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The yeast  Lachancea thermotolerans  (formerly  Kluyveromyces thermotolerans ) is a species with remarkable, yet underexplored, biotechnological potential. This ubiquist occupies a range of natural and anthropic habitats covering a wide geographic span. To gain an insight into  L .  thermotolerans  population diversity and structure, 172 isolates sourced from diverse habitats worldwide were analysed using a set of 14 microsatellite markers. The resultant clustering revealed that the evolution of  L .  thermotolerans  has been driven by the geography and ecological niche of the isolation sources. Isolates originating from anthropic environments, in particular grapes and wine, were genetically close, thus suggesting domestication events within the species. The observed clustering was further validated by several means including, population structure analysis, F-statistics, Mantel’s test and the analysis of molecular variance (AMOVA). Phenotypic performance of isolates was tested using several growth substrates and physicochemical conditions, providing added support for the clustering. Altogether, this study sheds light on the genotypic and phenotypic diversity of  L .  thermotolerans , contributing to a better understanding of the population structure, ecology and evolution of this non- Saccharomyces  yeast.

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems