1. Despite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystallized methodological questions is the ‘orthologue conjecture’, the hypothesis that function evolves faster after duplication (i.e. in paralogues), and conversely is conserved between orthologues. Since the mode of functional evolution after duplication is not well known, we investigate under which reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologues and paralogues.
2. We investigate three different simulation models, which represent reasonable but simplified hypotheses about the evolution of a gene function trait. These are time-dependent trait acceleration, correlated changes in rates of both sequence and trait evolution and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age.
3. Both approaches lose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication for trees with many duplications, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the orthologue conjecture under orthologue conjecture simulations, by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well under rapid shifts in traits.
4. Considering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution.

中文翻译：

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在物种形成和复制后的不同性状进化情景下，系统发育独立对比方法和改进的成对比较的性能

1. 尽管基因功能对进化生物学很重要，但比较方法对基因功能的适用性却知之甚少。一个使方法论问题具体化的具体案例是“直向同源物猜想”，即功能在复制后（即在旁系同源物中）进化得更快的假设，相反在直向同源物之间是守恒的。由于复制后的功能进化模式尚不清楚，我们研究了在哪些合理的进化场景下，系统发育独立对比或成对比较可以恢复直向同源物和旁系同源物之间不同功能进化的假定信号。
2. 我们研究了三种不同的模拟模型，它们代表了关于基因功能特征进化的合理但简化的假设。这些是依赖于时间的性状加速、序列和性状进化速率的相关变化以及不对称性状跳跃。对于每个模型，我们测试了系统发育独立对比和改进的成对比较方法，该方法说明了事件和节点年龄之间的相互作用。
3. 当具有许多重复的树的功能特征在重复后长时间加速时，两种方法都失去了检测功能进化趋势的能力，在中间情景下具有更好的系统发育对比能力。通过系统发育独立对比，序列和性状的进化速率在复制后同时增加会导致在性状进化的空模拟下错误拒绝零值，以及在直向同源物猜想模拟下错误拒绝直向同源物猜想。改进的成对比较对这种偏差是稳健的。在性状快速变化的情况下，这两种方法的表现同样出色。
4. 考虑到我们对基因功能进化的无知，以及在简单模型下存在偏差的可能性，我们建议在研究基因家族进化时采用方法论多元化。功能系统基因组学很复杂，只有一种方法支持的结果应谨慎对待。