Mining various genomic resources to resolve old alpha-taxonomy questions: A test of the species hypothesis of the Proteocephalus longicollis species complex (Cestoda: Platyhelminthes) from salmonid fishes

High-throughput sequencing strategies became commonly employed to study non-model parasites, but the corresponding genomes and transcriptomes were seldom mined following the original publication. Similar to the data generated with genome skimming techniques based on shallow-depth shotgun gen-omes, various genomic and transcriptomic resources can be screened for useful molecular phylogenetic markers traditionally characterised with Sanger sequencing. Here, we provide an example of a strategy using reduced-representation genomic as well as transcriptomic data to obtain broad insights into the molecular diversity of the cestode Proteocephalus longicollis, a common parasite of salmonids distributed throughout the Holarctic region. We extract popular mitochondrial and nuclear ribosomal markers from various genomic resources for hundreds of parasite specimens from multiple European whitefish popu-lations and compare those with Proteocephalus representatives from other species of salmonids and var-ious geographical regions. In contrast with the previous morphology-based assessments, molecular phylogeny reveals a high degree of genetic divergence between Proteocephalus isolates from different sal-monids, contrastingly low genetic differentiation within the parasite's populations hosted by the European whitefish (Coregonus lavaretus species complex), and a sister species relationship of Proteocephalus from European whitefish and Proteocephalus percae, a parasite of European perch (Perca fluviatilis). Proteocephalus spp. from North American lake whitefish, brown trout and Arctic charr each formed clearly distinct lineages. These results advance our understanding of the interrelationships of the Proteocephalus-aggregate, a well-recognized clade of Holarctic freshwater fish proteocephalids, and support resurrection of some of the nominal species of Proteocephalus, including Proteocephalus exiguus La Rue, 1911 from North American coregonids and Proteocephalus fallax La Rue, 1911 from European C. lavaretus, reserving Proteocephalus longicollis (Zeder, 1800) exclusively for parasites of Salmo trutta. (c) 2023 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Automated summary

High-throughput sequencing strategies have been commonly used to study non-model parasites, but the corresponding genomes and transcriptomes are seldom explored. In this study, reduced-representation genomic and transcriptomic data were used to investigate the molecular diversity of the cestode Proteocephalus longicollis. Molecular phylogeny revealed high genetic divergence between Proteocephalus isolates from different salmonids, low genetic differentiation within the parasite's populations hosted by the European whitefish, and distinct lineages for Proteocephalus spp. from North American lake whitefish, brown trout, and Arctic charr. These findings advance our understanding of the interrelationships within the Proteocephalus-aggregate and support the resurrection of some nominal species.