PhD Studentship: A Genomic approach to the Genetic Impact of an Invasive Congener on a threatened native pond fish

Daniel Jeffries

University of Hull & Cefas-Lowestoft

Supervisor(s): Bernd Hänfling, Lori Lawson-Handley & Gordon Copp

Research on invasive species and invaded communities is essential to understanding and predicting biodiversity change. Furthermore, introduced species are excellent model systems with which to address fundamental questions in biology. However, biological invasions can have dramatic impacts on native species and this appears to be the case for the crucian carp Carassius carassius, which is native to northwestern Europe (including southeast England), and under threat from non-native congeners goldfish C. auratus and gibel (a.k.a. Prussian) carp C. gibelio. Conservation efforts for C. carassius are hampered by the taxonomic ambiguity which exists between C. carassius, C. auratus and C. gibelio; the problems in classifying and identifying separate Carassius spp. have introduced doubt regarding the current distributions of all Carassius spp. Consequently, impact assessment has been difficult; for example, it has only recently been demonstrated that around 70% of pure C. carassius populations in Norfolk, UK have been replaced by non-native Carassius species in the past 30 years.

In order to provide impact assessments in invasive systems, conservation geneticists have previously concentrated their studies on the lowered fitness and adaptability of native species in small populations due to the loss of genetic variability. These studies almost exclusively use near-neutral genetic markers, which cannot be a proxy for genetic variation in genes which have selectively important functions. Furthermore, neutral markers will lose genetic variation more rapidly than those under selection, with there being no correlation between molecular marker heterozygosity and heritabilities. There is likely therefore to be a difference between the impact of bottlenecks and/or climate change on genetic variation in neutral and non-neutral genes. Additionally, the study of hybridisation has been carried out previously using mainly only a small number of molecular markers, which do not have sufficient power to reveal the introgression of single genes. These limitations have left two fundamental evolutionary questions unanswered: to what extent is adaptively important genetic variation affected by bottlenecks in small, isolated populations, and, what are the genetic effects associated with environmental change (through invasive species and climate change) on fragmented populations?

With the development of next-generation sequencing, it is now feasible to address these research gaps. Next generation sequencing techniques allow for genome-wide sequencing, including selectively functional genes, thus providing a better representation of the genetic variation within individuals and populations and allowing for comparison between the behaviour of these genome regions during bottlenecks. Furthermore, these techniques allow for the identification of small regions in the genome of native species that have introgressed from non-natives or vice versa. Simultaneously, the genomic analyses of this system, in conjunction with microsatellite analyses, will shed light on the genetic structure of C. carassius populations in both the UK and continental Europe, providing the means to put forward comprehensive and much needed Biodiversity action plans for this threatened species.


Daniel Jeffries
Evolutionary Biology Group
Hardy Building
University of Hull