Trier University, Department of Biogeography, Universitätsring 15, 54296 Trier, Germany.
Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
Mol Phylogenet Evol. 2019 May;134:211-225. doi: 10.1016/j.ympev.2019.02.013. Epub 2019 Feb 21.
Reconstructing reliable timescales for species evolution is an important and indispensable goal of modern biogeography. However, many factors influence the estimation of divergence times, and uncertainty in the inferred time trees remains a major issue that is often insufficiently acknowledged. We here focus on a fundamental problem of time tree analysis: the combination of slow-evolving (nuclear DNA) and fast-evolving (mitochondrial DNA) markers in a single time tree. Both markers differ in their suitability to infer divergences at different time scales (the 'genome-timescale-dilemma'). However, strategies to infer shallow and deep divergences in a single time tree have rarely been compared empirically. Using Mediterranean amphibians as model system that is exceptional in its geographic and taxonomic completeness of available genetic information, we analyze 202 lineages of western Palearctic amphibians across the entire Mediterranean region. We compiled data of four nuclear and five mitochondrial genes and used twelve fossil calibration points widely acknowledged for amphibian evolution. We reconstruct time trees for an extensive lineage-level data set and compare the performances of the different trees: the first tree is based on primary fossil calibration and mitochondrial DNA, while the second tree is based on a combination of primary fossil and on secondary calibrations taken from a nuclear tree using mitochondrial DNA (two-step protocol). Focusing on a set of nodes that are most likely explained by vicariance, we statistically compare the reconstructed alternative time trees by applying a biogeographical plausibility test. Our two-step protocol outperformed the alternative approach in terms of spatial and temporal plausibility. It allows us to infer scenarios for Mediterranean amphibian evolution in eight geographic provinces. We identified several tectonic and climatic events explaining the majority of Mediterranean amphibian divergences, with Plio-Pleistocene climatic fluctuations being the dominant driver for intrageneric evolution. However, often more than one event could be invoked for a specific split. We give recommendations for the use of secondary calibrations in future molecular clock analyses at the community level.
重建物种进化的可靠时间尺度是现代生物地理学的一个重要和不可或缺的目标。然而，许多因素影响着分歧时间的估计，推断时间树上的不确定性仍然是一个主要问题，而这个问题往往没有得到足够的承认。我们在这里关注时间树分析的一个基本问题：在单个时间树上结合慢速进化（核 DNA）和快速进化（线粒体 DNA）的标记。这两种标记在推断不同时间尺度上的分歧时的适用性不同（“基因组-时间尺度困境”）。然而，在单个时间树上推断浅层和深层分歧的策略很少被经验性地比较。使用地中海两栖动物作为模型系统，该系统在其可用遗传信息的地理和分类完整性方面非常特殊，我们分析了整个地中海地区的 202 个西部古北界两栖动物谱系。我们编译了四个核基因和五个线粒体基因的数据，并使用了广泛认可的 12 个化石校准点来研究两栖动物的进化。我们为广泛的谱系水平数据集重建时间树，并比较了不同树木的性能：第一棵树基于主要化石校准和线粒体 DNA，而第二棵树基于主要化石和使用线粒体 DNA 从核树中获取的次要校准的组合（两步协议）。我们专注于一组最有可能通过隔离解释的节点，通过应用生物地理可能性测试来统计比较重建的替代时间树。我们的两步协议在空间和时间上的可能性方面优于替代方法。它使我们能够推断出八种地理区域中地中海两栖动物进化的情景。我们确定了几个构造和气候事件，这些事件解释了大多数地中海两栖动物的分歧，其中上新世-更新世气候波动是种内进化的主要驱动因素。然而，对于特定的分裂，通常可以援引多个事件。我们为未来在社区层面进行分子钟分析中使用次要校准提供了建议。
