Genetic and genomic approaches to the conservation of the threatened crucian carp Carassius carassius (L.) : phylogeography, hybridisation and introgression

Biological invasions can have dramatic detrimental impacts on ecosystems, however they also represent rich opportunities to study the evolutionary processes associated with them. Hybridisation and subsequent introgression are two such processes and are common among native and non-native species. The crucian carp, Carassius carassius (L.), is a European freshwater fish that is threatened throughout much of its native range by several factors including hybridisation and introgression with three non-native species, the goldfish, Carassius auratus (L.), the gibel carp, Carassius gibelio (Bloch), and the common carp, Cyprinus carpio (L.). The conservation of C. carassius is hampered by a lack of phylogeographic knowledge for the species and no knowledge of the extent or impact of hybridisation and introgression. Contemporary genomic approaches such as Restriction Site Associated DNA sequencing (RADseq) can offer unprecedented insights into such research areas, however RADseq comes with several sources of potential bias. Exploratory analyses in Chapter 2 show that two sources of bias in particular, null alleles and over merged ohnolog loci, are highly important in this dataset, but can be filtered using population genetics statistics. The filtered dataset is used in phylogeographic analyses in Chapter 3, along with microsatellite and mitochondrial DNA and show that C. carassius exists as two major lineages in Europe, which diverged approximately 2.26 million years ago, and should be treated as separate units for conservation. These lineages result from the C. carassius postglacial recolonisation routes thtough Europe, which are highly distinct from the general patterns seen in other freshwater fish species. These phylogeographic results showed high similarity between C. carassius in England and those in continental Europe, calling into question the presently assumed native status of C. carassius in England, which has been contentious in the past. Empirical tests of this status using microsatellites showed that, in fact, C. carassius is most likely introduced in England around the 15th century, raising interesting discussions pertaining to their conservation in the England. Lastly, in Chapter 5, microsatellite and RADseq approaches show that hybridisation between C. carassius and non-native species is prevalent where they are sympatric, however backcrosses are rare, and there is no evidence of further introgression between the species studied. Taken together, these results suggest that postzygotic mechanisms of isolation limit interspecific gene flow, and conservationists should focus further research on the direct impacts of non-native species and F1 hybrids