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Global distribution of cryptic native, introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida

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Abstract

Biological invasions can pose a severe threat to coastal ecosystems, but are difficult to track due to inaccurate species identifications and cryptic diversity. Here, we clarified the cryptic diversity and introduction history of the marine amphipod Ampithoe valida by sequencing a mtDNA locus from 683 individuals and genotyping 10,295 single-nucleotide polymorphisms (SNPs) for 349 individuals from Japan, North America and Argentina. The species complex consists of three cryptic lineages: two native Pacific and one native Atlantic mitochondrial lineage. It is likely that the complex originated in the North Pacific and dispersed to the north Atlantic via a trans-arctic exchange approximately 3 MYA. Non-native A. valida in Argentina have both Atlantic mitochondrial and nuclear genotypes, strongly indicating an introduction from eastern North America. In two eastern Pacific estuaries, San Francisco Bay and Humboldt Bay, California, genetic data indicate human-mediated hybridization of Atlantic and Pacific sources, and possible adaptive introgression of mitochondrial loci, nuclear loci, or both. The San Francisco Bay hybrid population periodically undergoes population outbreaks and profoundly damages eelgrass Zostera marina thalli via direct consumption, and these ecological impacts have not been documented elsewhere. We speculate that novel combinations of Atlantic and Pacific lineages could play a role in A. valida’s unique ecology in San Francisco Bay. Our results reinforce the notion that we can over-estimate the number of non-native invasions when there is cryptic native structure. Moreover, inference of demographic and evolutionary history from mitochondrial loci may be misleading without simultaneous survey of the nuclear genome.

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Acknowledgements

This research was supported by the National Science Foundation (OCE-1357386 and OCE-1924599). The authors thank those listed in Table 2 for help with sample collection, and especially Stacy Krueger-Hadfield, Macarena Valinas, Glauco Machado, Ben Flanagan. We thank Chris Nice and Katie Bell for facilitating the RADseq analysis and providing barcoding primers, and Jonathon Stillman, Anna Sellas, Allan Strand, Gavin Naylor, and Amy Fowler for thoughtful advice and feedback.

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  1. Department of Biology, College of Charleston, 29412, Charleston, South Carolina, USA

    Katherine E. Harper & Erik E. Sotka

  2. Estuary & Ocean Science Center, Department of Biology, San Francisco State University, 94920, Tiburon, California, USA

    Lauren A. Scheinberg & Katharyn E. Boyer

  3. California Academy of Sciences, 94118, San Francisco, California, USA

    Lauren A. Scheinberg

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Harper, K.E., Scheinberg, L.A., Boyer, K.E. et al. Global distribution of cryptic native, introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida. Conserv Genet 23, 791–806 (2022). https://doi.org/10.1007/s10592-022-01452-8

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