Dactylogyrus species (Dactylogyridae: Monogenea) are a group of monogenean gill parasites that are highly specific to freshwater fish of the family Cyprinidae. Dactylogyrus species were sampled from 19 cyprinids and one percid collected in Europe. Using partial 18S rDNA and ITS1 sequences, a phylogeny of 51 Dactylogyrus species was reconstructed to investigate the patterns of parasite speciation and diversification. Three main Dactylogyrus lineages were recognized from all phylogenetic trees, that is, analysis of 18S rDNA alone and combined 18SrDNA and ITS1. The first lineage associates the Dactylogyrus species of Cyprinus carpio and Carassius auratus of the Cyprininae; the second associates Dactylogyrus species of the Gobioninae, Pseudorasbora parva of the Rasborinae, and Ctenopharyngodon idella of the Cyprininae; and the third associates Dactylogyrus species of the Leuciscinae and Alburninae and Barbus barbus of the Cyprininae. Our results suggest that the genus Dactylogyrus is of quite recent origin and that these three lineages separated from each other in a very short period of time. Host subfamily mapping onto the parasite tree inferred from analysis of the combined dataset showed that the Cyprininae could be plesiomorphic hosts for Dactylogyrus. Dactylogyrus parasites would have secondarily colonized the Percidae and representatives of the Leuciscinae, Alburninae, Gobioninae, and Rasborinae. Comparison of host and parasite phylogenetic relationships indicated that a very high number of parasite duplications occurred within two of the three Dactylogyrus lineages. Dactylogyrus diversification can be mainly explained by sympatric intrahost speciation events that seem to be correlated to strict host specificity. Moreover, the present study shows that the congeneric parasites speciating within one host tend to occupy niches within hosts differing at least in one niche parameter.
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