Our research interests include:
- The analysis of population genetic/genomic structure
- Phylogeography and phylogenetics
- Evolution of adaptive traits and functional analysis of genomes
- Molecular evolution of genes and genomes
- Ecological genetics of clonal animals
- Ancient/recovered DNA in molecular ecology
- Mechanisms of speciation, especially in tropical freshwater fishes
- Conservation genetics
- Genetic management of commercially exploited species
- DNA barcoding
- Metabarcoding of community and environmental DNA (eDNA)
- Metagenomics and microbiomes
- Wildlife forensics
- Traceability of fish and fish products
Fisheries research themes include stock structure analysis of exploited fishes, estimation of effective population size, assessing long-term changes in exploited species, the impact of genetics on stock recovery, DNA barcoding and conservation of genetic resources. Pioneering contributions, many in association with the Evolutionary Biology Group at the University of Hull (1996-2004), UK include:
- The first comparative analysis of resting egg bank and contemporary zooplankton populations using PCR-based DNA recovery, contesting classical models on the extent and maintenance of genetic diversity in cyclic parthenogens.
- Application of modern phylogeographic methods which have been part of a paradigm shift in consideration of zooplankter diversity and speciation.
- Provision of estimates of population structuring and the first comprehensive phylogeny of Lake Malawi cichlid fishes showing evidence for sympatric speciation.
- The first empirical demonstration that loss of genetic variability is associated with over-fishing in a marine fish.
- Technical developments which open up innovative approaches in molecular ecology, including: (a) rapid PCR-based protocol for microsatellite isolation (PIMA), (b) the first published accounts of DNA recovery, microsatellite and mtDNA amplification from sediment-borne resting eggs and archived fish otoliths dating back 45 years, (c) application of 454 sequencing (“massively parallel sequencing”), for the analysis of marine meiofaunal biodiversity, (d) SNP discovery in commercially exploited species, including cod, hake, herring and sole, (e) 454
- Roche transcriptome assembly and microarray design.
- Providing novel perspectives of marine metzoan biodiversity/macroecology using second-generation environmental sequencing.
- Among the first demonstrations of genomic signatures of directional selection in wild cod populations.