Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China

Abstract

The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages.Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus. Take away• S. paradoxus is distributed in temperate to subtropical climate zones in China.• A novel highly diverged ancient lineage of S. paradoxus is identified.• S. paradoxus exhibits higher genetic diversity in Eurasia than in America.

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

“…The influence of temperature during diversification might be one of the reasons why we observe frequent introgressions in the mitochondrial genome [45][46][47][48] , where speciesspecific mitotypes have been shown to strongly affect temperature tolerance 52,81 . Clear patterns of differentiation by geographic distribution and climatic conditions have also been detected for Saccharomyces mitotypes 26,33,67,82,83 .…”

“…Saccharomyces diversification within and outside of Asia in association with plants Several authors have postulated Asia as the geographical origin of S. cerevisiae and other species of Saccharomyces 13,22,25,28,37,66,67 . Our present results provide evidence to support several rounds of speciation in Asia, as well as potentially the origin of the genus itself: (i) the high genomic diversity in the Palearctic biogeographic realm, which includes Asia; (ii) the centrality of Palearctic mitochondrial haplotypes to the mitochondrial network; (iii) and ancestral polymorphisms in Asian strains that generate phylogenetic conflict and, in some cases, such as the GAL loci, phenotypic differences that are likely under strong selection.…”

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

“…The influence of temperature during the diversification might be one of the reasons why we observe frequent introgressions in the mitochondrial genome [44][45][46][47] , where speciesspecific mitotypes have been shown to strongly affect temperature tolerance 50,79 . Clear patterns of differentiation by geographic distribution and climatic conditions have also been detected for Saccharomyces mitotypes 26,33,65,80,81 .…”

“…Several authors have postulated Asia as the geographical origin of S. cerevisiae and other species of Saccharomyces 13, 22, 25, 28, 37, 64, 65 . Our present results provide evidence to support several rounds of speciation in Asia, as well as potentially the origin of the genus itself: i) the high genomic diversity in the Palearctic biogeographic realm, which includes Asia; ii) the centrality of Palearctic mitochondrial haplotypes to the mitochondrial network; iii) and ancestral polymorphisms in Asian strains that generate phylogenetic conflict and, in some cases, such as the GAL loci, phenotypic differences that are likely under strong selection.…”

Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages

“…In nature, single genetically homogenous fungal populations are generally found in distinct geographical regions as a result of isolation by distance (IBD) (Branco et al 2017;Chung et al 2017;He et al 2022). In contrast, the presence of multiple S. cerevisiae lineages at the same locality in Taiwan, even on the same tree, is striking (Fig.…”