28 results found
Koufopanou V, 2020, Population size, sex and purifying selection: comparative genomics of two sister taxa of the wild yeast Saccharomyces paradoxus, Genome Biology and Evolution, Vol: 12, Pages: 1636-1645, ISSN: 1759-6653
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 population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.
Koufopanou V, Lomas S, Tsai IJ, et al., 2015, Estimating the fitness effects of new mutations in the wild yeast Saccharomyces paradoxus, Genome Biology and Evolution, Vol: 7, Pages: 1887-1895, ISSN: 1759-6653
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 and polarize new mutations and estimate their fitness effects. By progressively restricting the analyses to narrower categories of sites, we further seek to characterize sites with predictable mutational effects, that is, unconditionally deleterious, neutral or beneficial. Consistent with previous studies on S. paradoxus, we have failed to find evidence for mutations with beneficial effects, even in regions that were divergent in two outgroup clades, perhaps a consequence of the relatively unchallenged, predominantly asexual and highly inbred lifestyle of this species. On the other hand, there is abundant evidence of deleterious mutations, varying in severity of effect from strongly deleterious to very mild, particularly in regions conserved in the outgroup taxa, indicating a history of persistent purifying selection. Narrowing the analysis down to individual amino acids reduces further the range of effects: for example, mutations changing cysteine are predicted to be nearly always strongly deleterious, whereas those changing arginine, serine, and tyrosine are expected to be nearly neutral. The proportion of mutations with deleterious effects for a particular amino acid is correlated with long-term stasis of that amino acid among highly divergent sequences from a variety of organisms, showing that functionality of sites tends to persist through the diversification of clades and that our findings are also relevant to longer evolutionary times and other taxa.
Koufopanou V, Swire J, Lomas S, et al., 2013, Primers for fourteen protein-coding genes and the deep phylogeny of the true yeasts, FEMS YEAST RESEARCH, Vol: 13, Pages: 574-584, ISSN: 1567-1356
Harrison E, Koufopanou V, Burt A, et al., 2012, The cost of copy number in a selfish genetic element: the 2-mu M plasmid of Saccharomyces cerevisiae, JOURNAL OF EVOLUTIONARY BIOLOGY, Vol: 25, Pages: 2348-2356, ISSN: 1010-061X
Tsai IJ, Burt A, Koufopanou V, 2010, Conservation of recombination hotspots in yeast, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 7847-7852, ISSN: 0027-8424
Replansky T, Koufopanou V, Greig D, et al., 2008, Saccharomyces sensu stricto as a model system for evolution and ecology, TRENDS IN ECOLOGY & EVOLUTION, Vol: 23, Pages: 494-501, ISSN: 0169-5347
Bensasson D, Zarowiecki M, Burt A, et al., 2008, Rapid evolution of yeast centromeres in the absence of drive, GENETICS, Vol: 178, Pages: 2161-2167, ISSN: 0016-6731
Tsai IJ, Bensasson D, Burt A, et al., 2008, Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 4957-4962, ISSN: 0027-8424
Koufopanou V, Hughes J, Bell G, et al., 2006, The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 361, Pages: 1941-1946, ISSN: 0962-8436
Koufopanou V, Burt A, 2005, Degeneration and domestication of a selfish gene in yeast: Molecular evolution versus site-directed mutagenesis, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 22, Pages: 1535-1538, ISSN: 0737-4038
Burt A, Koufopanou V, 2004, Homing endonuclease genes: the rise and fall and rise again of a selfish element, CURRENT OPINION IN GENETICS & DEVELOPMENT, Vol: 14, Pages: 609-615, ISSN: 0959-437X
Johnson LJ, Koufopanou V, Goddard MR, et al., 2004, Population genetics of the wild yeast Saccharomyces paradoxus, GENETICS, Vol: 166, Pages: 43-52, ISSN: 0016-6731
Posey KL, Koufopanou V, Burt A, et al., 2004, Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species, NUCLEIC ACIDS RESEARCH, Vol: 32, Pages: 3947-3956, ISSN: 0305-1048
Leroi AM, Koufopanou V, Burt A, 2003, Cancer selection, NATURE REVIEWS CANCER, Vol: 3, Pages: 226-231, ISSN: 1474-175X
Koufopanou V, Goddard MR, Burt A, 2002, Adaptation for horizontal transfer in a homing endonuclease, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 19, Pages: 239-246, ISSN: 0737-4038
Koufopanou V, Burt A, Szaro T, et al., 2001, Gene genealogies, cryptic species, and molecular evolution in the human pathogen Coccidioides immitis and relatives (Ascomycota, Onygenales), MOLECULAR BIOLOGY AND EVOLUTION, Vol: 18, Pages: 1246-1258, ISSN: 0737-4038
Koufopanou V, Reid DG, Ridgway SA, et al., 1999, A molecular phylogeny of the patellid limpets (Gastropoda : Patellidae) and its implications for the origins of their antitropical distribution, MOLECULAR PHYLOGENETICS AND EVOLUTION, Vol: 11, Pages: 138-156, ISSN: 1055-7903
Taylor JW, Geiser DM, Burt A, et al., 1999, The evolutionary biology and population genetics underlying fungal strain typing, CLINICAL MICROBIOLOGY REVIEWS, Vol: 12, Pages: 126-+, ISSN: 0893-8512
Taylor JW, Geiser DM, Burt A, et al., 1999, The evolutionary biology and population genetics underlying fungal strain typing., Clin Microbiol Rev, Vol: 12, Pages: 126-146, ISSN: 0893-8512
Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.
Koufopanou V, Burt A, Taylor JW, 1998, Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis (vol 94, pg 5478, 1997), PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 95, Pages: 8414-8414, ISSN: 0027-8424
Koufopanou V, Burt A, Taylor JW, 1997, Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 94, Pages: 5478-5482, ISSN: 0027-8424
KOUFOPANOU V, 1994, THE EVOLUTION OF SOMA IN THE VOLVOCALES, AMERICAN NATURALIST, Vol: 143, Pages: 907-931, ISSN: 0003-0147
KOUFOPANOU V, BELL G, 1993, SOMA AND GERM - AN EXPERIMENTAL APPROACH USING VOLVOX, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 254, Pages: 107-113, ISSN: 0962-8452
KOUFOPANOU V, BELL G, 1991, DEVELOPMENTAL MUTANTS OF VOLVOX - DOES MUTATION RECREATE THE PATTERNS OF PHYLOGENETIC DIVERSITY, EVOLUTION, Vol: 45, Pages: 1806-1822, ISSN: 0014-3820
BELL G, KOUFOPANOU V, 1991, THE ARCHITECTURE OF THE LIFE-CYCLE IN SMALL ORGANISMS, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 332, Pages: 81-89, ISSN: 0962-8436
KOUFOPANOU V, BELL G, 1984, MEASURING THE COST OF REPRODUCTION .4. PREDATION EXPERIMENTS WITH DAPHNIA-PULEX, OECOLOGIA, Vol: 64, Pages: 81-86, ISSN: 0029-8549
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