Epigenetic contributions to early life history variation in Chinook salmon

DNA methylation has been proposed as an epigenetic, evolutionary mechanism for acclimation, transgenerational plasticity, and local adaptation without changes in DNA sequence. In this thesis, I assess the highly targeted evolutionary nature of DNA methylation in Chinook salmon from the tissue to the population level, with important implications for organism survival and evolution. First, I developed a PCR-based bisulfite assay for Next-Generation sequencing for genes involved in growth, development, immune function, stress response, and metabolism (Chapter 2). Locus- and tissue-specific methylation was assessed in inbred and outbred Chinook salmon at two developmental stages (fry and yearling). This chapter established DNA methylation as a mechanism targeted to specific loci, tissues, levels of inbreeding, and developmental stages/environmental contexts. I assessed the role of DNA methylation in the propagation of maternal effects at three early developmental stages (egg, alevin, and fry; Chapter 3). Two 6x6 fully factorial Chinook salmon breeding crosses were used to estimate maternal effects. DNA methylation was assessed using bisulfite sequencing and both locus-specific and CpG-specific maternal effects were identified. This chapter established DNA methylation as a potential mechanism for the transmission of maternal effects, which can have important influences on offspring development and fitness. I quantified the effects of early environment on the genetic architecture of DNA methylation using 6x6 factorial crosses reared in two environments: a hatchery and a semi-natural channel (Chapter 4). Additive, non-additive, and maternal variance components, combined with environmental and GxE effects for DNA methylation were calculated. Rearing environment caused gene-specific plasticity in methylation, as well as differences in the genetic architecture of methylation. This chapter identified the importance of both genetic and environmental variation in controlling methylation, with important implications for methylation as an acclimation or adaptive mechanism. Finally, I characterized differences in locus-specific methylation among eight populations of Chinook salmon (Chapter 5). The significant population differences in locus-specific methylation were tested for correlation with environmental variables from natal streams, and pairwise FST estimates (microsatellite and SNP data). I identified no effects of rearing environment, but a weak among-population correlation between methylation and microsatellite FST indicating that genetic drift is influencing methylation. Population-level differences in DNA methylation suggest methylation may contribute to local adaptation and is certainly an important additional source of phenotypic variation. In conclusion, my doctoral research evaluated the role of DNA methylation from the tissue to the population level. My results support DNA methylation as a novel, potentially adaptive mechanism, contributing to normal organism function, transgenerational plasticity through maternal effects, plasticity, and population-level acclimation or adaptation

Epigenetics in Society

Would you take a potentially life-saving drug if you knew that your children and grandchildren might suffer the side effects? Would you change your lifestyle if it meant you could reverse disadvantages built into your genes? Would you be comfortable if corporations could infer intimate details about your life history without asking? What if that data could improve your quality of life? Epigenetics - our epigenome - controls how our genes behave without altering their sequence. Just about everything affects it, from nutrition, drugs, and toxins to child rearing, culture, and society. Many diseases, from obesity to addiction to cancer, can be linked to epigenetic modifications. Furthermore, throughout development and life, from conception to death, the exposures you have will not only affect your own epigenome, but potentially also your child’s, and your grandchild’s. This rapidly expanding field of biological, physiological, sociological, and psychological research could be key to discovering why, and more importantly how, we are the way we are. Epigenetics has consequences for medicine, pregnancy, childcare, law and how we live on an everyday basis. This book will provide a comprehensive introduction to the mechanisms and real-life consequences of epigenetics, and will arm the reader with the knowledge necessary to make informed decisions about the future of epigenetics in modern society. This is a call for serious consideration about the effects of epigenetics on society. Epigenetics has been independently peer-reviewed for accuracy by international experts. It is written by students of diverse disciplines, and intended for students and educated lay people.https://scholar.uwindsor.ca/emergingscholarspress/1000/thumbnail.jp

Venney_final_pct_meth_data

Final percent methylation data after outlier exclusion and quality control

Data from: Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon

Inbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth-, metabolic-, immune- and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates

Venney_et_al_geneseqs_bwameth

Gene sequences used for bwa-meth alignment and methylation analysis

Venney_et_al_inbreeding_fastq

Fastq files for each tissue in each individual split using mothur. File name includes the population (H=inbred, P=outbred), individual number (fry: P1-10, H1-11, yearling: P11-20, H12-21), and the tissue denoted by the first letter of each word (Fin, Gill, Liver, Spleen)

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

Epigenetic and genetic differentiation between Coregonus species pairs

International audiencePhenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and C. lavaretus) from four lakes (N=64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation

Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads

International audienceNascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Together, our results suggest that SVs may play an important role in speciation and that, by combining second- and third-generation sequencing, we now have the ability to integrate SVs into speciation genomics