Molecular approaches to trematode systematics: ‘best practice’ and implications for future study

Abstract

'Molecular approaches to trematode systematics: 'best practice' and implications for future study ', Systematic Parasitology, 93(3), 295-306. The final publication is available at Springer via http://dx.doi.org/10.1007/s11230-016-9631-2.The full details of the published version of the article are as follows: However, since the late-1980s we have seen an increased integration of genetic data to overcome problems encountered when morphological data are considered in isolation. Here, we provide advice regarding the 'best molecular practice' for trematode taxonomy and systematic studies, in an attempt to help unify the field and provide a solid foundation to underpin future work.Emphasis is placed on defining the study goals and recommendations are made regarding sample preservation, extraction methods, and the submission of molecular vouchers. We advocate generating sequence data from all parasite species/host species/geographic location combinations and stress the importance of selecting two independently evolving loci (one ribosomal and one mitochondrial marker). We recommend that loci should be chosen to provide genetic variation suitable to address the question at hand and for which sufficient 'useful' comparative sequence data already exist. Quality control of the molecular data via using proof-reading Taq polymerase, sequencing PCR amplicons using both forward and reverse primers, ensuring that a minimum of 85% overlap exists when constructing consensus sequences, and checking electropherograms by eye is stressed. We advise that all genetic results are best interpreted using a holistic biological approach, which considers morphology, host identity, collection locality, and ecology. Finally, we consider what advances next-generation sequencing holds for trematode taxonomy and systematics.

An updated look at the uneven distribution of cryptic diversity among parasitic helminths

“…In this group, the trend is to use a combination of molecular markers since half of the 64 cryptic species reports used both nuclear and mitochondrial markers to detect cryptic species. Just for trematodes, Blasco-Costa et al (2016) recently found that in the past 5 years most of the studies focusing on taxonomy, diversity, phylogeny and life cycles that generated mitochondrial sequences also reported nuclear DNA sequences. Actually, Blasco-Costa et al (2016) argued that the best practice for the discipline would be to obtain sequence data from at least two independently evolving or unlinked loci, i.e.…”

Two known and one new species of Proctoeces from Australian teleosts: Variable host-specificity for closely related species identified through multi-locus molecular data

“…However, the question of to which, if any, of the existing named species the five unnamed taxa can be identified is exceptionally problematic, given the issues identified by Bray & Gibson[39], Bray[16] and others -morphological plasticity, uncertainty regarding the extent to which species may be widespread and the reliability of their patterns of host-specificity. The ultimate solution to these issues can only lie in further study, ideally in the form of combined morphological and molecular analyses incorporating multiple biomarkers[41]. Studies that examine material from type-hosts and type-localities of existing species will be especially important.…”

Molecular identification of morphologically similar microcercous cercariae of two trematode families, Paragonimidae and Troglotrematidae, concurrently found in the same snail species of the subfamily Triculinae

“…A fragment of the internal transcribed spacer 2 region (ITS2) was chosen for analyses because this region has been proven to be a reliable marker and has been commonly used to identify digenean species (Esteban et al 2014, Blasco-Costa et al 2016, Chai 2019. Total genomic DNA was extracted from cercariae isolated from infected snails using the Dneasy Blood and Tissue Kit (QIAGEN, Hilden, Germany).…”

“…Generally, it is possible to identify cercarial specimens to the family level, and occasionally to the genus level, using morphological criteria, but it is not easy to differentiate cercariae of related genera/species based on their morphology alone (Frandsen and Christensen 1984). Alternatively, molecular techniques have been used to support the morphological identification (e.g., Bartoli et al 2000, Pina et al 2007, Chuboon and Wongsawad 2009, Kudlai et al 2015, Blasco-Costa et al 2016, Chontananarth et al 2017, Doanh et al 2018.…”