Phylogenomic inference of the interrelationships of Lake Baikal sponges

Abstract

The endemic sponges of Lake Baikal are vital components of one of the most unique ecosystems on the planet. To date we have yet to satisfactorily resolve their systematic relationships. Their relatively slow rates of molecular change, a short branch length to the common ancestor of extant species, and very plastic morphology in some species make robust species assignment and differentiation difficult. Using recently published genomic and transcriptomic resources, a novel Swartschewskia papyracea transcriptome and a phylogenomic approach, we have reassessed relationships within the Lubomirskiidae, a family of freshwater sponges endemic to Lake Baikal. After orthology assessment, paralog pruning and data curation, a concatenated 2710 orthogroup, 463,187 site alignment was used to infer phylogenetic interrelationships between four members of the Lubomirskiidae, several freshwater sponge species and outgroup taxa, using Bayesian and Maximum Likelihood methods. This approach conclusively answers a number of previously recalcitrant questions. It confirms the position of Swartschewskia papyracea as the sister taxon to genera Lubomirskia and Baikalospongia. It strongly supports Lubomirskia monophyly, with Baikalospongia bacillifera as the sister taxa to the two species of Lubomirskia sampled here. It also confirms the relative branching arrangement of other common freshwater taxa, including the issue of Spongillidae paraphyly. This is key for interpreting the evolution of the Spongillida as a whole, and in particular, for understanding the evolution of the still enigmatic sponges of Lake Baikal.

Key words:

• Lake Baikal
• sponges
• Porifera
• phylogenomics
• phylogeny
• transcriptome

Acknowledgements

We thank our co-workers in the Riesgo and Itskovich labs for their support and comments on this manuscript. We thank two unnamed reviewers, and the editors, Andrea Waeschenbach and Peter Olson, of this manuscript for their constructive comments on this work.

Disclosure statement

The authors have no declarations of interest to make, and have no financial interest or benefits arising from the direct applications of this research.

Supplemental data

Supplemental data for this article can be accessed here: https://dx.doi.org/10.1080/14772000.2020.1827077.

Associate Editor: Andrea Waeschenbach

Additional information

Funding

This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No 750937. Sample collection was performed under Limnological Institute, Siberian Branch of the Russian Academy of Sciences state project number 0345-2019-0002 and supported by the Russian Foundation for Basic Research (RFBR) and the Department of Science and Technology (DST) under research project No. 19-54-45034 and by the RFBR under research project No. 20-04-00868.