BMC Evol Biol. 2013 Aug 8;13:166. doi: 10.1186/1471-2148-13-166.
Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species.
The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record.
The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.
分子系统发生学为反刍动物进化树提供了前所未有的分辨率。然而，仅使用一个或少数几个（经常误用）化石校准点进行分子年龄估计，导致该分支内的许多重要进化事件的年龄产生了多样性的冲突。我在这里确定了与牛科和反刍动物系统发育相关的 16 个化石校准点，并通过重新分析 100 多种反刍动物的完整线粒体基因组，单独和共同使用这些点来构建一个有时间标记的分子系统发育。
新的多校准树提供的年龄总体上比以前的研究要年轻。其中包括冠反刍动物（39.3-28.8 Ma）和冠牛科（17.3-15.1 Ma）起源的年轻年龄。鉴于许多归入这些类群的基础化石实际上可能位于导致冠群的茎群中，从而夸大了以前的年龄估计，因此这些年龄被认为是合理的假设。然而，分子和化石日期之间仍然存在冲突领域，特别是在快速偶蹄类辐射的基部和麝香科与牛科的姐妹关系方面。单校准分析的结果还表明，使用不同的校准点可以获得非常广泛的分子年龄估计，并且校准点的选择会影响生成树的拓扑结构。与单校准树相比，多校准树的估计年龄方差较小，并且更好地反映了化石记录。
提倡使用大量经过验证的化石校准点和软边界，而不是仅使用一个或几个校准点，或者依赖内部一致性度量来丢弃良好的化石数据，作为一种更好的方法。本研究还强调了在定义高级分类群时考虑类群形态和生态特征的重要性。我还说明了在没有考虑化石记录的情况下，从仅包含现存分类群的树中推断出的系统发生和古环境假设可能会出现问题。纳入反刍动物的化石记录是未来旨在重建该分支进化历史的分析的必要步骤。
