Population genomics of domestic and wild yeasts

The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. _S. paradoxus_ populations are well delineated along geographic boundaries while the variation among worldwide _S. cerevisiae_ isolates show less differentiation and is comparable to a single _S. paradoxus_ population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of _S. cerevisiae_ shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation

ΕΞΕΛΙΞΗ ΚΑΙ ΑΝΑΠΤΥΞΗ ΣΤΑ ΜΑΣΤΙΓΩΤΑ ΠΡΑΣΙΝΑ ΦΥΚΗ (CHLOROPHYTA, VOLVOCALES)

THIS THESIS IS A STUDY OF THE EVOLUTION AND DEVELOPMENT OF THE FLAGELLATE GREENALGAE. THE FIRST PART IS A COMPARATIVE STUDY OF THE EVOLUTION OF BODY SIZE, MULTICELLULARITY AND SEGREGATED SOMA. THE ALLOMETRY OF MORPHOLOGICAL CHARACTERS, DEVELOPMENT, LIFE HISTORY AND THE LIFE CYCLE ARE ALSO CONSIDERED. THE SECOND PART IS AN EXPERIMENTAL TEST OF THE POTENTIAL ROLE OF MUTATION AS A DETERMINANT OF THE COURSE OF EVOLUTION. MUTATION IS DIRECTIONAL FOR ALL THE CHARACTERSSTUDIED. THE VARIANCES AND COVARIANCES CREATED BY MUTATION ARE COMPARED TO THOSE OF 30 SPECIES OF VOLVOCACEAE; THE CORRESPONDENCE BETWEEN THE TWO DEPENDS UPON THE CHARACTED EXAMINED. IN THE THIRD PART, THE GROWTH OF GERM CELLS GROWNWITH AND WITHOUT A SOMA IS COMPARED. THE RESPONSE TO NUTRIENT CONCENTRATION OF CELLS GROWN WITH AN INTACT SOMA IS STEEPER THAN THAT OF CELLS GROWN WITHOUT A SOMA. THIS RESULT DEMONSTRATES A PHYSIOLOGICAL ADVANTAGE OF SOMA IN VOLVOX, ATTRIBUTABLE TO A DIVISION OF LABOUR BETWEEN "SOURCE" AND "SINK".ΠΑΡΟΥΣΙΑΖΕΤΑΙ ΜΙΑ ΜΕΛΕΤΗ ΤΗΣ ΕΞΕΛΙΞΗΣ ΚΑΙ ΕΜΒΡΥΟΛΟΓΙΚΗΣ ΑΝΑΠΤΥΞΗΣ ΤΩΝ ΜΑΣΤΙΓΩΤΩΝ ΠΡΑΣΙΝΩΝ ΦΥΚΩΝ (CHLOROPHYTA, VOLVOCALES). ΤΟ ΠΡΩΤΟ ΜΕΡΟΣ ΠΕΡΙΛΑΜΒΑΝΕΙ ΤΗΝ ΣΥΓΚΡΙΤΙΚΗ ΜΕΛΕΤΗ ΤΗΣ ΕΞΕΛΙΞΗΣ ΤΟΥ ΜΕΓΕΘΟΥΣ ΣΩΜΑΤΟΣ, ΠΟΛΥΚΥΤΤΑΡΙΣΜΟΥ, ΚΑΙ ΤΟΥ ΔΙΑΧΩΡΙΣΜΟΥ ΤΟΥ ΣΤΕΙΡΟΥ ΣΩΜΑΤΟΣ ΑΠΟ ΤΟΝ ΓΟΝΟ. ΤΟ ΔΕΥΤΕΡΟ ΜΕΡΟΣ ΕΞΕΤΑΖΕΙ ΠΕΙΡΑΜΑΤΙΚΑ ΤΟ ΠΩΣ ΚΑΙ ΚΑΤΑ ΠΟΣΟΝ Η ΠΟΙΚΙΛΟΤΗΤΑ ΠΟΥ ΠΑΡΑΓΕΤΑΙ ΑΠΟ ΜΕΤΑΛΛΑΞΕΙΣ ΜΠΟΡΕΙ ΝΑ ΕΠΗΡΕΑΖΕΙ ΤΗΝ ΠΟΡΕΙΑ ΤΗΣ ΕΞΕΛΙΞΗΣ ΤΩΝ ΕΙΔΩΝ. Σ'ΑΥΤΗΝ ΤΗΝ ΜΕΛΕΤΗ, Η ΠΟΙΚΙΛΟΤΗΤΑ ΠΟΥ ΕΧΕΙ ΠΑΡΑΧΘΕΙ ΑΠΟ ΜΕΤΑΛΛΑΞΕΙΣ ΕΝΟΣ ΕΙΔΟΥΣ ΤΟΥ ΓΕΝΟΥΣ VOLVOX ΣΥΓΚΡΙΝΕΤΑΙ ΜΕ ΤΗΝ ΠΟΙΚΙΛΟΤΗΤΑ ΚΑΙ ΔΙΑΦΟΡΟΠΟΙΗΣΗ ΧΑΡΑΚΤΗΡΩΝ 30 ΕΙΔΩΝ ΤΗΣ ΟΙΚΟΓΕΝΕΙΑΣ VOLVOCACEAE. ΤΟ ΤΡΙΤΟ ΜΕΡΟΣ ΕΙΝΑΙ ΕΠΙΣΗΣ ΜΙΑ ΠΕΙΡΑΜΑΤΙΚΗ ΜΕΛΕΤΗ ΣΤΗΝ ΟΠΟΙΑ ΕΞΕΤΑΖΕΤΑΙ Η ΤΑΧΥΤΗΤΑ ΑΝΑΠΤΥΞΗΣ ΓΟΝΙΔΙΑΚΩΝ ΚΥΤΤΑΡΩΝ, ΤΑ ΟΠΟΙΑ ΜΕΓΑΛΩΝΟΥΝ ΜΕ Η ΧΩΡΙΣ ΤΟ ΣΩΜΑ ΤΟΥΣ. ΑΠΟΔΕΙΚΝΥΕΤΑΙ ΟΤΙ ΤΑ ΓΟΝΙΔΙΑΚΑ ΚΥΤΤΑΡΑ ΠΟΥ ΜΕΓΑΛΩΝΟΥΝ ΜΕ ΑΝΕΠΑΦΟ ΤΟ ΣΩΜΑ ΤΟΥΣ ΑΝΑΠΤΥΣΣΟΝΤΑΙ ΓΡΗΓΟΡΩΤΕΡΑ ΕΚΕΙΝΩΝ ΠΟΥ ΜΕΓΑΛΩΝΟΥΝ ΔΙΧΩΣ ΣΩΜΑ, ΣΕ ΠΛΟΥΣΙΕΣ ΤΡΟΦΙΚΕΣ ΣΥΝΘΗΚΕΣ, ΔΕΙΧΝΟΝΤΑΣ ΕΤΣΙ ΟΤΙ Ο ΔΙΑΧΩΡΙΣΜΟΣ ΤΟΥ ΣΩΜΑΤΟΣ ΑΠΟ ΤΟΝ ΓΟΝΟ Σ'ΑΥΤΟΥΣ ΤΟΥΣ ΑΠΛΟΥΣ ΟΡΓΑΝΙΣΜΟΥΣ ΜΠΟΡΕΙ ΝΑ ΕΞΗΓΗΘΕΙ ΜΕ ΤΗΝ ΘΕΩΡΙΑ ΔΙΑΧΩΡΙΣΜΟΥ ΕΡΓΑΣΙΑΣ ΚΥΤΤΑΡΩΝ ΜΕΤΑΞΥ "ΠΗΓΗΣ" ΚΑΙ "ΔΕΚΤΗ" ΤΡΟΦΙΚΩΝ ΟΥΣΙΩΝ

