Recombining your way out of trouble: the genetic architecture of hybrid fitness under environmental stress

Hybridization between species is a fundamental evolutionary force that can both promote and delay adaptation. There is a deficit in our understanding of the genetic basis of hybrid fitness, especially in non-domesticated organisms. We also know little about how hybrid fitness changes as a function of environmental stress. Here, we made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species, exposed populations to ten toxins, and sequenced the most resilient hybrids on low coverage using ddRADseq. We expected to find strong negative epistasis and heterozygote advantage in the hybrid genomes. We investigated three aspects of hybridness: 1) hybridity, 2) interspecific heterozygosity, and 3) epistasis (positive or negative associations between non-homologous chromosomes). Linear mixed effect models revealed strong genotype-by-environment interactions with many chromosomes and chromosomal interactions showing species-biased content depending on the environment. Against our predictions, we found extensive selection against heterozygosity such that homozygous allelic combinations from the same species were strongly overrepresented in an otherwise hybrid genomic background. We also observed multiple cases of positive epistasis between chromosomes from opposite species, confirmed by epistasis- and selection-free simulations, which is surprising given the large divergence of the parental species (~15% genome-wide). Together, these results suggest that stress-resilient hybrid genomes can be assembled from the best features of both parents, without paying high costs of negative epistasis across large evolutionary distances. Our findings illustrate the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of hybrid populations

Evidence for polarised boron in Co-B and Fe-B alloys

By exploiting the tunability of synchrotron radiation in measurements of spin-resolved photoemission it has proved possible to obtain information on the polarisation of the valence electrons of Co-B and Fe-B amorphous magnetic alloys, Both the spin-integrated and spin-resolved energy distribution curves show a marked dependence on photon energy indicating that the p states of boron hybridise with the d states of the transition metals giving rise to mixed states in the binding energy range 1 to 5 eV, The observed polarisation and spin-resolved densities of states imply that in the above restricted energy range there is a net negative polarisation of the boron states

The genetics of a putative social trait in natural populations of yeast

The sharing of secreted invertase by yeast cells is a well established laboratory model for cooperation, but the only evidence that such cooperation occurs in nature is that the SUC loci, which encode invertase, vary in number and functionality. Genotypes that do not produce invertase can act as “cheats” in laboratory experiments, growing on the glucose that is released when invertase producers, or “cooperators”, digest sucrose. However, genetic variation for invertase production might instead be explained by adaptation of different populations to different local availabilities of sucrose, the substrate for invertase. Here we find that, 110 wild yeast strains isolated from natural habitats, all contained a single SUC locus and produced invertase; none were “cheats”. The only genetic variants we found were three strains isolated instead from sucrose-rich nectar, which produced higher levels of invertase from three additional SUC loci at their sub-telomeres. We argue that the pattern of SUC gene variation is better explained by local adaptation than by social conflict

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter.

Although we understand the genetics of the laboratory model yeast Saccharomyces cerevisiae very well, we know little about the natural ecology and environment that shaped its genome. Most isolates of Saccharomyces paradoxus, the wild relative of S. cerevisiae, come from oak trees, but it is not known whether this is because oak is their primary habitat. We surveyed leaf litter in a forest in Northern Germany and found a strong correlation between isolation success of wild Saccharomyces and the proximity of the nearest oak. We compared the four most common tree genera and found Saccharomyces most frequently in oak litter. Interestingly, we show that Saccharomyces is much more abundant in oak leaf litter than on oak bark, suggesting that it grows in litter or soil rather than on the surfaces of oaks themselves. The distribution and abundance of Saccharomyces over the course of a year shows that oak leaf litter provides a stable habitat for the yeast, although there was significant tree-to-tree variation. Taken together, our results suggest that leaf litter rather than tree surfaces provide the better habitat for wild Saccharomyces, with oak being the preferred tree genus. 99.5% of all strains (633/636) isolated were S. paradoxus

Failure to progress

Experiments on yeast cells that are hosts to a killer virus confirm that natural selection can sometimes reduce fitness

A Saccharomyces paradox: chromosomes from different species are incompatible because of anti-recombination, not because of differences in number or arrangement

Many species are able to hybridize, but the sterility of these hybrids effectively prevents gene flow between the species, reproductively isolating them and allowing them to evolve independently. Yeast hybrids formed by Saccharomyces cerevisiae and Saccharomyces paradoxus parents are viable and able to grow by mitosis, but they are sexually sterile because most of the gametes they make by meiosis are inviable. The genomes of these two species are so diverged that they cannot recombine properly during meiosis, so they fail to segregate efficiently. Thus most hybrid gametes are inviable because they lack essential chromosomes. Recent work shows that chromosome mis-segregation explains nearly all observed hybrid sterility—genetic incompatibilities have only a small sterilising effect, and there are no significant sterilising incompatibilities in chromosome arrangement or number between the species. It is interesting that chromosomes from these species have diverged so much in sequence without changing in configuration, even though large chromosomal changes occur quite frequently, and sometimes beneficially, in evolving yeast populations

The ecology and evolution of non-domesticated Saccharomyces species

Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae: the seven species in the genus Saccharomyces. The best-studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the Saccharomyces genus have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression, and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography, and ecology are only beginning. Much remains to understand about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context, and to develop the Saccharomyces genus as a model clade for ecology and evolution

Saccharomyces cerevisiae: a nomadic yeast with no niche?

Different species are usually thought to have specific adaptations, which allow them to occupy different ecological niches. But recent neutral ecology theory suggests that species diversity can simply be the result of random sampling, due to finite population sizes and limited dispersal. Neutral models predict that species are not necessarily adapted to specific niches, but are functionally equivalent across a range of habitats. Here we evaluate the ecology of S. cerevisiae, one of the most important microbial species in human history. The artificial collection, concentration, and fermentation of large volumes of fruit for alcohol production produces an environment in which S. cerevisiae thrives, and therefore it is assumed that fruit is the ecological niche that S. cerevisiae inhabits and has adapted to. We find very little direct evidence that S. cerevisiae is adapted to fruit, or indeed to any other specific niche. We propose instead a neutral nomad model for S. cerevisiae, which we believe should be used as the starting hypothesis in attempting to unravel the ecology of this important microbe

Asynchronous spore germination in isogenic natural isolates of Saccharomyces paradoxus

Spores from wild yeast isolates often show great variation in the size of colonies they produce, for largely unknown reasons. Here we measure the colonies produced from single spores from six different wild Saccharomyces paradoxus strains. We found remarkable variation in spore colony sizes, even among spores that were genetically identical. Different strains had different amounts of variation in spore colony sizes, and variation was not affected by the number of preceding meioses, or by spore maturation time. We used time-lapse photography to show that wild strains also have high variation in spore germination timing, providing a likely mechanism for the variation in spore colony sizes. When some spores from a laboratory strain make small colonies, or no colonies, it usually indicates a genetic or meiotic fault. Here, we demonstrate that in wild strains spore colony size variation is normal. We discuss and assess potential adaptive and non-adaptive explanations for this variation