Vassiliki Koufopanou

Genomic characterization and diversity of dsRNA viruses and their killer satellites in a natural population of the yeast Saccharomyces paradoxus

Mahsan Nematbakhsh, Vassiliki Koufopanou, Anthony Cass, Austin Burt

Abstract Killer yeasts secrete protein toxins that inhibit other yeast strains, a trait often encoded by M satellites of L-A dsRNA viruses. These systems serve as important molecular models, yet their adaptive significance in natural settings remains unclear. This study surveyed 60 …

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Identifying Single-Origin Rare Variants in Population Genomic Data

Jennifer E. Reynolds, Vassiliki Koufopanou, Austin Burt

Genomic analyses have shown that some mutations in large population genomic datasets may be the result of repeated, independent events at the same locus. However, the possibility of recurrent mutation is often ignored, even when it has the potential to introduce errors, …

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Identifying single origin rare variants in population genomic data

Vassiliki Koufopanou, Austin Burt

Abstract Genomic analyses have shown that some mutations in large population genomic datasets may be the result of repeated, independent events at the same locus. However, the possibility of recurrent mutation is often ignored, even when it has the potential to introduce …

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Yeasts from temperate forests

Simone Mozzachiodi, Feng‐Yan Bai, Petr Baldrián, Graham Bell et autres

Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They …

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Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

Vassiliki Koufopanou, Susan Lomas, O. Pronina, Pedro Almeida et autres

This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their …

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Estimating the fitness effects of new mutations in the wild yeast Saccharomyces paradoxus

Vassiliki Koufopanou, Susan Lomas, Isheng Jason Tsai, Austin Burt

The nature of selection acting on a population is in large measure determined by the distribution of fitness effects of new mutations. In this study, we use DNA sequences from four closely related clades of Saccharomyces paradoxus and Saccharomyces cerevisiae to identify …

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Metabolic variation in natural populations of wild yeast

Pedram Samani, Étienne Low‐Décarie, Kyra McKelvey, Thomas Bell et autres

Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on …

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Sex drives intracellular conflict in yeast

Ellie Harrison, R. Craig MacLean, Vassiliki Koufopanou, Austin Burt

Theory predicts that sex can drive the evolution of conflict within the cell. During asexual reproduction, genetic material within the cell is inherited as a single unit, selecting for cooperation both within the genome as well as between the extra-genomic elements within …

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Primers for fourteen protein-coding genes and the deep phylogeny of the true yeasts

Vassiliki Koufopanou, Jonathan Swire, Susan Lomas, Austin Burt

The Saccharomycetales or 'true yeasts' consist of more than 800 described species, including many of scientific, medical and commercial importance. Considerable progress has been made in determining the phylogenetic relationships of these species, largely based on rDNA sequences, but many nodes for …

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The cost of copy number in a selfish genetic element: the 2‐μ m plasmid of S accharomyces cerevisiae

Ellie Harrison, Vassiliki Koufopanou, Austin Burt, R. Craig MacLean

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The …

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Conservation of recombination hotspots in yeast

Isheng Jason Tsai, Austin Burt, Vassiliki Koufopanou

Meiotic recombination does not occur randomly along a chromosome, but instead tends to be concentrated in small regions, known as "recombination hotspots." Recombination hotspots are thought to be short-lived in evolutionary time due to their self-destructive nature, as gene conversion favors recombination-suppressing …

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Population genomics of domestic and wild yeasts

Gianni Liti, David M. Carter, Alan M Moses, Jonas Warringer et autres

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