DISCUSSION
Large-scale population genomics studies performed onSaccharomyces spp. allowed us to understand yeast dynamics in
nature and their association with anthropogenic environments (Peter and
Schacherer, 2016). In this sense, the analysis of complete genomes and
the use of molecular markers aided the understanding of the natural
genetic diversity in Saccharomyces populations and highlights how
they adapt to the environments which they inhabit (Almeida et al., 2015;
Almeida et al., 2014; Bendixsen et al., 2021; Parts et al., 2021; Peter
and Schacherer, 2016). In the last decade, advances in sequencing
technologies have made it possible to extrapolate this type of study to
non-model species that have long been overlooked (Bansal and Boucher,
2019; Dujon and Louis, 2017). L. cidri , a non-model species, is
an attractive model to study since it’s a Crabtree-positive yeast
located phylogenetically before the whole-genome duplication (Porter et
al., 2019b; Vakirlis et al., 2016), and which exhibits substantial
biotechnological potential for fermentation (Villarreal et al., 2021).
In contrast to Saccharomyces spp., which are mostly diploid in
nature (Almeida et al., 2014; Nespolo et al., 2020b; Peter et al.,
2018), L. cidri isolates are haploids, which might be indicative
of a different reproductive cycle. It has been reported that even with
identical genomes, ploidy itself is known to have different effects on
yeasts. Therefore, understanding how ploidy affects the ecology and
evolution of organisms has long been a topic of interest (Gerstein et
al., 2011; Gerstein and Otto, 2009). Haploid yeasts have a competitive
advantage over diploid yeasts. For example, one of the main differences
between the two ploidy levels is cell size, where differences in volume
have been shown to directly affect relative fitness in some
environments. Under nutrient stress, for example, where a limited
concentration of nutrients diffuses across the cell membrane, haploid
organisms would have a greater advantage, likely favoring their survival
under extreme environmental conditions (Gerstein et al., 2011).
Our results demonstrate that L. cidri is widely-distributed in
Patagonia. In fact, L. cidri is found between latitudes 35 °S and
45 °S in Australia and Patagonia, which in general are considered
non-Mediterranean (cold regions). However, L. cidri was not found
in extreme southern regions such as Tierra del Fuego (54 °S), probably
due to southern Patagonia’s extreme cold climatic conditions, where the
temperature is below freezing for a large fraction of the year (Ponce JF
and M., 2014). Samples obtained in South America were collected from
tree species belonging to the genera Nothofagus andAraucaria in National Parks from Chile, covering approximately
1,000 km of territory. Then, the biogeographical history of the South
American population of L. cidri correlates well with the history
and distribution of the Nothofagus forest, comparable to reports
for other species isolated in Patagonia (Saccharomyces and
non-Saccharomyces ) (Nespolo et al., 2020b). Our results agree
with previous findings, where it has been demonstrated that L.
cidri exhibits significant host preference, being more frequently
isolated from N. dombeyi in Patagonia (Nespolo et al., 2020b;
Villarreal et al., 2021). In this way, this study, together with
previous studies in Saccharomyces yeasts from forests ecosystems
(Cadez et al., 2021; Langdon et al., 2020; Libkind et al., 2011; Nespolo
et al., 2020b) demonstrate the impact of the Nothofagus biome
(Woodward et al., 2004) across the southern hemisphere on the current
distribution of the Lachancea genus throughout Patagonia.
The phylogenomic analysis of wild L. cidri strains demonstrates
the remarkable genetic diversity present in South America. Unlike
Australia, where isolates were collected from a smaller territory and
showed relatively low genetic variation (Varela et al., 2020), in South
America, a broad geographic distribution with varied seasonal and
spatial variation generated an enormous genetic differentiation and
nucleotide diversity. Therefore, our population structure analysis,
developed with different strategies, generated a consistent phylogenetic
picture: two populations depending on geographic origin (SoAm and Aus),
with the Australian isolates forming a tight cluster with the reference
strain from France (CBS2950). The Australian population shows a low
genetic diversity (π = 0,00005), indicating a recent common ancestor.
Despite the large geographic distance between Australian isolates and
the French reference strain, we found a low genetic differentiation
between both, which would suggest a recent exchange between Australia
and Europe, likely coalescing between 405 to 51 years ago. In contrast,
the variability found within the South American population is in
accordance with the different localities from which the isolates were
obtained. The different environmental conditions and the extensive
distribution of the Nothofagus forest in Patagonia likely
facilitated the presence of a unique genetic diversity (Cadez et al.,
2019; Cubillos et al., 2019; Nespolo et al., 2020b; Villarreal et al.,
2021), which is reflected in our study. In the same way, the phenotypic
data corroborates the large genetic diversity observed in Patagonia.
Although it has been reported that genetic diversity is not always a
reflection of diversity at the physiological level (Banilas et al.,
2016; Pfliegler et al., 2014), we were able to demonstrate how a greater
diversity at the genetic level is determinant when performing phenotypic
analyses under natural and stressful conditions.
The divergence between Australian and South America strains is
interesting and deserves attention. The split could have originated in
the Cretaceous-Early Tertiary interchange when Nothofagusoriginated, and continents were separated (Hill, 1992). The absence of
fossil records for yeasts complicates the interpretation, but the
geographic origin of our samples, the high association with native
forests with a well-documented phylogeographic history (e.g., (Acosta et
al., 2014; Hinojosa et al., 2016), and the genetic differences found inL. cidri from South America permit to delineate some hypotheses.
The last glacial maximum (LGM) during the Late Pleistocene
(~35,000 years ago, see Davies et al. 2020)(Davies et
al., 2020) resulted in an ice cover that expanded through the south of
South America from latitude 53°S to 38ºS, leaving only few areas free of
ice, such as Altos de Lircay (Hewitt, 2000; Hinojosa, 1997). Thus, most
areas including Coyhaique were covered by the ice, and present-day
plants and animals are young populations that colonized the area either
from Argentina or from coastal refuges, during the last
~10,000 years. This large isolation barrier would
explain the divergence observed between the South American L.
cidri populations, unlike the French and Australian strains that likely
migrated because of human movements.
In summary, our results demonstrate the presence of two
genetically-different populations in L. cidri . In the same way,
it is possible to suggest that the geographic location and the
ecological niche (host) where each isolate was found are essential
factors in determining the genetic differentiation and nucleotide
diversity observed in this species. Our results show a high
phylogeographic structure among the localities of South America. The
high diversity, species delimitation method and genetic differences
between Altos de Lircay populations and southern populations in
Patagonia suggest that the former represents a different evolutionary
unit. This is a striking result, since the unique conditions of
Patagonia during the Late Pleistocene could have contributed to the
differentiation of L. cidri populations in South America.
Furthermore, we propose that there was a recent exchange between
Australia and France due to the low genetic differentiation between
strains from both regions. In conclusion, this work provides a valuable
insight into the genetic and phenotypic diversity of L. cidri ,
contributing to a better understanding of phylogeography, population
structure, ecology, and divergence time of this underexplored yeast
species, with remarkable biotechnological potential.