Abstract
Assessing genomic diversity and population structure of non-indigenous species is crucial to develop adequate management strategies. However, in species with scarce material for DNA extraction, applying genomic techniques can be a difficult task. Here we set a protocol for small DNA samples combining whole genome amplification (WGA) and genotyping-by-sequencing (GBS). This protocol was applied to the worldwide invasive colonial ascidian Didemnum vexillum using a single zooid per colony. WGA–GBS performance was tested using half zooids, providing empirical demonstration for genotyping reliability. We analysed 296 individuals from 12 localities worldwide including native and the main invaded areas. Polymorphic loci datasets generated by locality, area and globally, identified genetic differentiation at all levels. The two groups found in Japan, the native area, matched Cytochrome Oxidase I clades and were strongly differentiated at the genomic level suggesting reproductive isolation. Our genomic analyses confirmed that only one clade spread worldwide. We also detected some clones, always within the same locality. Genetic diversity was high in both the introduced and in the native area. Three independent colonisation events determined the global distribution of the species, although population pairwise comparisons within each introduced genetic cluster were significant. Human-mediated transportation seems to drive the distribution pattern of this species worldwide and regionally, as there is a lack of isolation by distance within introduced areas. Diverse and well differentiated populations point to a high expansion potential of this worrisome worldwide invader.
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Acknowledgements
We are deeply indebted to all people that contributed providing samples for this study: Gretchen Lambert, Ian Davidson, Mike Page, Judith Pederson, and Frédérique Viard. We specially thank Margarita Fernández, Carles Bori, Davide Tagliapietra, Marco Sigovini and Irene Guarneri for their help during sampling in Ebro Delta and Venice; Marc Rius for help while sampling in UK, and Gaku Kumano for assistance with the Aomori sampling. This research was funded by the projects CHALLENGEN and PopCOmics (CTM2013-48163 and CTM2017-88080, MCIU/AEI/FEDER/UE) from the Spanish Government. MC was funded by a predoctoral FPI contract of the Spanish Government. This is a contribution from the Consolidated Research Group “Benthic Biology and Ecology” SGR2017-1120 (Catalan Government).
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XT and MP designed research. MC and XT collected samples. MC performed laboratory work, ran the bioinformatics pipeline, and wrote the first draft of the manuscript. All authors contributed to analyses, discussed and interpreted results, and revised the manuscript.
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Raw reads from all individuals, including information of location of all samples, can be found at NCBI SRA Bioproject PRJNA555829. The genotypic data used in the analyses of global, clade A and clade B individuals is available in Appendices S9 to S11. All loci datasets will be available upon request to the authors.
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Casso, M., Turon, X. & Pascual, M. Single zooids, multiple loci: independent colonisations revealed by population genomics of a global invader. Biol Invasions 21, 3575–3592 (2019). https://doi.org/10.1007/s10530-019-02069-8
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DOI: https://doi.org/10.1007/s10530-019-02069-8