Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae.

"Synthetic recombinant" populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In the latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.

Corrigendum: Heat Shock Improves Random Spore Analysis in Diverse Strains of Saccharomyces cerevisiae.

[This corrects the article DOI: 10.3389/fgene.2020.597482.].

Heat Shock Improves Random Spore Analysis in Diverse Strains of Saccharomyces cerevisiae.

Random spore analysis (RSA) is a classic method in yeast genetics that allows high-throughput purification of recombinant haploid spores following specific crosses. RSA typically involves a number of steps to induce sporulation, purge vegetative cells that fail to sporulate, and disrupt the ascus walls of sporulated cells to release haploid spores. These steps generally require expensive chemicals and/or enzymes that kill diploid cells but have few effects on spores. In the fission yeast Schizosaccharomcyes pombe, heat shock has been reported as an effective addition to RSA protocols, but to our knowledge heat shock has not been used for this purpose in the budding yeast Saccharomyces cerevisiae. Here, we evaluate the effects of heat shock on vegetative and sporulated cultures of four diverse yeast strains: a European wine strain (DBVPG6765), a Japanese sake strain (Y12), a West African palm wine strain (DBVPG6044) and a North American strain isolated from the soil beneath an oak tree (YPS128). We characterize this phenotype under multiple combinations of temperature and incubation time, and find specific conditions that lead to the exclusion of vegetative cells and an enrichment in spores, which differ by strain. We also collected genome sequence data from a recombinant population that experienced multiple rounds of RSA, including one round with a heat shock treatment. These data suggest that when incorporated into an RSA protocol, heat shock leads to increased genetic diversity among the cells that survive and mate. Ultimately, our work provides evidence that short heat treatments can improve existing RSA protocols, though in a strain-specific manner. This result informs applications of high-throughput RSA protocols, such as QTL mapping and experimental evolution research.

Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change.

"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms such as bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling-the number of discrete time points sequence data are collected from evolving populations. Using data from an E&R experiment with outcrossing Saccharomyces cerevisiae in which populations were sequenced 17 times over ~540 generations, we address the following questions: (a) Do more time points improve the ability to identify candidate regions underlying selection? And (b) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e., models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e., models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling eight or more time points has clear benefits for studying complex evolutionary dynamics.

Y-chromosomes can constrain adaptive evolution via epistatic interactions with other chromosomes.

BACKGROUND: Variation in the non-coding regions of Y-chromosomes have been shown to influence gene regulation throughout the genome in some systems; a phenomenon termed Y-linked regulatory variation (YRV). This type of sex-specific genetic variance could have important implications for the evolution of male and female traits. If YRV contributes to the additive genetic variation of an autosomally coded trait shared between the sexes (e.g. body size), then selection could facilitate sexually dimorphic evolution via the Y-chromosome. In contrast, if YRV is entirely non-additive (i.e. interacts epistatically with other chromosomes), then Y-chromosomes could constrain trait evolution in both sexes whenever they are selected for the same trait value. The ability for this phenomenon to influence such fundamental evolutionary dynamics remains unexplored. RESULTS: Here we address the evolutionary contribution of Y-linked variance by selecting for improved male geotaxis in populations possessing multiple Y-chromosomes (i.e. possessed Y-linked additive and/or epistatic variation) or a single Y-chromosome variant (i.e. possessed no Y-linked variation). We found that males from populations possessing Y-linked variation did not significantly respond to selection; however, males from populations with no Y-linked variation did respond. These patterns suggest the presence of a large quantity of Y-linked epistatic variance in the multi-Y population that dramatically slowed its response. CONCLUSIONS: Our results imply that YRV is unlikely to facilitate the evolution of sexually dimorphic traits (at least for the trait examined here), but can interfere with the rate of trait evolution in both males and females. This result could have real biological implications as it suggests that YRV can affect how quickly a population responds to new selective pressures (e.g. invasive species, novel pathogens, or climate change). Considering that YRV influences hundreds of genes and is likely typical of other independently-evolved hemizygous chromosomes, YRV-like phenomena may represent common and significant costs to hemizygous sex determination.

