How Brewer's Yeast Evolves UpdatesUnravelling the genetic basis of the remarkable phenotypic diversity observed in natural populations remains a central challenge in biology. That's the opening sentence of a deep genomic analysis of Brewer's yeast, a species comprising a wide range of different strains. The genomic analysts, coordinated at the University of Strasbourg, France, promise, This study addresses a critical gap in our understanding of how different types of genetic variation contribute to phenotypic diversity. Great. High time (1, 2).Right away, the research team observes that structural variants (SVs), including insertions, deletions, duplications and rearrangements, are far more important than single-nucleotide polymorphisms (SNPs - which are easier to study. (It's worth remembering that SNPs were once the putative source of all phenotpic variation in life, but no longer.)) Are SVs the source of yeast's diversity? Apparently so, because this study can correlate them with the phenotypic differences they produce. First, the yeast genes fall into definite categories, much like the "core genome" and "pan genome" of prokaryotes (3). Here however, the core genome is far larger than that observed in prokaryotes, and the pan genes are divided into three subgroups. Only 129 "singletons" were noticed. The "U-shape" of the bargraph of panel a below is especially pronounced (compare to ref 3). The analysis is insightful and "open access." The deep coverage of this study makes it especially edifying.
Where do the genes come from?Panel d of the figure above includes a "Gene origin" listing with five categories. First, Reference genes were already known to be existing yeast genes, so no "origin" is proposed for them. Next, To investigate the origin of non-reference genes, we aligned novel gene sequences to a curated eukaryotic database. Most of them were apparently close relatives of known Saccharomyces genes, suggesting "Introgression" from related species. Next, 358 were most similar to genes from unrelated species, which would indicate horizontal gene transfers (HGTs). In another category, 516 genes appear to have diverged from non-reference Saccharomyces genes; these were labeled "Fast-evolving." Finally, 92 De novo genes seemed to have come from nowhere — or possibly by HGT from an undiscovered source?The "Gene origin" heading should instead be "Gene source," because no origins are explained. Only the "Fast-evolving" ones have even the potential to provide an origin, and they are still classified wih their apparent paralogs. Perhaps the most they exemplify is microevolution, or exploration and optimization within a limited range. The only certifiable "new" genes in the study are the de novo ones, and even they lack identifiable "origins." Meanwhile, evolution by the acquisition of existing genes gets robust support in the study. Updates 24 Oct 2025: Fungi evolved much earlier than the fossil record indicates?
References1. "From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes," by Loegler, V., Thiele, P., Teyssonnière, E. et al, doi:10.1038/s41586-025-09637-0, Nature, 15 Oct 2025.
2. "From Genomes to Traits: 1,086 Yeast Mapped," Bioengineer, 16 Oct 2025.
3. How Prokaryotes Evolve
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