Figures
Figure 1. Geographic distribution and phylogeny of L. cidri isolates. (a) World map depicting the different locations whereL. cidri were isolated. In Chile, strains were obtained from seven sampling locations. (b) Maximum likelihood tree depicting the genetic relationships between 56 strains using 218,266 biallelic SNPs (substitution model GTR+F+ASC) and manually-rooted with L. fermentati as the outgroup.
Figure 2. Population structure of L. cidri. (a) Plot of the genomic variation distribution of 56 L. cidri strains based on the first two components of a PCA performed using 13,275 unlinked SNPs. Each dot represents a single strain. The black arrow denotes strains from Altos de Lircay National Park (AL). (b) PCA only considering strains from Patagonia. The colored PCA reflects the grouping by location. Villarrica National Park (VI), Huilo-Huilo Biological Reserve (HH), Valdivian Coastal Reserve (VCR), Osorno Volcano (OV), Chiloé National Park (CH), and Coyhaique National Reserve (CY).(c) STRUCTURE and ADMIXTURE. An optimum K = 2 group is shown in both cases. (d) Heat map of a Co-ancestry matrix obtained using fineSTRUCTURE chunk counts. Each row and column represents an isolated color indicating genetic sharing (yellow = low sharing, blue = high sharing). The tree shows the clusters inferred from the co-ancestry matrix. (e) F ST values between localities, using the same abbreviations shown in (b) as well as Central Plateau of Tasmania (CP), Australia. (f) IBD (Isolation by distance) estimates considering seven localities of southern Chile. The density of data points is indicated by colors.
Figure 3. Species delimitation and divergence time analysis inL. cidri populations . (a) DensiTrees gathered in the Bayesian analyses using StarBEAST calculated from 13 concatenated genes. Color blocks identify distinct candidate species based on genetic groups. Values in nodes correspond to the Bayesian inference result of the species tree. CBS2959 (French reference strain), and strains from Australia (Aus), Altos de Lircay National Park (AL), Huilo-Huilo Biological Reserve (HH), and Coyhaique National Reserve (CY).(b) Estimation of the divergence time since the last common ancestor between groups. Time between (1) Australia lineage and SoAm lineage; Time between (2) Australia lineage and CBS2950. Timeline in Million’s years (Ky).
Fig. 4. Phenotypic diversity across L. cidri populations. (a) Heat map depicting the phenotypic diversity in L. cidriobtained from growth parameter using 12 different microculture conditions. Strains are grouped by hierarchical clustering; colors indicate the lineages (Australia (Aus) and South America (SoAm)), locality (Altos de Lircay National Park (AL), Villarrica National Park (VI), Huilo-Huilo Biological Reserve (HH), Valdivian Coastal Reserve (VCR), Osorno Volcano (OV), Chiloé National Park (CH), Coyhaique National Reserve (CY), Central Plateau of Tasmania (CP), Australia, and France (FR)) and isolation altitude (high altitude (HA) and low altitude (LA)). The heat map was elaborated based on the z-score of µmax (h-1). (b) Fitness (µmax h-1) variation in 6% v/v ethanol. Asterisks indicate statistically-significant differences according to the t-test (*p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001).