Cold temperature preference in bacterially infected Drosophila melanogaster improves survival but is remarkably suboptimal.

Altering one's temperature preference (e.g. behavioral fever or behavioral chill) is a common immune defense among ectotherms that is likely to be evolutionarily conserved. However, the temperature chosen by an infected host may not be optimal for pathogen defense, causing preference to be inefficient. Here we examined the efficiency of temperature preference in Drosophila melanogaster infected with an LD50 of the gram negative bacteria Pseudomonas aeruginosa. To this end, we estimated the host's uninfected and infected temperature preferences as well as their optimal survival temperature. We found that flies decreased their preference from 26.3°C to 25.2°C when infected, and this preference was stable over 48h. Furthermore, the decrease in temperature preference was associated with an increased chance of surviving the infection. Nevertheless, the infected temperature preference did not coincide with the optimum temperature for infection survival, which lies at or below 21.4°C. These data suggest that the behavioral response to P. aeruginosa infection is considerably inefficient, and the mechanisms that may account for this pattern are discussed. Future studies of infected temperature preferences should document its efficiency, as this understudied aspect of behavioral immunity can provide important insight into preference evolution.

Y-linked variation for autosomal immune gene regulation has the potential to shape sexually dimorphic immunity.

Sexually dimorphic phenotypes arise from the differential expression of male and female shared genes throughout the genome. Unfortunately, the underlying molecular mechanisms by which dimorphic regulation manifests and evolves are unclear. Recent work suggests that Y-chromosomes may play an important role, given that Drosophila melanogaster Ys were shown to influence the regulation of hundreds of X and autosomal genes. For Y-linked regulatory variation (YRV) to facilitate sexually dimorphic evolution, however, it must exist within populations (where selection operates) and influence male fitness. These criteria have seldom been investigated, leaving the potential for dimorphic evolution via YRV unclear. Interestingly, male and female D. melanogaster differ in immune gene regulation. Furthermore, immune gene regulation appears to be influenced by the Y-chromosome, suggesting it may contribute to dimorphic immune evolution. We address this possibility by introgressing Y-chromosomes from a single wild population into an isogenic background (to create Y-lines) and assessing immune gene regulation and bacterial defence. We found that Y-line males differed in their immune gene regulation and their ability to defend against Serratia marcescens. Moreover, gene expression and bacterial defence were positively genetically correlated. These data indicate that the Y-chromosome has the potential to shape the evolution of sexually dimorphic immunity in this system.

Thermoregulatory strategy may shape immune investment in Drosophila melanogaster.

As temperatures change, insects alter the amount of melanin in their cuticle to improve thermoregulation. However, melanin is also central to insect immunity, suggesting that thermoregulatory strategy may indirectly impact immune defense by altering the abundance of melanin pathway components (a hypothesis we refer to as thermoregulatory-dependent immune investment). This may be the case in the cricket Allonemobius socius, where warm environments (both seasonal and geographical) produced crickets with lighter cuticles and increased pathogen susceptibility. Unfortunately, the potential for thermoregulatory strategy to influence insect immunity has not been widely explored. Here we address the relationships between temperature, thermoregulatory strategy and immunity in the fruit fly Drosophila melanogaster. To this end, flies from two separate Canadian populations were reared in either a summer- or autumn-like environment. Shortly after adult eclosion, flies were moved to a common environment where their cuticle color and susceptibility to a bacterial pathogen (Pseudomonas aeruginosa) were measured. As with A. socius, individuals from summer-like environments exhibited lighter cuticles and increased pathogen susceptibility, suggesting that the thermoregulatory-immunity relationship is evolutionarily conserved across the hemimetabolous and holometabolous clades. If global temperatures continue to rise as expected, then thermoregulation might play an important role in host infection and mortality rates in systems that provide critical ecosystem services (e.g. pollination), or influence the prevalence of insect-vectored disease (e.g. malaria).