Angiosperm divergence times:: The effect of genes, codon positions, and time constraints
Angiosperm divergence times:: The effect of genes, codon positions, and time constraints
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DOI：
10.1554/04-565.1
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发表时间：
2005-08-01
期刊：
影响因子：
3.3
通讯作者：
Sanderson, MJ
中科院分区：
文献类型：
--
作者：
Magallón, SA;Sanderson, MJ
要了解现代陆地生态系统的进化，就必须了解与被子植物进化相关的动力学，包括它们的起源时间和多样化到今天非同寻常的多样性。对被子植物年龄的分子估计有很大的不同，许多估计在早白垩纪化石出现之前就已经存在了。在本研究中，研究了不同基因、密码子位置和时间限制对节点年龄的影响，并对种子植物的分化时间估计进行了研究，特别关注被子植物。惩罚似然被用来估计种子植物的系统发育假设上的发散时间，从贝叶斯分析中得到，用最大似然估计分支长度。质体基因atpB、psaA、psbB和rbcL被单独或组合使用，使用第一、第二、第三和三个密码子位置，包括和排除20个节点的年龄限制，这些节点来自陆地植物化石记录的严格检查。采用惩罚似然法对每个无约束和约束数据集进行最优平滑。对分子钟的测试显示，在所有数据集中都有明显的类似解锁的速率。再加上化石的限制，导致更大程度上偏离了恒常性。与时钟的显著偏差一致，估计的最佳平滑值很低，但没有发现速率异质性与最佳平滑值之间的严格相关性。整个系统发育中节点的年龄估计随着基因和密码子的位置而变化，有时很大。然而，基于四个连接基因的估计与四个单个基因估计的平均值非常相似。对于任何给定的节点，不受约束的年龄估计比受约束的估计更不稳定，而且往往比得到充分证实的进化分支的化石成员更年轻。对进化枝年龄的有约束估计比无约束估计和最古老的化石代表更古老，有时两者相差甚远。随着速率平滑的增加，被子植物的年龄估计值降低。尽管无约束的被子植物年龄估计的范围跨越了该分支的化石时代，但约束估计的范围比最早的被子植物化石更窄（也更古老）。结果明确地表明，约束因素在减少来自不同数据分区的年龄变异性和减少平滑参数的影响方面具有相关性。在整个系统发育中，对分化时间和替代率的约束优化表明被子植物和裸子植物的进化动力学明显不同。裸子植物的冠群在种子植物出现后不久就出现了，而冠群被子植物的出现则经过了很长一段时间。尽管被子植物和被子植物枝的绝对年龄估计比它们最早的化石要早，但系统发育多样化的估计速度在很大程度上与地层序列中被子植物谱系的快速出现一致。
An understanding of the evolution of modern terrestrial ecosystems requires an understanding of the dynamics associated with angiosperm evolution, including the timing of their origin and diversification into their extraordinary present-day diversity. Molecular estimates of angiosperm age have varied widely, and many substantially predate the Early Cretaceous fossil appearance of the group. In this study, the effect of different genes, codon positions, and chronological constraints on node ages are examined on divergence time estimates across seed plants, with a special focus on angiosperms. Penalized likelihood was used to estimate divergence times on a phylogenetic hypothesis for seed plants derived from Bayesian analysis, with branch lengths estimated with maximum likelihood. The plastid genes atpB, psaA, psbB, and rbcL were used individually and in combination, using first and second, third, and the three codon positions, including and excluding age constraints on 20 nodes derived from a critical examination of the land-plant fossil record. The optimal level of rate smoothing according to each unconstrained and constrained dataset was obtained with penalized likelihood. Tests for a molecular clock revealed significantly unclocklike rates in all datasets. Addition of fossil constraints resulted in even greater departures from constancy. Consistently with significant deviations from a clock, estimated optimal smoothing values were low, but a strict correlation between rate heterogeneity and optimal smoothing value was not found. Age estimates for nodes across the phylogeny varied, sometimes substantially, with gene and codon position. Nevertheless, estimates based on the four concatenated genes are very similar to the mean of the four individual gene estimates. For any given node, unconstrained age estimates are more variable than constrained estimates and are frequently younger than well-substantiated fossil members of the clade. Constrained estimates of ages of clades are older than unconstrained estimates and oldest fossil representatives, sometimes substantially so. Angiosperm age estimates decreased as rate smoothing increased. Whereas the range of unconstrained angiosperm age estimates spans the fossil age of the clade, the range of constrained estimates is narrower (and older) than the earliest angiosperm fossils. Results unambiguously indicate the relevance of constraints in reducing the variability of ages derived from different partitions of the data and diminishing the effect of the smoothing parameter. Constrained optimizations of divergence times and substitution rates across the phylogeny suggest appreciably different evolutionary dynamics for angiosperms and for gymnosperms. Whereas the gymnosperm crown group originated shortly after the origin of seed plants, a long time elapsed before the origin of crown group angiosperms. Although absolute age estimates of angiosperms and angiosperm clades are older than their earliest fossils, the estimated pace of phylogenetic diversification largely agrees with the rapid appearance of angiosperm lineages in stratigraphic sequences.