Data from: Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals

Convergent evolution occurs when the same trait arises independently in multiple lineages. In most cases of phenotypic convergence such transitions are adaptive, so finding the underlying molecular causes of convergence can provide insight into the process of adaptation. Convergent evolution at the genomic level also lends itself to study by comparative methods, though molecular convergence can also occur by chance, adding noise to this process. Parker et al. (2013) studied convergence across the genomes of several mammals, including echolocating bats and dolphins. Based on a null distribution of site-specific likelihood support (SSLS) generated using simulated topologies, they concluded that there was evidence for genome-wide adaptive convergence between echolocating taxa. Here we demonstrate that methods based on SSLS do not adequately measure convergence, and reiterate the use of an empirical null model that directly compares convergent substitutions between all pairs of species. We find that when the proper comparisons are made there is no surprising excess of convergence between echolocating mammals, even in sensory genes.趋同演化（Convergent evolution）指同一性状在多个独立演化支系中独立出现的现象。在多数表型趋同（phenotypic convergence）案例中，这类演化转变均为适应性的，因此探明趋同现象背后的分子机制，可为理解适应性演化过程提供重要洞见。基因组水平的趋同演化同样可通过比较方法（comparative methods）开展研究，但分子趋同（molecular convergence）也可能因随机事件发生，为该类研究引入噪声。Parker等人（2013年）对包括回声定位蝙蝠（echolocating bats）与海豚在内的多种哺乳动物的基因组趋同现象展开了研究。其基于模拟拓扑结构生成的位点特异性似然支持值（site-specific likelihood support, SSLS）的零分布，得出回声定位类群间存在全基因组范围适应性趋同的结论。本研究表明，基于SSLS的方法无法充分衡量趋同演化水平，并重申应采用可直接比对所有物种对间趋同替换（convergent substitutions）的经验零模型（empirical null model）。我们发现，在采用恰当比对方式后，并未发现回声定位哺乳动物间存在异常显著的趋同演化过剩现象，即便在感官基因（sensory genes）中亦是如此。