fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs

Infection phenotypes of a coevolving parasite are highly diverse, structured, and specific

Understanding how diversity is maintained in natural populations is a major goal of evolutionary biology. In coevolving hosts and parasites, negative frequency-dependent selection is one mechanism predicted to maintain genetic variation. While much is known about host diversity, parasite diversity remains understudied in coevolutionary research. Here, we survey natural diversity in a bacterial parasite by characterizing infection phenotypes for over 50 isolates in relation to 12 genotypes of their host, Daphnia magna. We find striking phenotypic variation among parasite isolates, and we discover the parasite can infect its host through at least five different attachment sites. Variation in attachment success at each site is explained to varying degrees by host and parasite genotypes. A spatial correlation analysis showed that infectivity of different isolates does not correlate with geographic distance, meaning isolates from widespread populations are equally able to infect the host. Overall, our results reveal that infection phenotypes of this parasite are highly diverse. Our results are consistent with the prediction that under Red Queen coevolutionary dynamics both the host and the parasite should show high genetic diversity for traits of functional importance in their interactions.

Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and nonadditive genetic variance in hatchery fish and greater maternal effects in seminatural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.

DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects

The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood. Despite recent work identifying DNA methylation as a potential mechanism of nongenetic inheritance, currently proposed links between DNA methylation and parental effects are indirect and primarily involve genomic imprinting. We combined a factorial breeding design and gene-targeted sequencing methods to assess inheritance of methylation during early life stages at 14 genes involved in growth, development, metabolism, stress response, and immune function of Chinook salmon (Oncorhynchus tshawytscha). We found little evidence for additive or nonadditive genetic effects acting on methylation levels during early development; however, we detected significant maternal effects. Consistent with conventional maternal effect data, maternal effects on methylation declined through development and were replaced with nonadditive effects when offspring began exogenous feeding. We mapped methylation at individual CpG sites across the selected candidate genes to test for variation in site-specific methylation profiles and found significant maternal effects at selected CpG sites that also declined with development stage. While intergenerational inheritance of methylated DNA is controversial, we show that CpG-specific methylation may function as an underlying molecular mechanism for maternal effects, with important implications for offspring fitness.

Do whitefish (Coregonus lavaretus) larvae show adaptive variation in the avoidance of microplastic ingestion?

The presence of microplastics in aquatic ecosystems has recently received increased attention. Small plastic particles may resemble natural food items of larval fish and other aquatic organisms, and create strong selective pressures on the feeding traits in exposed populations. Here, we examined if larval ingestion of 90 μm polystyrene microspheres, in the presence of zooplankton (Artemia nauplii, mean length = 433 μm), shows adaptive variation in the European whitefish (Coregonus lavaretus). A full-factorial experimental breeding design allowed us to estimate the relative contributions of male (sire) and female (dam) parents and full-sib family variance in early feeding traits, and also genetic (co)variation between these traits. We also monitored the magnitude of intake and elimination of microplastics from the alimentary tracts of the larvae. In general, larval whitefish ingested small numbers of microplastics (mean = 1.8, range = 0-26 particles per larva), but ingestion was marginally affected by the dam, and more strongly by the full-sib family variation. Microsphere ingestion showed no statistically significant additive genetic variation, and thus, no heritability. Moreover, microsphere ingestion rate covaried positively with the ingestion of Artemia, further suggesting that larvae cannot adaptively avoid microsphere ingestion. Together with the detected strong genetic correlation between food intake and microplastic intake, the results suggest that larval fish do not readily possess additive genetic variation that would help them to adapt to the increasing pollution by microplastics. The conflict between feeding on natural food and avoiding microplastics deserves further attention.

Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures

Climate change is leading to altered temperature regimes which are impacting aquatic life, particularly for ectothermic fish. The impacts of environmental stress can be translated across generations through maternally derived glucocorticoids, leading to altered offspring phenotypes. Although these maternal stress effects are often considered negative, recent studies suggest this maternal stress signal may prepare offspring for a similarly stressful environment (environmental match). We applied the environmental match hypothesis to examine whether a prenatal stress signal can dampen the effects of elevated water temperatures on body size, condition, and survival during early development in Chinook salmon Oncorhynchus tshawytscha from Lake Ontario, Canada. We exposed fertilized eggs to prenatal exogenous egg cortisol (1,000 ng/ml cortisol or 0 ng/ml control) and then reared these dosed groups at temperatures indicative of current (+0°C) and future (+3°C) temperature conditions. Offspring reared in elevated temperatures were smaller and had a lower survival at the hatchling developmental stage. Overall, we found that our exogenous cortisol dose did not dampen effects of elevated rearing temperatures (environmental match) on body size or early survival. Instead, our eyed stage survival indicates that our prenatal cortisol dose may be detrimental, as cortisol-dosed offspring raised in elevated temperatures had lower survival than cortisol-dosed and control reared in current temperatures. Our results suggest that a maternal stress signal may not be able to ameliorate the effects of thermal stress during early development. However, we highlight the importance of interpreting the fitness impacts of maternal stress within an environmentally relevant context.

No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout (Salmo trutta)

One of the most common and potent pollutants of freshwater habitats is 17-alpha-ethynylestradiol (EE2), a synthetic component of oral contraceptives that is not completely eliminated during sewage treatment and that threatens natural populations of fish. Previous studies found additive genetic variance for the tolerance against EE2 in different salmonid fishes and concluded that rapid evolution to this type of pollution seems possible. However, these previous studies were done with fishes that are lake-dwelling and hence typically less exposed to EE2 than river-dwelling species. Here, we test whether there is additive genetic variance for the tolerance against EE2 also in river-dwelling salmonid populations that have been exposed to various concentrations of EE2 over the last decades. We sampled 287 adult brown trout (Salmo trutta) from seven populations that show much genetic diversity within populations, are genetically differentiated, and that vary in their exposure to sewage-treated effluent. In order to estimate their potential to evolve tolerance to EE2, we collected their gametes to produce 730 experimental families in blockwise full-factorial in vitro fertilizations. We then raised 7,302 embryos singly in 2-ml containers each and either exposed them to 1 ng/L EE2 (an ecologically relevant concentration, i.e., 2 pg per embryo added in a single spike to the water) or sham-treated them. Exposure to EE2 increased embryo mortality, delayed hatching time, and decreased hatchling length. We found no population differences and no additive genetic variance for tolerance to EE2. We conclude that EE2 has detrimental effects that may adversely affect population even at a very low concentration, but that our study populations lack the potential for rapid genetic adaptation to this type of pollution. One possible explanation for the latter is that continuous selection over the last decades has depleted genetic variance for tolerance to this synthetic stressor.

Genetic architecture of gene transcription in two Atlantic salmon (Salmo salar) populations

Gene expression regulation has an important role in short-term acclimation and long-term adaptation to changing environments. However, the genetic architecture of gene expression has received much less attention than that of traditional phenotypic traits. In this study, we used a 5 × 5 full-factorial breeding design within each of two Atlantic salmon (Salmo salar) populations to characterize the genetic architecture of gene transcription. The two populations (LaHave and Sebago) are being used for reintroduction efforts into Lake Ontario, Canada. We used high-throughput quantitative real-time PCR to measure gene transcription levels for 22 genes in muscle tissue of Atlantic salmon fry. We tested for population differences in gene transcription and partitioned the transcription variance into additive genetic, non-additive genetic and maternal effects within each population. Interestingly, average additive genetic effects for gene transcription were smaller than those reported for traditional phenotypic traits in salmonids, suggesting that the evolutionary potential of gene transcription is lower than that of traditional traits. Contrary to expectations for early life stage traits, maternal effects were small. In general, the LaHave population had higher additive genetic effects for gene transcription than the Sebago population had, indicating that the LaHave fish have a higher adaptive potential to respond to the novel selection pressures associated with reintroduction into a novel environment. This study highlights not only the profound variation in gene transcription possible among salmonid populations but also the among-population variation in the underlying genetic architecture of such traits.