Evolution of a selfish genetic element : the 2 micron plasmid of saccharomyces spp

The 2 Micron plasmid is a multicopy DNA circle inhabiting the genome of the budding yeasts, Sacchormyces spp. The plasmid confers no known benefits to the host, but imposes a small fitness cost. However the plasmid is able to drive, i.e. to transmit to >50% of sexual offspring, which allows the element to spread through an outcrossing host population. Therefore we can consider the plasmid a selfish genetic element of yeast. Here we draw on a number of approaches to improve our understanding of this element. Firstly, we examined the relationship between the cost of plasmid carriage and copy number by experimentally manipulating the number of plasmids in the host. We find that host fitness decreases at a rate of ~0.09% per additional plasmid. Secondly we use experimentally evolving yeast populations to test the hypothesis that sexual reproduction, which is fundamental to the evolution of selfish genetic elements, will drive increasing virulence in the plasmid. We find that 2 Micron copy number increased in outcrossing populations but remained constant in asexual populations. We also find that sex allowed the invasion of non-functional mitochondria in to the populations, showing that sex has the capacity to generate a driving selfish genetic element from one of the most fundamental endosymbionts of the eukaryotic cell. In addition, we have investigated plasmid variation from global populations of Saccharromyces spp. in order to better understand the population biology and evolution of this plasmid. Here we find evidence that the plasmid is able to move between species, recombine with other plasmids within the cell, and exist at a surprisingly wide range of copy numbers in different host populations. Understanding the population structure and evolution of this element allows us to view the plasmid as an autonomous unit evolving in its own right in the genomes of its hosts.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Growth rate data

Growth rate dat

Rapid evolution of yeast centromeres in the absence of drive

To find the most rapidly evolving regions in the yeast genome we compared most of chromosome III from three closely related lineages of the wild yeast Saccharomyces paradoxus. Unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even faster than DNA sequences unlikely to be under selective constraint (i.e., synonymous sites after correcting for codon usage bias and remnant transposable elements). Centromeres on other chromosomes also show an elevated rate of nucleotide substitution. Rapid centromere evolution has also been reported for some plants and animals and has been attributed to selection for inclusion in the egg or the ovule at female meiosis. But Saccharomyces yeasts have symmetrical meioses with all four products surviving, thus providing no opportunity for meiotic drive. In addition, yeast centromeres show the high levels of polymorphism expected under a neutral model of molecular evolution. We suggest that yeast centromeres suffer an elevated rate of mutation relative to other chromosomal regions and they change through a process of “centromere drift,” not drive

Data from: The cost of copy number in a selfish genetic element: the 2µM plasmid of Saccharomyces cerevisiae

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 2µm is a multi-copy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2µm is that plasmid copy number evolves as a tradeoff between selection for increased vertical transmission, favoring high copy number, and selection for decreased virulence, favoring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2µm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (±0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast/2µm associations, and pave the way for future studies examining how selection can shape the cost of multi-copy elements