Most organisms belonging to the Saccharomycotina subphylum have high
genetic diversity and a vast repertoire of metabolisms and lifestyles,
which explains its ecological versatility. The yeast Lachancea
cidri is an ideal model for exploring the interplay between genetics,
ecological function and evolution. L. cidri is a species that
diverged from the Saccharomyces lineage before the whole-genome
duplication and exhibits a broad distribution across the South
Hemisphere, thus displaying an important ecological success. Here, we
applied phylogenomics to investigate the adaptive genetic variation of
L. cidri isolates obtained from natural environments in Australia
and South America. Our approach revealed the presence of two main
lineages according to their geographic distribution (Aus and SoAm).
Estimation of the divergence time suggest that South American and
Australian lineages diverged near the last glacial maximum event during
the Pleistocene (64-8 KYA), consistent with the presence of multiple
glacial refugia. Interestingly, we found that the French reference
strain belongs to the Australian lineage, with a recent divergence
(405-51 YA), likely associated to human movements. Additionally, species
delimitation analysis identified different evolutionary units within the
South American lineage and, together with parameters like Pi (π) and
FST, revealed that Patagonia contains most of the genetic diversity of
this species. These results agree with phenotypic characterizations,
demonstrating a greater phenotypic diversity in the South American
lineage. These findings support the idea of a Pleistocene-dated
divergence between South Hemisphere lineages, where the Nothofagus and
Araucaria ecological niches likely favored the extensive distribution of
L. cidri in Patagonia.
Genetic diversity of Geophagus brasiliensis from the South American Atlantic Rainforest
