Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.
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DOI：
10.1186/1741-7007-6-6
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发表时间：
2008-01-28
期刊：
影响因子：
5.4
通讯作者：
Mindell DP
中科院分区：
文献类型：
--
作者：
Brown JW;Rest JS;García-Moreno J;Sorenson MD;Mindell DP
确定鸟类进化史的绝对时间尺度已被证明是有争议的。现有的两个信息来源，古生物学数据和从现存分子遗传序列推断化石记录支持大多数现代谱系起源于新生代，而分子遗传学估计表明，这些相同的谱系起源于白垩纪深处，并在K-Pg中幸存下来。（白垩纪-古近纪;以前的白垩纪-第三纪或K-T）大规模灭绝事件。因此，这两个数据来源似乎支持根本不同的鸟类进化模型。这一悖论被推测为反映了化石记录中的缺陷，遗传数据处理中未被认识到的偏见，或者两者兼而有之。在这里，我们试图探索不确定性和限制偏见进入分子分歧时间估计通过：（i）改进的分类群（n = 135）和字符（n = 4594 bp mtDNA）取样;（ii）包括多个分支学测试的内部化石校准点（n = 18）;（iii）使用多种方法校正谱系特异性速率异质性（n = 5）;（iv）适应树拓扑结构中的不确定性;（v）测试情节演化的可能影响。各种“放松时钟”的方法都表明，现代鸟类的主要（基础）谱系起源于白垩纪深处，虽然时间intraordinal多样化模式不同的方法。我们发现，拓扑的不确定性有一个系统的，但主要分支的起源日期估计的影响较小，贝叶斯分析假设固定的拓扑结构提供类似的结果与无约束的拓扑结构分析。我们还发现，与预期相反，替代率是不自相关的整个树的祖先后代的方式。最后，我们没有发现与物种形成事件或K-Pg边界相关的情节性分子进化的特征，这些特征可能会系统地误导遗传数据的推断。一些人认为“岩石时钟”的缺口是由于分子遗传分歧时间估计的变幻莫测。然而，尽管采取措施，探索不同形式的不确定性，在几个关键参数，我们未能调和分子遗传分歧的时间估计与化石记录的日期，相反，我们发现有力的支持现代鸟类谱系的古老起源，与许多现存的订单和家庭出现在白垩纪中期，与以前的分子估计一致。虽然有足够的空间来改善双方的'岩石时钟'鸿沟（例如，解释化石记录中的“幽灵”谱系，并为分子遗传序列开发更现实的速率进化模型），这两个数据来源之间的一致和明显的分歧更可能反映了（i）茎群起源和（ii）冠-组形态多样性，分别。在这个问题上的进一步进展将受益于古生物学家和分子生物学遗传学家在解释鸟类谱系年龄估计错误方面的更多交流。
Determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, 'rocks' and 'clocks'), have appeared irreconcilable; the fossil record supports a Cenozoic origin for most modern lineages, whereas molecular genetic estimates suggest that these same lineages originated deep within the Cretaceous and survived the K-Pg (Cretaceous-Paleogene; formerly Cretaceous-Tertiary or K-T) mass-extinction event. These two sources of data therefore appear to support fundamentally different models of avian evolution. The paradox has been speculated to reflect deficiencies in the fossil record, unrecognized biases in the treatment of genetic data or both. Here we attempt to explore uncertainty and limit bias entering into molecular divergence time estimates through: (i) improved taxon (n = 135) and character (n = 4594 bp mtDNA) sampling; (ii) inclusion of multiple cladistically tested internal fossil calibration points (n = 18); (iii) correction for lineage-specific rate heterogeneity using a variety of methods (n = 5); (iv) accommodation of uncertainty in tree topology; and (v) testing for possible effects of episodic evolution. The various 'relaxed clock' methods all indicate that the major (basal) lineages of modern birds originated deep within the Cretaceous, although temporal intraordinal diversification patterns differ across methods. We find that topological uncertainty had a systematic but minor influence on date estimates for the origins of major clades, and Bayesian analyses assuming fixed topologies deliver similar results to analyses with unconstrained topologies. We also find that, contrary to expectation, rates of substitution are not autocorrelated across the tree in an ancestor-descendent fashion. Finally, we find no signature of episodic molecular evolution related to either speciation events or the K-Pg boundary that could systematically mislead inferences from genetic data. The 'rock-clock' gap has been interpreted by some to be a result of the vagaries of molecular genetic divergence time estimates. However, despite measures to explore different forms of uncertainty in several key parameters, we fail to reconcile molecular genetic divergence time estimates with dates taken from the fossil record; instead, we find strong support for an ancient origin of modern bird lineages, with many extant orders and families arising in the mid-Cretaceous, consistent with previous molecular estimates. Although there is ample room for improvement on both sides of the 'rock-clock' divide (e.g. accounting for 'ghost' lineages in the fossil record and developing more realistic models of rate evolution for molecular genetic sequences), the consistent and conspicuous disagreement between these two sources of data more likely reflects a genuine difference between estimated ages of (i) stem-group origins and (ii) crown-group morphological diversifications, respectively. Further progress on this problem will benefit from greater communication between paleontologists and molecular phylogeneticists in accounting for error in avian lineage age estimates.
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DOI：
10.1046/j.1095-8312.2003.00222.x
发表时间：
2003-09-01
影响因子：
1.9
作者：
Cubo, J
通讯作者：
Cubo, J
影响因子：
1.5
作者：
Clarke, Julia A.;Chiappe, Luis M.
通讯作者：
Chiappe, Luis M.
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：
64.8
作者：
Benton, MJ;Wills, MA;Hitchin, R
通讯作者：
Hitchin, R
影响因子：
3.3
作者：
Castric, V;Bonney, F;Bernatchez, L
通讯作者：
Bernatchez, L