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).