scholarly journals The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus

2006 ◽  
Vol 361 (1475) ◽  
pp. 1941-1946 ◽  
Author(s):  
Vassiliki Koufopanou ◽  
Joseph Hughes ◽  
Graham Bell ◽  
Austin Burt
Keyword(s):  
Genetic Differentiation ◽  
Population Genomics ◽  
Model Organism ◽  
Physical Distance ◽  
Saccharomyces Paradoxus ◽  
Population Genetic Differentiation ◽  
Wild Yeast ◽  
Oak Trees ◽  
Eukaryotic Microbes ◽  
Well Differentiated

Little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. We studied the spatial distribution of genetic variation in Saccharomyces paradoxus , the wild relative of Saccharomyces cerevisiae , from the scale of a few centimetres on individual oak trees to thousands of kilometres across different continents. Genealogical analysis of six loci shows that isolates from Europe form a single recombining population, and within this population genetic differentiation increases with physical distance. Between different continents, strains are more divergent and genealogically independent, indicating well-differentiated lineages that may be in the process of speciation. Such replicated populations will be useful for studies in population genomics.

scholarly journals Brewing potential of the wild yeast species Saccharomyces paradoxus

2020 ◽  
Vol 246 (11) ◽  
pp. 2283-2297 ◽  
Author(s):  
Jarkko Nikulin ◽  
Virve Vidgren ◽  
Kristoffer Krogerus ◽  
Frederico Magalhães ◽  
Seija Valkeemäki ◽  
...  
Keyword(s):  
Pilot Scale ◽  
Lag Phase ◽  
Yeast Fermentation ◽  
Lager Yeast ◽  
Saccharomyces Paradoxus ◽  
Beer Brewing ◽  
Wild Yeast ◽  
Oak Trees ◽  
Wild Strains ◽  
Selling Point

Abstract Saccharomyces paradoxus is commonly isolated from environmental samples in Northern Europe and North America, but is rarely found associated with fermentation. However, as novelty has become a selling point in beer markets, interest toward non-conventional and local yeasts is increasing. Here, we report the first comprehensive investigation of the brewing potential of the species. Eight wild strains of S. paradoxus were isolated from oak trees growing naturally in Finland, screened in a series of fermentation trials and the most promising strain was selected for lager beer brewing at pilot scale (40 l). Yeasts were evaluated according to their ability to utilize wort sugars, their production of flavour-active aroma volatiles, diacetyl and organic acids, and sensorial quality of beers produced. All strains could assimilate maltose but this occurred after a considerable lag phase. Once adapted, most wild strains reached attenuation rates close to 70%. Adaptation to maltose could be maintained by re-pitching and with appropriate handling of the adapted yeast. Fermentation at 15 °C with the best performing strain was completed in 17 days. Maltose was consumed as efficiently as with a reference lager yeast, but no maltotriose use was observed. Bottled beers were evaluated by a trained sensory panel, and were generally rated as good as, or better than, reference beers. S. paradoxus beers were considered full-bodied and had a relatively clean flavour profile despite the presence of the clove-like 4-vinyl guaiacol. In conclusion, S. paradoxus exhibits a number of traits relevant to brewing, and with appropriate handling could be applied industrially.

scholarly journals Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

2008 ◽  
Vol 105 (12) ◽  
pp. 4957-4962 ◽  
Author(s):  
I. J. Tsai ◽  
D. Bensasson ◽  
A. Burt ◽  
V. Koufopanou
Keyword(s):  
Life Cycle ◽  
Population Genomics ◽  
Saccharomyces Paradoxus ◽  
Wild Yeast

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals Loss-of-function in IRF2BPL is associated with neurological phenotypes

2018 ◽  
Author(s):  
Paul C. Marcogliese ◽  
Vandana Shashi ◽  
Rebecca C. Spillmann ◽  
Nicholas Stong ◽  
Jill A. Rosenfeld ◽  
...  
Keyword(s):  
Nervous System ◽  
Population Genomics ◽  
Stop Codon ◽  
Ectopic Expression ◽  
Premature Stop Codon ◽  
Model Organism ◽  
Global Developmental Delay ◽  
Mendelian Disease ◽  
Loss Of Function ◽  
Missense Variants

AbstractThe Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) gene encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals affected with neurological symptoms who carry damaging heterozygous variants in IRF2BPL. Five cases carrying nonsense variants in IRF2BPL resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The bioinformatics signature for IRF2BPL based on population genomics is consistent with a gene that is intolerant to variation. We show that the IRF2BPL ortholog in the fruit fly, called pits (protein interacting with Ttk69 and Sin3A), is broadly expressed including the nervous system. Complete loss of pits is lethal early in development, whereas partial knock-down with RNA interference in neurons leads to neurodegeneration, revealing requirement for this gene in proper neuronal function and maintenance. The nonsense variants in IRF2BPL identified in patients behave as severe loss-of-function alleles in this model organism, while ectopic expression of the missense variants leads to a range of phenotypes. Taken together, IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.

scholarly journals The Timing and Direction of Introgression Under the Multispecies Network Coalescent

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 1059-1073 ◽  
Author(s):  
Mark S. Hibbins ◽  
Matthew W. Hahn
Keyword(s):  
Statistical Methods ◽  
Biological Process ◽  
Genomic Data ◽  
Hybrid Speciation ◽  
Saccharomyces Paradoxus ◽  
Genomic Signatures ◽  
Wild Yeast ◽  
Other Information ◽  
Homoploid Hybrid ◽  
New Statistics

Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus—a proposed example of HHS—demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

scholarly journals Spatial Structure and Genetic Variation of a Mangrove Species (Avicennia marina (Forssk.) Vierh) in the Farasan Archipelago

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1287
Author(s):  
Rahmah N. Al-Qthanin ◽  
Samah A. Alharbi
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Conservation ◽  
Natural Populations ◽  
Avicennia Marina ◽  
Conservation Strategies ◽  
Isolated Populations ◽  
Mangrove Species ◽  
Population Genetic Differentiation ◽  
Sea Currents

Avicennia marina (Forssk.) Vierh is distributed in patches along the Farasan archipelago coast and is the most common mangrove species in the Red Sea. However, to date, no studies have been directed towards understanding its genetic variation in the Farasan archipelago. In this investigation, genetic variations within and among natural populations of Avicennia marina in the Farasan archipelago were studied using 15 microsatellite markers. The study found 142 alleles on 15 loci in nine populations. The observed (Ho) and expected (He) heterozygosity values were 0.351 and 0.391, respectively, which are much lower than those of earlier studies on A. marina in the Arabian Gulf. An inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (FST = 0.301) was similar to other mangrove species. Our findings suggest that the sea current direction and coastal geomorphology might affect genetic dispersal of A. marina. The more isolated populations with fewer connections by sea currents exhibited lower genetic variation and differentiation between populations. The genetic clustering of populations fell into three main groups—Group 1 (populations of Farasan Alkabir Island), Group 2 (populations of Sajid Island), and Group 3 (mix of one population of Farasan Alkabir Island and a population of Zifaf Island). More genetic variation and less genetic differentiation occurred when the population was not isolated and had a direct connection with sea currents. Both of these factors contributed to limited propagule dispersal and produced significant structures among the population. It is expected that the results of this research will be useful in determining policy and species-conservation strategies and in the rehabilitation of A. marina mangrove stands on the Farasan islands in an effort to save this significant natural resource.

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