DaveLunt.net - Dr Dave Lunt | PDRA Evolutionary Comparative Genomics
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PDRA Evolutionary Comparative Genomics



A PDRA position is available in my lab to work on the project ‘The evolutionary genomics of sexual recombination’. The research project is a large, 3-year, multi-centre NERC-funded collaboration using modern evolutionary comparative genomics approaches to study the rate and pattern of genome sequence change with and without the action of meiosis, and across different levels of inbreeding. The project will be carried out in a phylogenetic design, on a newly generated nematode multi-genome data set, leading to advances in understanding the role of reproductive mode in shaping the structure and diversity of genomes.

The postdoc based in Hull will examine transposable elements, gene families and the type of mutational patterns found across the nematode genomes. This will require a good understanding of evolutionary biology (molecular evolution, population genetics, bioinformatics etc), an interest in the causes and consequences of sexual reproduction, and an ability for large-scale data analysis. This is an exciting project using an enormous data set to address really fundamental biological questions, and I anticipate it could produce some very substantial publications.

The project is a collaboration with Prof Mark Blaxter at the University of Edinburgh with a postdoc on each campus. The Edinburgh PDRA will be responsible for genome assembly and annotation, and the Hull  PDRA evolutionary analysis of transposons, gene families, and mutational processes (although there will be extensive collaboration and some overlap of roles).

Brief details of the project are below and you are welcome to contact me to discuss the position, but your application will need to go through the official channels.

Vacancy Reference: FS0217
Salary range: £25,251 – £30,122 pa Closing Date: 12 August 2012
Informal enquiries to Dr Dave Lunt: d.h.lunt@ hull.ac.uk, dave.lunt@gmail.com
Official info and online application: http://bit.ly/PYo0QJ


The Evolutionary Genomics of Sexual Recombination

Meiotic recombination is one of the fundamental forces of evolution and plays a very significant role in both generating and mixing the genetic diversity present in sexual organisms. Recombination is also instrumental in shaping the content of eukaryotic genomes through processes such as unequal crossing over and gene duplication, concerted evolution, allelic sequence divergence, and the spread of transposable elements. The puzzling predominance of sexual reproduction amongst animals has been repeatedly identified as one of the major outstanding questions in biology and has received an enormous amount of study, particularly from a theoretical perspective. Empirical data, however, has lagged behind, and large-scale data sets able to contribute to our understanding of the mechanisms and action of sexual recombination in the wild are particularly needed to generate novel hypotheses and test existing predictions. Up until recently, it was almost inconceivable that such empirical studies could consist of whole genome sequences of multiple closely related species chosen for their specific utility in addressing the problem at hand. With the advent of second generation sequencing such comparative evolutionary genomic studies are now a reality.

In this project we will to study the role of meiotic recombination and reproductive mode in shaping the content and diversity of animal genomes using an exceptionally diverse and powerful natural system- the Root Knot Nematodes. We will analyze the genomes of 19 species of nematode in a single genus, Meloidogyne, in a phylogenetic design incorporating a range of reproductive modes both with and without meiosis. We will characterize genome evolution in a phylogenetic framework by studying, firstly, taxa defining multiple phylogenetically independent losses of meiosis, and secondly, closely related species that inbreed (meiotic parthenogenesis) or outbreed (sexual amphimixis).


The Evolutionary Genomics of Sexual Recombination

A 3-year PDRA position is now available at the University of Hull as part of a large, NERC-funded project entitled ‘The Evolutionary Genomics of Sexual Recombination’. Using modern evolutionary comparative genomics approaches we aim to study the rate and pattern of genome sequence change with and without the action of meiosis, and across different levels of inbreeding. The project will be carried out in a phylogenetic design, on a newly generated nematode multi-genome data set, leading to advances in understanding the role of reproductive mode in shaping the structure and diversity of genomes.

The puzzling predominance of sexual reproduction amongst animals has been repeatedly identified as one of the major outstanding questions in biology and has received an enormous amount of study. Meiotic recombination is one of the fundamental forces of evolution and plays a very significant role in both generating and mixing the genetic diversity present in sexual organisms. Recombination is also suggested to be instrumental in shaping the content of eukaryotic genomes. We are embarking on a three year project to study the role of breeding system and recombination in shaping the content and diversity of animal genomes using an exceptionally powerful natural system – the Root Knot Nematodes (Meloidogyne spp.). We will, for the first time, be able to take a comparative genomic view of radically different reproductive modes in a phylogenetic design. Together these studies will give us a novel and powerful understanding of the role sexual reproduction plays in shaping genome content.

This project is a collaboration between Dr Dave Lunt at the University of Hull and Prof Mark Blaxter at the University of Edinburgh. The goals of the project are to generate complete, annotated genome sequences for a set of Meloidogyne species (at least 16 genomes), carefully chosen to represent independent evolutionary contrasts in reproductive mode, and then to use these whole genome data to characterise the effect of organismal breeding system on abundance, diversity and distribution of transposable elements between amphimicts, automicts, and apomicts. We will also test for adaptive evolution of genes and gene families using statistical models of gene family evolution, and test sequence based signatures of adaptive evolution, relating these to loci involved in reproduction and plant-parasite interactions.

PDRA2- MOLECULAR EVOLUTIONARY ANALYSIS; UNIVERSITY OF HULL

Applicants with a strong background in evolutionary biology, bioinformatics and population genetics are invited for this PDRA position to analyse the new genome datasets. The post-holder will use modern evolutionary bioinformatic approaches to analyse transposable elements, gene families and the type of mutational patterns found across the phylogeny of nematode genomes generated in Edinburgh.

The PDRA will be based in the Evolutionary Biology Group at Hull University. The group is a large and interactive community of evolutionary biologists, with excellent facilities, and provides a great environment for investigating questions in genomics and breeding system.

We anticipate the successful candidate will work proactively and flexibly across the research groups to gain most from this enormous data set, address fundamental biological questions, and produce some very substantial publications.

You must have, or shortly obtain, a PhD in evolutionary biology, bioinformatics, population genetics or other directly relevant subject. An excellent understanding of the genetic consequences of sexual reproduction and the bioinformatic skills suitable to analyse large datasets would be advantageous.

Vacancy Reference: FS0217 Closing Date: 12 August 2012
Salary range: £25,251 – £30,122 pa
Informal enquiries to Dr Dave Lunt: d.h.lunt @hull.ac.uk, dave.lunt@gmail.com
Official info and online application: http://bit.ly/PYo0QJ

PDRA1- GENOME ASSEMBLY, ANNOTATION, AND ANALYSIS; UNIV OF EDINBURGH
Applications for this position are now closed.

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