Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes

publisher: Elsevier articletitle: Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes journaltitle: Molecular Phylogenetics and Evolution articlelink: http://dx.doi.org/10.1016/j.ympev.2017.03.004 content_type: article copyright: Crown Copyright © 2017 Published by Elsevier Inc. All rights reserved.The file attached is the final draft version of the article

Platyhelminth systematics and the emergence of new characters

Since the inclusion of molecular data in modern phylogenetic analyses, significant progress in resolving the origins and radiation of flatworms has been made, although some key problems remain. Here I review developments in the supply and use of systematic characters that provide the basis for diagnosis and phylogeny reconstruction, that in turn have driven systematic revisions and the interpretation of broader evolutionary patterns and processes; focus is placed on the parasitic taxa. Although useful tools have been refined to the point of becoming established systematic markers of broad utility, attention to the need for denser gene and taxon sampling is addressed in the light of unresolved questions and current trends in molecular systematics, from nucleotide to genome. Tradition and the nature of available comparative information tends to dictate the choice of systematic markers, but faced with incongruent phylogenies, the emergence of new technologies and the need for rapid species diagnosis, there is a pressing need to assess and standardize our choice of tools so they are fit for purpose, available to all and used widely. I present a brief review of existing and potential sources of phylogenetic characters and discuss their likely value in the context of the systematics and diagnostics of parasitic flatworms

The mitochondrial genome of <i>Gyrodactylus derjavinoides</i> (Platyhelminthes: Monogenea) - A mitogenomic approach for <i>Gyrodactylus</i> species and strain identification

Systematists and evolutionary biologists are constantly on the lookout for new sources of characters to discriminate amongst taxa and estimate interrelationships within and between taxa. Entire mitochondrial genomes provide a wealth of data, both at the nucleotide and amino acid level. Molecular markers are of particular utility when applied to small, morphologically conserved taxa, as is the case for many monogenean ectoparasites of fish. Gyrodactylus species display a considerable degree of anatomical conservatism, complicating diagnostics based solely on morphology, and some are significant pests of wild and cultured fish. Here we sequenced the complete mitochondrial genome of Gyrodactylus derjavinoides Malmberg, Collins, Cunningham & Behiar 2007, one of the most frequently found gyrodactylid species on salmonids in Scandinavia, and compared it with the recently published genomes of Gyrodactylus salaris Malmberg, 1957 and Gyrodactylus thymalli Zitnan 1960. Through comparative sliding window analysis we identified regions of high sequence variability and designed new primer sequences. In total, 6 new primer pairs have been developed, amplifying fragments of cox1, cox3, nad1, nad2, nad4, nad5 and atp6. Together, they amplify regions capturing almost half the nucleotide variability present in the complete mitochondrial genome. These degenerate primers should also work for other Gyrodactylus species parasitizing salmonids. In addition, we developed a multiplex assay that simultaneously amplifies four fragments in a single PCR reaction. Besides the diagnostic value, these fragments can be used for studying the transmission dynamics of Gyrodactylus, providing crucial information for an improved understanding of the spread and epidemiology of these important fish pathogens

Diverse Applications of Environmental DNA Methods in Parasitology

Nucleic acid extraction and sequencing of genes from organisms within envi- ronmental samples encompasses a variety of techniques collectively referred to as environmental DNA or ‘eDNA’. The key advantages of eDNA analysis include the detection of cryptic or otherwise elusive organisms, large-scale sampling with fewer biases than specimen-based methods, and generation of data for molecular systematics. These are particularly relevant for parasitology because parasites can be difficult to locate and are morphologically intractable and genetically divergent. However, parasites have rarely been the focus of eDNA studies. Focusing on eukaryote parasites, we review the increasing diversity of the ‘eDNA toolbox’. Combining eDNA methods with complementary tools offers much potential to understand parasite communities, disease risk, and parasite roles in broader ecosystem processes such as food web structuring and com- munity assembly