Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation.
Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation.
复制标题
DOI：
10.1371/journal.pone.0027138
复制
发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Morin PA
中科院分区：
文献类型：
--
作者：
Duchêne S;Archer FI;Vilstrup J;Caballero S;Morin PA
由于分子生物学的最新技术进步，线粒体基因组序列的可用性正在增长。在系统发育分析中，完整的有丝分裂基因组正日益成为首选的标记，通常提供更好的系统发育分辨率和精度相对于传统的标记，如细胞色素B（CYTB）和控制区（CR）。在某些情况下，有丝分裂基因组标记和单基因标记之间的系统发育估计的差异产生了不一致的结论。通过比较不同基因的系统发育估计，我们确定了信息量最大的线粒体区域，并评估了复制与有丝分裂基因组相同结果所需的最小数据量。我们比较了个别基因和最近发表的完整的有丝分裂基因组数据集选定的飞燕（Delphinidae）和虎鲸（属Orcinus）的结果。使用贝叶斯系统发育方法，我们调查了两个数据集的基因之间的拓扑结构，分歧日期和时钟行为的估计差异。尽管每个分类群的最具信息性的区域并不相同（巨鲸属的COX1、CYTB、ND3和ATP 6，以及海豚科的ND1、COX1和ND4），但在这两种情况下，它们都相当于不到完整有丝分裂基因组的四分之一。这表明，基因信息内容可以在组之间变化，但可以充分代表的一部分完整的序列。虽然我们的研究结果表明，完整的有丝分裂基因组提供了最高的系统发育分辨率和最精确的日期估计，最小量的数据可以选择使用我们的方法时，完整的序列不可用。基于单基因的研究可以受益于添加更多的线粒体标记，产生类似于使用整个有丝分裂基因组获得的拓扑结构和日期估计。
The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.
登录
查看更多内容
DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
3.3
作者：
Foote, Andrew D.;Morin, Phillip A.;da Fonseca, Rute R.
通讯作者：
da Fonseca, Rute R.
影响因子：
--
作者：
Ho, Simon Y. W.;Lanfear, Robert
通讯作者：
Lanfear, Robert
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
DOI：
10.1098/rstb.1986.0011
发表时间：
1986-01-29
期刊：
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES
影响因子：
--
作者：
AVISE, JC
通讯作者：
AVISE, JC