An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.
An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.
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DOI：
10.1093/sysbio/syx061
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发表时间：
2018-01-01
影响因子：
6.5
通讯作者：
Yang Z
中科院分区：
文献类型：
--
作者：
Angelis K;Álvarez-Carretero S;Dos Reis M;Yang Z
分子序列数据的爆炸性生长使使用带有许多基因基因座的基因组规模数据集在松弛的锁定模型下估计物种差异时间。为了改善模型现实主义和最佳提取有关序列数据中相对差异时间的信息，重要的是要说明跨基因或基因组区域的进化过程中的异质性。分区是实现这些目标的常用方法。我们将具有相似进化特征的站点分组到同一分区中，而具有不同特征的分区中的站点则将不同的分区分组，然后使用不同的模型或模型参数的不同值进行不同分区来说明分区之间的异质性。但是，如何在实用系统发育分析中分配数据，尤其是在放松的锁定分析中，比科学更重要。在这里，我们使用计算机仿真和实际数据分析来研究分区方案对差异时间估计的影响。当先前的假设正确并且时钟没有严重侵犯时，分区方案对后时间估计的准确性有相对较小的影响，但是当时钟被严重违反时，化石校准处于冲突或不正确时，或者在速率上遇到了很大的差异，或者当速率是错误的情况下。串联产生的后间隔最大，精度最低。如《无限位置理论》所预测的那样，许多分区的使用提高了精度，但是由于化石校准或错误指定的速率先验，后间隔可能无法包括真实年龄。我们分析了来自15种植物物种的78个质体基因的数据集，这些植物违反了严重的时钟，并表明分区方案之间的时间估计值显着差异，而与使用的速率漂移模型无关。多重和精确的化石校准减少了分区方案之间的差异，对于提高差异时间估计的精度很重要。尽管使用许多分区是减少后时间估计中不确定性的重要方法，但鉴于当前汇率漂移模型对分区数据的局限性以及解释化石证据以构建准确且内容丰富的校准的挑战，我们不建议其对当前的一般使用。
The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into different partitions, and then use different models or different values of model parameters for different partitions to account for the among-partition heterogeneity. However, how to partition data in practical phylogenetic analysis, and in particular in relaxed-clock dating analysis, is more art than science. Here, we use computer simulation and real data analysis to study the impact of the partition scheme on divergence time estimation. The partition schemes had relatively minor effects on the accuracy of posterior time estimates when the prior assumptions were correct and the clock was not seriously violated, but showed large differences when the clock was seriously violated, when the fossil calibrations were in conflict or incorrect, or when the rate prior was mis-specified. Concatenation produced the widest posterior intervals with the least precision. Use of many partitions increased the precision, as predicted by the infinite-sites theory, but the posterior intervals might fail to include the true ages because of the conflicting fossil calibrations or mis-specified rate priors. We analyzed a data set of 78 plastid genes from 15 plant species with serious clock violation and showed that time estimates differed significantly among partition schemes, irrespective of the rate drift model used. Multiple and precise fossil calibrations reduced the differences among partition schemes and were important to improving the precision of divergence time estimates. While the use of many partitions is an important approach to reducing the uncertainty in posterior time estimates, we do not recommend its general use for the present, given the limitations of current models of rate drift for partitioned data and the challenges of interpreting the fossil evidence to construct accurate and informative calibrations.
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先验率对多个基因座发散时间的贝叶斯估计的影响。
影响因子：
6.5
作者：
Dos Reis M;Zhu T;Yang Z
通讯作者：
Yang Z
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
9.4
作者：
Clarke, John T.;Warnock, Rachel C. M.;Donoghue, Philip C. J.
通讯作者：
Donoghue, Philip C. J.
影响因子：
10.7
作者：
Kainer, David;Lanfear, Robert
通讯作者：
Lanfear, Robert
影响因子：
--
作者：
Ho, Simon Y. W.;Lanfear, Robert
通讯作者：
Lanfear, Robert