Bernice Sepers

Bernice Sepers MSc

PhD Student
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands

About

The aim of my PhD project is to identify genetic and environmental control mechanism underlying genome-wide DNA methylation and possible functional consequences of gene methylation for natural variation in great tit personality.

Biography

Bernice Sepers (1991) studied Biology (Bachelor of Science) and Environmental Biology (specialisation programme Behavioural Ecology, Master of Science) at Utrecht University. During her major internship at Stichting AAP, she studied the effect of intervention on the abnormal behaviour of ex-laboratory chimpanzees. In her final year she visited the Nova Scotia Department of Natural Resources in Canada to study the environmental conditions that influenced snowmobile trail use by coyotes within lynx home ranges at Cape Breton Island (Nova Scotia, Canada). Her master thesis consisted of an extensive literature review on the effect of epigenetic changes on the behaviour of animals in natural populations (NIOO-KNAW). Bernice graduated in 2016, after which she was funded by a Startersbeurs to study the effect of experimental brood size manipulation on DNA methylation and exploratory behaviour in the great tit at the NIOO-KNAW. After this, she worked as a soil consultant and ecologist at Antea Group (the Netherlands) before starting her PhD at the NIOO-KNAW in 2018. This PhD project focuses on the epigenetics of animal personality, in particular DNA methylation and its influence on exploratory behaviour in great tits. By using established selection lines of fast and slow exploratory birds and several long-term natural populations, this projects aims to identify genetic and environmental control mechanism underlying genome-wide DNA methylation and possible functional consequences of gene methylation for natural variation in great tit personality.

Research groups

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Publications

Peer-reviewed publications

  • Molecular Ecology Resources
    2022

    An ecologist's guide for studying DNA methylation variation in wild vertebrates

    Veronika Laine, Bernice Sepers, Melanie Lindner, F. Gawehns, Suvi Ruuskanen, Kees van Oers

    The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.

    https://doi.org/10.1111/1755-0998.13624
  • Molecular Ecology Resources
    2022

    epiGBS2

    F. Gawehns, Maarten Postuma, Morgane Van Antro, Adam Nunn, Bernice Sepers, Samar Fatma, Thomas Van Gurp, Niels C. A. M. Wagemaker, A.C. Mateman, Slavica Milanovic-Ivanovic, Ivo Groβe, Kees van Oers, Philippine Vergeer, Koen Verhoeven

    Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost- and time-efficient and the computational workflow is designed in a user-friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the Snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with Freebayes (epiFreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).

    https://doi.org/10.1111/1755-0998.13597
  • Frontiers in Ecology and Evolution
    04-03-2021

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

    Bernice Sepers, Jolijn Erven, F. Gawehns, Veronika Laine, Kees van Oers
    Early developmental conditions are known to have life-long effects on an individual’s behavior, physiology and fitness. In altricial birds, a majority of these conditions, such as the number of siblings and the amount of food provisioned, are controlled by the parents. This opens up the potential for parents to adjust the behavior and physiology of their offspring according to local post-natal circumstances. However, the mechanisms underlying such intergenerational regulation remain largely unknown. A mechanism often proposed to possibly explain how parental effects mediate consistent phenotypic change is DNA methylation. To investigate whether early life effects on offspring phenotypes are mediated by DNA methylation, we cross-fostered great tit (Parus major) nestlings and manipulated their brood size in a natural study population. We assessed genome-wide DNA methylation levels of CpG sites in erythrocyte DNA, using Reduced Representation Bisulfite Sequencing (RRBS). By comparing DNA methylation levels between biological siblings raised in enlarged and reduced broods and between biological siblings of control broods, we assessed which CpG sites were differentially methylated due to brood size. We found 32 differentially methylated sites (DMS) between siblings from enlarged and reduced broods, a larger number than in the comparison between siblings from control broods. A considerable number of these DMS were located in or near genes involved in development, growth, metabolism, behavior and cognition. Since the biological functions of these genes line up with previously found effects of brood size and food availability, it is likely that the nestlings in the enlarged broods suffered from nutritional stress. We therefore conclude that early life stress might directly affect epigenetic regulation of genes related to early life conditions. Future studies should link such experimentally induced DNA methylation changes to expression of phenotypic traits and assess whether these effects affect parental fitness to determine if such changes are also adaptive.
    https://doi.org/10.3389/fevo.2021.609061
  • Integrative and Comparative Biology
    2020

    Epigenetics of animal personality

    Kees van Oers, Bernice Sepers, W. Sies, F. Gawehns, Koen Verhoeven, Veronika Laine
    The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. 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 be transferred from one generation to the next and can thereby be a component of the heritable 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 the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the 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.
    https://doi.org/10.1093/icb/icaa138
  • Journal of Ornithology
    10-07-2019

    Avian ecological epigenetics: pitfalls and promises

    Bernice Sepers, Krista van den Heuvel, Melanie Lindner, Heidi Viitaniemi, Arild Husby, Kees van Oers
    Epigenetic mechanisms can alter gene expression without a change in the nucleotide sequence and are increasingly recognized as important mechanisms that can generate phenotypic diversity. Most of our current knowledge regarding the origin and role of epigenetic variation comes from research on plants or mammals, often in controlled rearing conditions. Epigenetic research on birds in their natural habitats is still in its infancy, but is needed to answer questions regarding the origin of epigenetic marks and their role in phenotypic variation and evolution. Here we review the potential for studying epigenetic variation in natural bird systems. We aim to provide insights into (1) the origin of epigenetic variation, (2) the relationship between epigenetic variation and trait variation, and (3) the possible role of epigenetic variation in adaptation to changing environments. As there is currently little research on epigenetics in wild birds, we examine how findings on other taxa such as plants and mammals relate to birds. We also examine some of the pros and cons of the most commonly used methods to study patterns of DNA methylation in birds, and suggest some topics we believe need to be addressed to develop the field of wild avian epigenetics further.
    https://doi.org/10.1007/s10336-019-01684-5

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