Integrating fossil flowers into the angiosperm phylogeny using molecular and morphological evidence

Fossils are essential to infer past evolutionary processes. The assignment
of fossils to extant clades has traditionally relied on morphological
similarity and on apomorphies shared with extant taxa. The use of explicit
phylogenetic analyses to establish fossil affinities has so far remained
limited. In this study, we built a comprehensive framework to investigate
the phylogenetic placement of 24 exceptionally preserved fossil flowers.
For this, we assembled a new species-level dataset of 30 floral traits for
1,201 extant species that were sampled to capture the stem and crown nodes
of all angiosperm families. We explored multiple analytical approaches to
integrate the fossils into the phylogeny, including different phylogenetic
estimation methods, topological-constrained analyses, and combining
molecular and morphological data of extant and fossil species. Our results
were widely consistent across approaches and showed minor differences in
the support of fossils at different phylogenetic positions. The placement
of some fossils agrees with previously suggested relationships, but for
others, a new placement is indicated. We also identified fossils that are
well supported within particular extant families, whereas others showed
high phylogenetic uncertainty. Finally, we present recommendations for
future analyses combining molecular and morphological evidence, regarding
the selection of fossils and appropriate methodologies, and provide some
perspectives on how to integrate fossils into the investigation of
divergence times and the temporal evolution of morphological traits.

化石对于推断古演化进程至关重要。长期以来，将化石划归至现生支系（extant clades）的传统依据为形态相似性，以及与现生类群共有的衍征（apomorphies）。截至目前，借助明确的系统发育分析确定化石亲缘关系的应用仍较为有限。本研究构建了一套综合分析框架，用于探究24枚保存极为完好的化石花的系统发育位置。为此，我们汇编了一套全新的物种级数据集，涵盖1201个现生物种的30项花部性状，采样覆盖了所有被子植物科的茎节点与冠节点。我们探索了多种将化石整合入系统发育树的分析方法，包括不同的系统发育估计方法、拓扑约束分析，以及结合现生与化石物种的分子与形态学数据。不同分析方法下的结果整体一致性较高，仅在不同化石的各系统发育位置支持度上存在细微差异。部分化石的位置与此前提出的亲缘关系假说相符，但另有一些化石则被提示存在新的系统发育位置。我们还发现，部分化石在特定现生科内获得了较高的支持度，而另一些化石则呈现较高的系统发育不确定性。最后，我们就化石筛选与合适方法选择等方面，为未来结合分子与形态学证据的研究提出了建议，并就如何将化石整合进分化时间与形态性状的时间演化研究提供了研究展望。