Paternal identity impacts embryonic development for two species of freshwater fish

Paternal, compared to maternal, contributions were believed to have only a limited influence on embryonic development and larval fitness traits in fishes. Therefore, the perspective of male influence on early life history traits has come under scrutiny. This study was conducted to determine parental effects on the rate of eyed embryos of Ide Leuciscus idus and Northern pike Esox lucius. Five sires and five dams from each species were crossed using a quantitative genetic breeding design and the resulting 25 sib groups of each species were reared to the embryonic eyed stage. We then partition variation in embryonic phenotypic performance to maternal, paternal, and parental interactions using the Restricted Maximum Likelihood (REML) model. Results showed that paternal, maternal, and the paternal×maternal interaction terms were highly significant for both species; clearly demonstrating that certain family combinations were more compatible than others. Paternal effects explained 20.24% of the total variance, which was 2-fold higher than the maternal effects (10.73%) in Ide, while paternal effects explained 18.9% of the total variance, which was 15-fold higher than the maternal effects (1.3%) in Northern pike. Together, these results indicate that male effects are of major importance during embryonic development for these species. Furthermore, this study demonstrates that genetic compatibility between sires and dams plays an important role and needs to be taken into consideration for reproduction of these and likely other economically important fish species.

Tactic-specific benefits of polyandry in Chinook salmon Oncorhynchus tshawytscha

This study examined whether polyandrous female Chinook salmon Oncorhynchus tshawytscha obtain benefits compared with monandrous females through an increase in hatching success. Both of the alternative reproductive tactics present in male O. tshawytscha (large hooknoses and small, precocious jacks) were used, such that eggs were either fertilized by a single male (from each tactic) or multiple males (using two males from the same or different tactics). The results show that fertilized eggs from the polyandrous treatments had a significantly higher hatching success than those from the monandrous treatments. It is also shown that sperm speed was positively related with offspring hatching success. Finally, there were tactic-specific effects on the benefits females received. The inclusion of jacks in any cross resulted in offspring with higher hatching success, with the cross that involved a male from each tactic providing offspring with the highest hatching success than any other cross. This study has important implications for the evolution of multiple mating and why it is so prevalent across taxa, while also providing knowledge on the evolution of mating systems, specifically those with alternative reproductive tactics.

Prenatal Stress Exposure Generates Higher Early Survival and Smaller Size without Impacting Developmental Rate in a Pacific Salmon

Prenatal exposure to elevated glucocorticoids can act as a signal of environmental stress, resulting in modifications to offspring phenotype. While "negative" phenotypic effects (i.e., smaller size, slower growth) are often reported, recent research coupling phenotype with other fitness-related traits has suggested positive impacts of prenatal stress. Using captive Chinook salmon (Oncorhynchus tshawytscha), we treated eggs with biologically relevant cortisol levels-low (300 ng mL^-1 ), high (1,000 ng mL^-1 ), or control (0 ng mL^-1 )-to examine the early-life impacts of maternally transferred stress hormones on offspring. Specifically, we measured early survival, rate of development, and multiple measures of morphology. Low and high cortisol dosing of eggs resulted in significantly higher survival compared to controls (37% and 24% higher, respectively). Fish reared from high dose eggs were structurally smaller compared to control fish, but despite this variation in structural size, exposure to elevated cortisol did not impact developmental rate. These results demonstrate that elevations in egg cortisol can positively influence offspring fitness through an increase in early survival while also altering phenotype at a critical life-history stage. Overall, these results suggest that exposure to prenatal stress may not always produce apparently negative impacts on offspring fitness and further proposes that complex phenotypic responses should be examined in relevant environmental conditions.

Genetic architecture and maternal contributions of early-life survival in lake trout Salvelinus namaycush

The influences of additive, non-additive and maternal effects on early survival (uneyed embryo survival, eyed embryo survival, alevin survival and overall survival to first feeding) were quantified in lake trout Salvelinus namaycush using a 7 × 7 full-factorial breeding design. Maternal effects followed by non-additive genetic effects explained around one third of the phenotypic variance of the survival traits. Although the amount of additive genetic effects were low (<1%), suggesting a limited potential of the traits to respond to new selection pressures, how maternal and non-additive genetic effects may respond to selection under certain circumstances are discussed.