Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird

Abstract

The search for the hereditary mechanisms underlying quantitative traits traditionally focussed on the identification of underlying genomic polymorphisms such as Single Nucleotide Polymorphisms (SNPs). It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably transferred from one generation to the next and can thereby be a component of the heritbale variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.

Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major)

“…Since a DMS in HSPA2 might also indicate a bias in brood temperature, because HSPA2 expression is affected by temperature in chicken testes (Wang et al, 2013(Wang et al, , 2015, we do not expect our main findings to be affected by a potential sex-bias. Another possible, but unlikely explanation could be that the differences were caused by genetic variation between the pools, since a large fraction of erythrocyte DNA methylation is similar between relatives (Viitaniemi et al, 2019;van Oers et al, 2020). However, since the samples in one pool were, to our knowledge, unrelated and the samples in Control1 originated from siblings of the samples in Control2, we expect the genetic diversity to be larger within than between the pools, although we did not check for extra-pair paternity, which is estimated at about 10% for this population (van Oers et al, 2008).…”

“…From the three control pairs, four samples (N = 12) per cross-foster pair were chosen for further analysis (biological sibling pairs being raised in different control broods). Since siblings are more similar to each other in their methylation profile than to nestlings from other broods (Viitaniemi et al, 2019;van Oers et al, 2020), this approach allowed us to control for prehatching differences in DNA methylation by only comparing DNA methylation levels between siblings raised in enlarged and reduced broods and between siblings raised in control broods. This approach resulted in a total sample size of 26 samples from 26 individuals ( Supplementary Table 1).…”

Does Arsenic Contamination Affect DNA Methylation Patterns in a Wild Bird Population? An Experimental Approach

“… 71 Yet, our initial models suggested that sex explained only a very minor part of the variation in DNA methylation (and was therefore dropped from the final model), which suggests that in our data, sex-bias is unlikely to strongly mask the effects. DNA methylation is known to be heavily influenced by the genetic background, for example, in van Oers et al, 62 the majority of the variation between individuals was explained by genetic similarity. In the future, split-brood experimental designs may be used to distinguish genetic effects from the environment.…”

Does arsenic contamination affect DNA methylation patterns in a wild bird population? An experimental approach

“…Yet, our initial models suggested that sex explained only a very minor part of the variation in DNA methylation (and was therefore dropped from the final model), which suggests that in our data sex-bias is unlikely to strongly mask the effects. DNA methylation is known to be heavily influenced by the genetic background, for example in van Oers et al (62), the majority of the variation between individuals was explained by genetic similarity. In the future, split-brood experimental designs may be used to distinguish genetic effects from environmental.…”

“…We chose the RRBS approach because with the use of MspI as restriction enzyme, the method targets regions that are enriched for CpG sites. These regions are typically situated in or near the promotor regions, which has the advantage that CpGs in a relatively large proportion of the genes are covered (22,62) making this a cost-effective method for detecting sites that are likely functional (16). It was previously shown in the study species that a vast majority of methylated Cs (97%) were derived from CpG sites in blood (48).…”