Are we missing the boat? Time for using multiple independent loci in trematode diversity studies.

Over the years, the number of parasitic helminth species discoveries has not ceased to increase and the popularisation of the use of molecular methods has contributed greatly to sustain the growth in knowledge. However, molecular approaches evolved rapidly in the last 20 years. I argue that the research community working on parasitic helminths has lagged behind in the application of molecular methods that examine multiple loci to study species diversity. In this paper, I review the recent historical trends in the molecular markers used to study trematode diversity. Except for the emergence of pioneer mitogenome studies, the use of markers has not changed in the past 10 years. It is still restricted to single locus or a combination of two, rarely three, mitochondrial and ribosomal loci. I identify past and current molecular approaches providing data on multiple loci across the genome which have found resistance in the trematode and the helminth parasitology fields over the last four decades. I discuss how the knowledge gained from the analysis of genome-wide markers would benefit research on parasite diversity today, in particular for cases of species complexes, cryptic (or nearly cryptic) species, recently diverged species, and species with a complex taxonomic history, or a history of suspected mitonuclear discordance as well as for taxa with wide geographical distributions or species with disjoint distributions. Furthermore, I argue that both, studies with classical markers and reduced-representation genome studies providing genome-wide markers should not walk different paths but feedback on each other to advance the field forward. I examine some challenges and make recommendations for obtaining high-throughput molecular data of parasitic helminths.