Epigenetic adaptation

1 PhD project offered in the IPP summer call 2019 field Evolution & Gene Regulation

Scientific Background

Hybrid origins followed by clonal reproduction has been demonstrated for all parthenogenetic species within the lizard genus Aspidoscelis. Interspecific hybridization endows offspring with high levels of heterozygosity, but lack of genetic diversity and limited ability to evolve. Clonal reproduction should thus condemn such obligate unisexuals to rapid extinction. However, information on genetic and epigenetic diversity within unisexual populations is sparse, and the ages of most parthenogenetic vertebrate lineages are unknown. Hybrids that reproduce "clonally" may diversify by mutation accumulation and epigenetic effects on gene expression. Here we propose to test the hypothesis that epigenetic mechanisms result in widespread allele-specific gene expression in parthenogenetic lizard species of hybrid origin. Ploidy elevation further increases heterozygosity, and the additional genomes in triploid and tetraploid lineages expand the genetic repertoire that permits further adaptation through allele-specific gene expression.
The side-by-side comparison of first-generation hybrids with parthenogenetic individuals that originated from the same parental species in nature many generations ago provides a unique opportunity to examine adaptation to the presence of divergent genomes in the same organism.

PhD project 4: Epigenetic adaptation

The incoming student will use RNA seq, ChIP seq and bioinformatics to analyze the extent and distribution of allele-specific gene. This will provide the foundation to investigate the regulatory mechanisms that underlie allele-specific expression in hybrids and parthenogenetic species. Instances where allele-specific expression is seen either in first generation hybrids or parthenogenetic animals - but not in both - will be a particular focus as these are prime candidates for epigenetic adaptation. We will examine the DNA methylation status of affected promoter regions and probe for differences in chromatin modifications. These studies will provide insights into how allele-specific gene expression is established, fixed and maintained over generations. In addition, it will provide the first high-resolution analysis of epigenetic diversity in clonally reproducing vertebrate lineages

Relevant publications

Lutes, A.A., Neaves, W.B., Baumann, D.P., Wiegraebe, W., and Baumann, P. (2010). Sister chromosome pairing maintains heterozygosity in parthenogenetic lizards. Nature 464, 283-286.

Lutes, A.A., Baumann, D.P., Neaves, W.B., and Baumann, P. (2011). Laboratory synthesis of an independently reproducing vertebrate species. Proc Natl Acad Sci U S A 108, 9910-9915.

Neaves, W.B., and Baumann, P. (2011). Unisexual reproduction among vertebrates. Trends in Genetics 27, 81-88.

Newton, A.A., Schnittker, R.R., Yu, Z., Munday, S.S., Baumann, D.P., Neaves, W.B., and Baumann, P. (2016). Widespread failure to complete meiosis does not impair fecundity in parthenogenetic whiptail lizards. Development 143, 4486-4494.

Contact Details

Prof. Peter Baumann