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.