Data from: Gene tree discordance causes apparent substitution rate variation

Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide data sets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as Substitutions Produced by ILS (SPILS). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant topologies are most affected by SPILS. Finally, we use data from multiple Drosophila species to show that SPILS can be detected in nature. Although the effects of SPILS are modest per gene, it has the potential to affect substitution rate variation whenever high levels of ILS are present, particularly in rapid radiations. The problems outlined here have implications for character mapping of any type of trait, and for any biological process that causes discordance. We discuss possible solutions to these problems, and areas in which they are likely to have caused faulty inferences of convergence and accelerated evolution.

已知由于多种复杂的生物学过程，不同基因、染色体、物种及演化支系间的替换速率存在显著差异。本研究探讨了另一类替换速率变异的来源，即与基因树不一致（gene tree discordance）相关的技术偏倚。全基因组数据集内普遍存在基因树不一致现象，其主要诱因是不完全谱系分选（incomplete lineage sorting, ILS）。当在单一固定的物种树框架下分析存在于冲突基因树上的替换时，便会产生此类表观替换速率变异。这类替换需要通过在物种树上引入多重替换来解析，因此我们将这一现象命名为不完全谱系分选产生的替换（Substitutions Produced by ILS, SPILS）。我们通过模拟实验证实，SPILS的效应随ILS水平升高而增强，且在类群数量更多的系统发育树中更为显著。物种树的特定演化支会被一致但错误地推断为更长或更短，我们证明可基于冲突树的拓扑结构预测这些支系。此外，我们发现，在开展正选择检验时固定物种树拓扑结构会提升假阳性率，尤其对于那些冲突拓扑结构受SPILS影响最为显著的基因。最后，我们利用多个果蝇（Drosophila）物种的基因组数据证实，SPILS现象可在自然种群中被检测到。尽管单个基因的SPILS效应较为微弱，但只要存在高水平的ILS，尤其是在快速辐射演化的类群中，SPILS便有可能对替换速率变异产生影响。本文阐述的问题对任何类型性状的特征映射，以及任何会引发基因树不一致的生物学过程均具有参考意义。我们讨论了这类问题的可能解决方案，以及它们可能导致趋同演化和加速演化的错误推断的研究领域。