Wednesday, August 26, 2020

New Paper: Acanthocephalans from Australian Marine Fish

I've got a new paper out, this time on Acanthocephalans. This was one of those projects that started off simple and then snowballed into a serious undertaking.

D.C. Huston . T.H. Cribb and L.R. Smales. 2020. Molecular characterisation of acanthocephalans from Australian marine teleosts: proposal of a new family, synonymy of another and transfer of taxa between orders. Systematic Parasitology.

Acanthocephalans are a strange group of obligate endoparasites. Generally, they have two-host life cycles, with an invertebrate intermediate and vertebrate definitive host. Despite being worm-like and traditionally lumped in with the parasitic 'helminths', molecular phylogenetic study has demonstrated that acanthocephalans are most closely related to the rotifers. A most curious evolutionary trajectory for an ancient rotifer-like beast.

A lot of the specimens I was after for my PhD research came from species of an unusual family of fishes, the Kyphosidae. Well, many of the kyphosids I found had heavy infections of acanthocephalans. This project began because I wanted to identify them. Next thing I knew I was taking all the acanthocephalans from the Marine Parasitology Lab at The University of Queensland to the South Australian Museum to work with Dr Lesley Smales identifying them. I noticed that, at that time, there weren't any molecular sequences available for any Australian acanthocephalan. Thus I started sequencing all the species in my collection. This took years - I was doing this work as a side-project to my PhD on digenetic trematodes, and more and more acanthocephalan specimens kept getting added as the years wore on. It was worth it in the end - we got some interesting phylogeny results which led us to do some much needed taxonomic revisions and we even got to propose a new family.

Publishing this paper also allowed me to experience the joys of making a mistake in something I've put out on public record. Well, I say mistake, but really it was mistakes... I requested a correction shortly after some things were brought to my attention - and its just come out ( Somehow a couple typos made it all the way through drafting, revision and peer review. You would think that after reading through a draft you've been writing 10-20+ times you would notice these things, but I guess sometimes its easy to glaze over as you go, especially when reading over convoluted scientific names (note to self - always add scientific names to the word processor dictionary). 

As if that wasn't enough, I found myself greatly embarrassed when another researcher let me know that two of the cox1 sequences I uploaded to GenBank were coming up in odd places in the phylogeny they were building. Well, I double checked them and sure enough they were contaminated with DNA from other acanthocephalans from the same sequencing batch. I immediately contacted GenBank and had them flag those sequences - so they are no longer available for download. This problem seems to be a result of a labeling error in the spreadsheet I was using to track the sequences as I generated them over the many years of the project. I provided the cox1 sequences as part of the project, but didn't actually do anything with them for the paper, so I didn't notice their odd phylogentic positions myself. (second note to self - always double check each sequence via a quick tree and BLAST before uploading). All the analyses in the paper used only 18S and/or 28S sequences. Anyway, embarrassing, but at least the error didn't impact any of the results of the study...! So overall a bit of a lesson to self. It is easy to make silly mistakes even with a doctorate and huge amounts of experience writing and doing science. Accepting mistakes and making corrections is part of the scientific endeavor - transparency and honesty are key. I've heard it said somewhere, in discussions on corrections to scientific works: 'to err is human, to correct divine' !

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