecular level, these estimates provide congruence between the molecular results, paleontological analyses and morphological expectations. The programs developed here are provided along with sample data that reproduce the results of this study and are especially applicable studies using genome-scale sequence lengths.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
4.1
作者：
Nikaido, M;Cao, Y;Hasegawa, M
通讯作者：
Hasegawa, M
DOI：
10.1073/pnas.95.21.12386
发表时间：
1998-10-13
影响因子：
11.1
作者：
Bromham, L;Rambaut, A;Penny, D
通讯作者：
Penny, D
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
影响因子：
3.5
作者：
Cao, Y;Fujiwara, M;Hasegawa, M
通讯作者：
Hasegawa, M