Pleistocene dated divergence between the main evolutionary units in L. cidri
Given the genetic divergence of the AL clade and considering the distribution of SNPs according to the PCA, the clustering in the co-ancestry matrix in fineSTRUCTURE and the highF ST values compared to the rest of the SoAm populations, we evaluated the possibility that the group of isolates from AL could represent a different lineage or evolutionary unit in the species. For this, we performed a species delimitation analyses according to the different models generated, and hypothesized the presence of 1 to 4 genetically-different linages or groups utilizing CBS2950, Aus, AL, HH and CY as representatives of the different lineages (Fig. 3a). The Bayes factor species delimitation (SNAPP) analysis supported the scenario where AL represents a different evolutionary unit in the species (model 4, Fig 3a), exhibiting the highest Bayes factor (-180457.18) (Table S2) and a high Bayesian support (IB = 1, Fig 3a). In addition, this analysis also predicts the presence of 4 different groups separating HH and CY as a different unit (Table S2); however, the Bayesian support in the species tree was low and therefore these could not be considered as different evolutionary unit (IB= 0.75, Fig 3a). Altogether, this suggests the presence of 3 different evolutionary units in L. cidri : Aus, AL and SoAm.
Considering the results obtained, we use the population genomic data to estimate the divergence time since the most recent common ancestor between lineages. Following the same strategy as previously used forL. kluyveri and S. cerevisiae (Friedrich et al., 2015; Ruderfer et al., 2006) we predicted the number of generations that have passed since the divergence of any two groups. Our data lead to an estimation of 23.9 x 106 generations since the most recent common ancestor in L. cidri . In the Australian lineage, we obtained an estimation of 1.5 x 105 generation since the most recent common ancestor of the Australian strains and the reference CBS2950 strain. In contrast to this, when we analyzed the number of generations of the AL most recent common ancestor, we obtain 23 x 106 generations. Considering that cell division of yeast in the wild ranges from 1 to 8 generations per day (Fay and Benavides, 2005), the divergence time of the Australia and South America lineage correspond to approximately 64-8 KYA (Fig 3b), dating back to the upper Pleistocene. On the other hand, the divergence of the Australian strains and the CBS2950 strain is very recent and corresponds to approximately 405-51 YA (Fig 3b). Finally, the coalescence time of the AL lineage would correspond to approximately 62-7.8 KYA.