Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Genetics, Evolution and Environment, University College London, London, UK.
J Evol Biol. 2022 Dec;35(12):1646-1658. doi: 10.1111/jeb.14013. Epub 2022 May 4.
Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.
研究性染色体系统在分化的早期阶段对于理解重组抑制的初始过程和潜在原因至关重要。然而，由于 X 染色体和 Y 染色体之间存在高度的序列相似性，因此识别同形性性染色体的分化特征可能具有挑战性。方法精确性和基础数据的差异可能会导致检测微妙的分化模式或完全错过它们之间存在差异。最近在孔雀鱼中测试 X-Y 序列分化的努力导致了相互矛盾的结果。在这里，我们将不同的分析方法应用于同一数据集，以测试不同方法在识别孔雀鱼性染色体分化模式中的准确性。我们的比较分析表明，不同分析结果的最大变异来源在于所使用的参考基因组。使用焦点种群或物种的定制基因组组装进行的分析成功地在不同的方法中恢复了分化信号。相比之下，使用与孔雀鱼和剑尾鱼之间存在序列进化和结构变异的远缘 Xiphophorus 参考基因组，会导致结果产生可变的模式。映射和过滤参数的变化还会引入噪声并模糊信号。我们的结果说明了分析差异如何改变感知结果，并强调了研究新生性染色体的最佳实践。
