3 PhD positions at the University of Edinburgh (UK)

Project 1: Parent-of-origin specific genomic exclusion in insects
For most organisms, the two copies of a gene - one from their mother, the other from their father - are interchangeable. But sometimes this rule is violated. In a process called genomic imprinting the expression of one of the two copies of a gene is privileged, depending on its parental origin. Genomic imprinting is studied extensively in mammals and plants and most biologists consider it exclusive to these groups. In fact imprinting was first discovered in a different group, the insects, in the 1950s, decades before its discovery elsewhere. Since then however, the instances of genomic imprinting in insects have hardly been addressed and are unknown to most biologists.

The occurrence of genomic imprinting in some groups of insects is striking, as it involves a whole genome rather than just a couple of hundred genes as in mammals and plants. In males all genes inherited from his father are first silenced and subsequently eliminated from his sperm. So males can only pass their mothers genes to their offspring. This process seems regulated by some of the same epigenetic machinery (methylation, histone modification) as imprinting in mammals but many questions remain: How is the parental origin of chromosomes recognized? How are the chromosomes marked (differential methylation?), by which parent and at which stage in development? Why does imprinting only happen in males? Is the genomic imprinting also involved in sex determination, as sex is not genetically determined? Understanding the mechanisms of imprinting in these insects will allow for a better understanding of the evolution of this phenomenon, which is found in 10.000s of insects and has evolved repeatedly in different insect orders. Furthermore this study will provide insight in which aspects of the imprinting machinery are evolutionarily conserved across all animals.
This project will use an interdisciplinary approach by taking the methods developed for studying genomic imprinting in mammals and applying them to a promising new study system, the citrus mealybug (Planococcus citri). These small plant-feeding insects are easy to keep in the laboratory and uniquely suited for the proposed project. The project will involve the use of next generation sequencing approaches to 1) determine the methylation landscape across the genome, comparing the maternal and paternal chromosomes in males as well as sperm and eggs. 2) manipulate the methylation status of the genome (directly or by knocking out the responsible genes) and study the phenotypic effects on genomic imprinting 3) compare the transcriptome of male and female embryos, before and after the parental genome is silenced. The student will combine these data with the use of modern cytogenetic techniques to identify the factors involved in the silencing of the paternal genome in males and study the difference between male and female embryos to understand the understand the role of imprinting in sex determination.
more info at: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=48265&LID=455

Project 2: Paternal genome elimination in insects
Multicellular organisms can be regarded as nested hierarchies of cooperating entities. Genes live in genomes, genomes live in cells, and cells live in bodies. But under the surface of this apparent harmony is a hidden world of evolutionary conflict. The overarching aim of this project is to understanding how these conflicts can explain reproductive variability across life. In order to address this question the project will focus on reproductive systems that are characterized by "Genomic exclusion". Here, individuals discard the chromosomes they inherited from one parent, and only transmit those from the other. This creates conflict between the genomes of different parental origin, as the discarded chromosomes from one parent are less likely to be transmitted than those from the other. In the majority of cases the discarded chromosome are of paternal origin. This unusual type of reproduction, Paternal Genome Elimination (PGE), is found in thousands of species and has evolved at least six times independently across insects and mites (Normark 2003). It gives rise to sons in which genes inherited from their father are suppressed and eliminated, while those from the mother enjoy a transmission advantage. The main objective of this proposal is to understand how PGE evolves and how it shapes conflict between males and females and genes of maternal and paternal origin within them.

The project uses a small plant-parasite, the citrus mealybugs as a model system to study these questions. Mealybugs have a long evolutionary history of PGE, yet several lines of evidence indicate that the victory of the maternal genome is not always complete (Ross et al. 2010). To study this the project will combine both experimental and genomic approaches to test whether the paternal genome can escape elimination and/or transcriptional suppression in current and historical populations. Dependent on their interest, the student will be involved in laboratory experiments, genotyping and analysis of sequence and transcriptome data.

more info at: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=48206&LID=455


Project 3: The evolutionary origin of hermaphrodites in insects
Why there is such great variation in the ways that animals reproduce remains an unsolved mystery in evolutionary biology. This project aims to study this question by focusing on a group of insects whose reproduction is incredibly variable and in which evolutionary innovations have reduced the importance of males (Ross et al. 2010). Specifically it focuses on a small plant feeding insect - the cottony cushion scale insect Icerya purchasi - in which evolution appears to have driven the male to become a parasite living in the body of the female, producing sperm and fertilising her from within. This turns females into functional hermaphrodites. Recent evolutionary theory suggests that this system might have evolved from conflict between males and females over how many eggs a male gets to fertilize (Gardner and Ross 2012). However many questions remain: based on our current understanding we would expect that all reproduction happens through self-fertilization of hermaphrodites. However we do find true males in natural populations, and these males have been shown to mate with the hermaphrodites in the laboratory. This raises the question, can the sperm of these males compete with the sperm already present within the hermaphrodite and can these male infect their daughters with new parasitic male tissue? Other questions include, the role of bacteria living within the cells of Icerya purchasi and why and when mothers produce sons instead of hermaphrodites.

This project will combine laboratory experiments and genetic analyses. Depending on the interest of the student these results can be combined with observations of mating behavioural, microscopy of early embryogenesis to study the establishment of the male cells, antibiotics experiments and evolutionary theory.

more info at: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=48404&LID=455

Dr Laura Ross
NERC Independent Research fellow

Institute of Evolutionary Biology
University of Edinburgh
Ashworth Laboratories
Kings Buildings
West Mains Road
Edinburgh
EH9 3JT

email: laura.ross@ed.ac.uk