Cryptic lineages and hybridization in a cosmopolitan marine invertebrate
Harper, Katherine Elizabeth
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Some biological invasions pose a severe threat to marine coastal ecosystems, but can be difficult to track due to inaccurate species identifications and unrecognized cryptic diversity. Expanding on the published work of Pilgrim and Darling, we employed both mtDNA and nuclear genotypes to clarify the historical and recent introduction history of the benthic marine amphipod <i>Ampithoe valida</i>. We Sanger sequenced a subunit of the mitochondrial cytochrome oxidase I (COI) for 703 individuals and genotyped a single-nucleotide polymorphism (SNP) from each of 10,295 anonymous restriction-digested genomic fragments for 349 individuals. We confirmed that <i>Ampithoe valida</i> is comprised of three cryptic mitochondrial lineages. With few exceptions, clade C haplotypes were confined to the western United States and northern Japan, clade B dominated southern Japan and clade A dominated the eastern United States. Individuals with these mitochondrial lineages were also strongly divergent at nuclear SNPs in nearly all populations. It seems likely that <i>A. valida</i> originated somewhere in the North Pacific where it ultimately diverged into two lineages and dispersed to the north Atlantic via a trans-arctic exchange approximately 3 MYA. More recently, three introduction events with distinct genetic outcomes have occurred. In Argentina, individuals have both Atlantic mitochondrial and nuclear genotypes indicating that <i>A.valida</i> was introduced from the northwest Atlantic. Populations with evidence of hybridization occurred in two estuaries of the western United States. San Francisco individuals were composed of Pacific clade B and a largely Atlantic nuclear genome, while Humboldt Bay individuals were Atlantic haplotype A and a mix of Atlantic and Pacific nuclear backgrounds. Mito-nuclear discordance suggests recent hybridization of Atlantic and Pacific sources in these estuaries and possibly adaptive introgression of mitochondrial loci, nuclear loci, or both. More generally, we find that mitochondrial loci alone generate a mistaken demographic and evolutionary history that can be resolved with nuclear SNPs.