Lavin Alvar A, Rivas-Santisteban Juan
Department of Systems Biology, Centro Nacional de Biotecnología, Madrid, Spain.
Department of Biology and Biochemistry, University of Bath Milner Centre for Evolution, Bath, UK.
Open Biol. 2025 Mar;15(3):240302. doi: 10.1098/rsob.240302. Epub 2025 Mar 19.
The molecular clock rests upon the assumption that the observed changes among sequences capture the differentiation of lineages, or kinship, as dissimilarity increases with time. Although it has been questioned over the years, this paradigmatic principle continues to underlie the idea that the polymorphic space of a gene is so vast that it is unattainable in evolutionary time. Thus, the molecular clock has been used to obtain taxonomic annotations, proving to be very effective at delivering testable results. In this article, however, we ask how often this assumption leads to inaccuracies when inferring the lineage of prokaryotic genes. Thus, we open an interesting discussion by simulating, in realistic scenarios, the critical times in which specific 5S rRNA sequences of two distant lineages are exhausting the polymorphic space. We contend that certain genes in one lineage will become increasingly similar to those in another over time, as the space for new variants is finite, mimicking phylogenetic features by convergence or by chance, without implying true kinship.
分子钟基于这样一种假设，即随着时间的推移，序列间观察到的变化反映了谱系的分化或亲缘关系，因为差异会随着时间增加。尽管多年来一直受到质疑，但这一范式原则仍然是这样一种观点的基础，即基因的多态空间如此巨大，以至于在进化时间内是无法达到的。因此，分子钟已被用于获得分类注释，事实证明在提供可检验的结果方面非常有效。然而，在本文中，我们要问的是，在推断原核基因谱系时，这种假设导致不准确的情况有多频繁。因此，我们通过在现实场景中模拟两个远缘谱系的特定5S rRNA序列耗尽多态空间的关键时间，展开了一场有趣的讨论。我们认为，随着新变异的空间是有限的，一个谱系中的某些基因会随着时间的推移变得越来越类似于另一个谱系中的基因，通过趋同或偶然模仿系统发育特征，而不意味着真正的亲缘关系。
