Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages

The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast''s geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species’ diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

The yeast genus Saccharomyces, which includes S. cerevisiae, is a powerful model system for revealing patterns of genomic variation underlying reproductive isolation and adaptation in eukaryotic microorganisms. Surveys of population genetic data have been used in S. cerevisiae to date the origin of key domestication events (Gallone et al. 2016; Duan et al. 2018; Peter et al. 2018), to determine life cycle frequencies in nature (Tsai et al. 2008), to determine the genomic basis of adaptation at continental scale (Duan et al. 2018; Peter et al. 2018), and, more recently, to establish its geographical origin and dispersal history (Xia et al. 2017). Phylogenomic analyses of the Saccharomyces sensu stricto complex and extensive sequencing of collections across the world suggest that S. cerevisiae originated in East Asia (Duan et al. 2018; Peter et al. 2018). The 1011 Genome Project—the most broad large-scale yeast population genomic study—discovered that three wild isolates from Taiwan showed an unprecedented high genetic diversity compared with populations from the rest of the world (Peter et al. 2018). Population genomics of 266 domestic and wild isolates in China revealed six wild lineages from primeval forests. The newly identified CHN-IX group represents the most diverged lineage (Duan et al. 2018). Isolates from this group and the three Taiwanese isolates were grouped into a single lineage that showed a disjunct geographic distribution (Bendixsen et al. 2021). Although considerable knowledge is available on the biogeography and population genetics of plants and animals across continents (Whittaker et al. 2017), little is known about how eukaryotic microorganisms such as S. cerevisiae disperse, establish, reproduce, and persist in nature (Liti 2015).Most S. cerevisiae biology has been based on experiments on a handful of laboratory domesticated strains, but comprehensive analyses of the ecology and evolutionary biology of S. cerevisiae in the wild are still unavailable. In nature, S. cerevisiae have been isolated from the bark, fruits, surrounding soil, and leaves of plants belonging to several different families (Naumov et al. 2013), with early reports suggesting that the yeast is most successfully isolated from the oak family Fagaceae (Sniegowski et al. 2002; Sampaio and Gonçalves 2008; Wang et al. 2012). S. cerevisiae contains high genetic diversity in certain populations, including lineage-specific variants that display clear population structures (Barnett 1992; Wang et al. 2012; Cromie et al. 2013; Strope et al. 2015; Gallone et al. 2016; Gonçalves et al. 2016; Zhu et al. 2016; Duan et al. 2018; Legras et al. 2018; Peter et al. 2018) and explain phenotypic variance similar to common variants (Fournier et al. 2019). Samples from natural habitats tend to be homozygous diploids forming unique populations with minimal genetic admixture, whereas lineages associated with human activities were likely heterozygous, containing higher ploidy and greater genetic admixture leading to a mosaic genome makeup (Diezmann and Dietrich 2009; Liti et al. 2009; Wang et al. 2012; Almeida et al. 2015). The diverse natural lineages of S. cerevisiae present in East Asia provide an excellent opportunity to study the natural diversity of this species, which was previously believed to be fully domesticated (Fay and Benavides 2005).Taiwan is a continental shelf island with the fifth highest tree density in the world (Crowther et al. 2015). Among the 13 climate-related forests types in Taiwan, five are Fagaceae-dominated natural forests on low- and mid-elevation mountains (Li et al. 2013), thus a potentially ideal natural habitat for S. cerevisiae. Taiwan also harbors a high phylogenetic diversity of flowering plants (53 out of 64 angiosperm orders present under the APG IV classification system) (Lin and Chung 2017) and endemism compared with other oceanic islands (Hsieh 2002), raising the possibility that the associated microbial populations are genetically different from their continental counterparts. Here, we set out to characterize the intra-genetic diversity, relative abundance, and distribution of S. cerevisiae in Taiwanese forests over 4 yr of broad sampling. Our study provides novel insights of the predomestication phase of S. cerevisiae and broadens our understanding of the ecological and biogeographic implications before anthropogenic impacts.     

Red-cell GSH regeneration and glutathione reductase activity in G6PD variants in the Ferrara area

Summary. Red-cell studies were carried out on three groups of G6PD-deficient subjects with different G6PD variants from the Ferrara area of Northern Italy. Red-cell GSH and activities of G6PD, glutathione reductase (GR), glutathione peroxidase (GPx) and superoxide dismutase (SOD) were measured. A method was developed to measure red-cell GSH regeneration after oxidation of endogenous GSH in whole blood by diamide and only this clearly distinguished the variants from each other and from normal. Regeneration by 1 h was lowest in the Mediterranean variant, 0–10.2% in contrast to 93–98% in normal. A predisposition to a haemolytic crisis after ingestion of fava beans was not clearcut, but subjects appeared to be at risk if GSH regeneration at 1 h was less than 30% of the endogenous level, and red-cell FAD⁺ was very high indicated by high in vitro GR activity and inhibition by added FAD⁺.
It is suggested that the most informative tests in G6PD deficiency are measurements of GSH regeneration in intact red cells plus GR activity and/or red-cell flavin compounds.     

Polymorphisms of the Z protein protease inhibitor and risk of venous thromboembolism: a meta-analysis

Two nonsense polymorphisms of Z-dependent protease inhibitor (ZPI; Serpina10) have been identified. To assess the risk of venous thromboembolism (VTE) associated with W303x and R67X Serpina10 mutations, we performed a meta-analysis of studies comparing the prevalence of these two mutations in VTE patients and in controls Odds Ratios (ORs) and 95% confidence intervals (CIs) were calculated for each trial and pooled using a random-effects model. Five studies involving 5000 patients were included. R67X and W303X mutations of Serpina10 were not associated with increased VTE risk (OR 1.63; 95% CI 0.84, 3.16 and OR 1.21; 95% CI 0.29, 4.98 respectively).     

How general practitioners perceive and grade the cardiovascular risk of their patients.

BACKGROUND: Although risk assessment charts have been proposed to identify patients at high cardiovascular risk, in everyday practice general practitioners (GPs) often use their knowledge of the patients to estimate the risk subjectively. DESIGN: A cross-sectional study aimed to describe how GPs perceive, qualify and grade cardiovascular risk in everyday practice. METHODS: General practitioners had to identify in a random sample of 10% of their contacts the first 20 consecutive patients perceived as being at cardiovascular risk. For each patient essential data were collected on clinical history, physical examination and laboratory tests, for the qualification of risk. At the end of the process GPs subjectively estimated the overall patient's level of risk. General practitioners grading was compared with the risk estimate from a reference chart. RESULTS: Over a mean time of 25 days 3120 patients perceived as being at cardiovascular risk were enrolled. According to the inclusion scheme each GP had contact with more than 200 patients at cardiovascular risk every month. Thirty percent of these patients had atherosclerotic diseases. Up to 72% of patients without any history of atherosclerotic diseases but perceived to be at risk could be classified according to a reference chart as being at moderate to very high risk. Comparing GPs' grading of risk with a chart estimate there was agreement in 42% of the cases. Major determinants of GPs' underestimation of risk were age, sex and smoking habits, while obesity and family history were independently associated with overestimation. CONCLUSIONS: On the basis of their perception GPs properly identify patients at cardiovascular risk in the majority of cases. General practitioners subjective grading of risk level only partially agreed with that given by a chart.