Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods, which use phylogenies to infer the evolution of traits. The development of ancestral state reconstruction (ASR) methods has provided the tools to reconstruct trait evolution, which are widely used in fields like evolutionary biology, macroecology and paleontology. As there are different elements involved in those analyses, with different levels of uncertainty (i.e. relating to branch length estimation, trait coding, statistical framework, taxon sampling or software), the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits, potentially leading to opposite conclusions. To assess the impact of these different elements in ASR, we performed a set of analyses, including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study, which was coded as a continuous or as a discrete character. Our results show that taxon sampling, character coding, tree shape, statistical framework and software all significantly affect ASR, both individually and in combination. Not all reconstructed tree nodes show discrepancies, but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results (zero migration vs fully migratory), thus challenging interpretations of trait evolution. We propose some possible solutions to partly inform decisions, involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve, but our results demand serious rethinking about how the research community currently uses ASR.

中文翻译：

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估计祖先国家重建的挑战：以西尔维亚莺为例的迁徙演变。

我们目前对物种如何进化的理解主要是基于比较系统进化方法，该方法使用系统进化论来推断性状的进化。祖先状态重建（ASR）方法的发展提供了重建性状进化的工具，这些工具广泛用于进化生物学，宏观生态学和古生物学等领域。由于这些分析涉及不同的元素，不确定性程度不同（即，与分支长度估计，性状编码，统计框架，分类群抽样或软件有关），因此这些元素的各种组合可能对重构的影响很大。特征的演变，可能导致相反的结论。为了评估这些不同元素对ASR的影响，我们进行了一系列分析，西尔维亚鸣鸟作为案例研究，被编码为连续字符或离散字符。我们的结果表明，分类单元抽样，字符编码，树形，统计框架和软件都对ASR产生了重大影响，无论是单独还是组合使用。并非所有重建的树节点都显示出差异，但是在关键的树节点之间，大多数成对比较都导致分析之间的冲突和出乎意料的拮抗结果（零迁移与完全迁移），从而挑战了性状进化的解释。我们提出了一些可能的解决方案，以部分地为决策提供依据，包括选择方法以及纳入有关性状如何进化的生物学或化石证据，但是我们的结果需要认真思考研究界当前如何使用ASR。