Fish Genomics: Testing for Fishing-Induced Evolution using Genotyping-by-Sequencing of Modern and Ancient Snapper

We are seeking a highly-motivated PhD student for a project that aims to test for fishing-induced evolution in New Zealand Snapper (Chrysophrys auratus) using Genotyping-by-Sequencing (GBS) of modern and ancient DNA.  

Project Supervisors  
Dr. Peter Ritchie, Victoria University of Wellington (VUW), New Zealand  
Dr. Nic Rawlence, Department of Zoology, University of Otago, New Zealand  
Dr. Maren Wellenreuther, Plant and Food Research (PFR), Nelson, New Zealand  

Fishing typically targets larger individuals and thus has the potential to increase the reproductive success of small fish that mature early. Numerous studies have reported a decrease in the average size of heavily fished species and the age of maturation, but there is uncertainty about whether this is caused by directional selection on allele frequencies (evolutionary change). The overall goal of this PhD project is to test for fishing-induced evolution in New Zealand snapper by comparing DNA isolated from contemporary populations, to the DNA isolated from bones of pre-industrial fish samples. New Zealand has a unique record of snapper bones that have been preserved in prehistoric New Zealand middens (i.e. places where food remains were dumped or buried). The successful candidate for this project will be responsible for collecting a GBS dataset of genome-wide SNPs using DNA extracted from contemporary samples. This position will be based at Victoria University of Wellington (New Zealand). The data set collected from contemporary samples will be combined with a comparable dataset recovered from snapper ancient DNA that will be obtained by researchers at the Otago Palaeogenetics Laboratory. The complete physical isolation of the ancient and modern part of the project will ensure there is minimal risk of cross-contamination. This ambitious and innovative approach will provide the level of resolution needed to identify genomic regions that have experienced selection and make precise population genetic and demographic inferences possible.

PhD Project Aims  
1. To test whether size-selective industrial fishing is associated with a signature of genetic selection,  
2. Determine levels of genetic diversity and differentiation,  
3. Test for loci under selection and adaptive genetic variation.  

This project will provide an excellent opportunity to develop skills in the areas of genomics, bioinformatics and population genetics, and how they can be used to support sustainable harvesting. The PhD student will gain experience working with collaborators in New Zealand (Professor Hamish Spencer), Australia (Professor Mike Bunce), and Norway (Dr. Bastiaan Star). The PhD student will be a member of a highly active and collaborative group of researchers, and help develop population genomics and an understanding of how human activity is changing the environment.  

The successful candidate will be a highly-motivated researcher, with a strong background and interest in genomics and molecular evolution. Experience with a coding and/or scripting languages will be an advantage. This position will be based at Victoria University of Wellington and comes with a three-year scholarship that provides a stipend (NZ$27,500 pa) and university tuition fees. This project is supported by the New Zealand Marsden Fund.