Many remarkable phenotypes 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 14,785 gene families from 993 Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we found that gene family expansion and contraction were significantly linked to trait gain and loss in 45/56 (80%) traits. While 595/739 (81%) 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. Strikingly, most of these families are known to encode metabolic enzymes and transporters, including all members of the industrially relevant MAL tose fermentation loci in the baker’s yeast Saccharomyces cerevisiae . These results indicate that convergent evolution on the gene family level may be more widespread across deeper timescales than previously believed.

中文翻译：

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关键基因家族的趋同扩增推动了酵母菌的代谢创新

许多显著的表型在巨大的进化距离中反复出现。当生命之树上出现趋同性状时，它们有时由相同的潜在基因家族驱动，而其他时候，则涉及许多不同的基因家族。相反，一个基因家族可能会因单个性状或许多不同的性状而被反复招募。为了了解在基因组和表型水平上控制收敛的一般规则，我们系统地测试了来自 993 个酵母菌属的 14,785 个基因家族中 56 种二元代谢性状与基因计数之间的关联。使用最近开发的减少虚假相关性的系统发育方法，我们发现基因家族的扩增和收缩与 45/56 （80%） 性状的性状获得和丢失显着相关。虽然 595/739 （81%） 的重要基因家族仅与一个性状相关，但我们还确定了几个“关键”基因家族，这些基因家族与高达 13/56 （23%） 的所有性状显著相关。引人注目的是，已知这些家族中的大多数编码代谢酶和转运蛋白，包括面包酵母酿酒酵母中工业相关的 MAL tose 发酵基因座的所有成员。这些结果表明，基因家族水平的趋同进化可能比以前认为的在更深的时间尺度上更广泛。