David Kyle T, Schraiber Joshua G, Crandall Johnathan G, Labella Abigal L, Opulente Dana A, Harrison Marie-Claire, Wolters John F, Zhou Xiaofan, Shen Xing-Xing, Groenewald Marizeth, Hittinger Chris Todd, Pennell Matt, Rokas Antonis
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles CA 90089, USA.
bioRxiv. 2024 Jul 23:2024.07.22.604484. doi: 10.1101/2024.07.22.604484.
Many remarkable innovations have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,710 gene families from 993 species of yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we discovered that gene family expansion and contraction was significantly linked to trait gain and loss in 45/56 (80%) of traits. While 601/746 (81%) of significant gene families were associated with only one trait, we also identified several 'keystone' gene families that were significantly associated with up to 13/56 (23%) of all traits. These results indicate that metabolic innovations in yeasts are governed by a narrow set of major genetic elements and mechanisms.
许多显著的创新在漫长的进化历程中反复出现。当趋同性状出现在生命之树上时，它们有时由相同的基础基因家族驱动，而有时则涉及许多不同的基因家族。相反，一个基因家族可能会被反复用于单一性状或许多不同性状。为了理解在基因组和表型水平上控制趋同现象的一般规律，我们系统地测试了993种酵母的14710个基因家族中56种二元代谢性状与基因数量之间的关联。使用一种最近开发的系统发育方法来减少虚假相关性，我们发现基因家族的扩张和收缩与45/56（80%）的性状获得和丧失显著相关。虽然601/746（81%）的显著基因家族仅与一种性状相关，但我们也鉴定出了几个“关键”基因家族，它们与多达13/56（23%）的所有性状显著相关。这些结果表明，酵母中的代谢创新受一组狭窄的主要遗传元件和机制的控制。
