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

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.

     

Genetic and historical evidence disagree on likely sources of the Atlantic amethyst gem clam Gemma gemma (Totten, 1834) in California

Aim Historical information about source populations of invasive species is often limited; therefore, genetic analyses are used. We compared inference about source populations from historical and genetic data for the oyster‐associated clam, Gemma gemma that invaded California from the USA Atlantic coast. Location Mid‐Atlantic (North Carolina, Maryland), Northeastern (New Jersey, New York, Massachusetts) and the California coasts (Elkhorn Slough, San Francisco Bay, Bolinas Lagoon, Tomales Bay, Bodega Harbor). Methods The documented history of transplantation of Eastern oysters to California was reviewed. Cytochrome c oxidase subunit I (COI) sequences from recent and archived clams were examined in a haplotype network. We used AMOVA to detect geographic genetic structure and a permutation test for significant reductions in diversity. Results Chesapeake Bay oysters were transplanted to New York prior to shipment to San Francisco Bay and from there to peripheral bays. Gemma in the Northeastern and Mid‐Atlantic regions were genetically differentiated. In California, populations in Bodega Harbor and Tomales Bay were genetically similar to those in the Mid‐Atlantic area while clams in San Francisco Bay, Elkhorn Slough and Bolinas Lagoon resembled populations in the Northeastern region. In California, genetic variation was not highest in San Francisco Bay despite greater magnitude of oyster plantings. Haplotypes varied over time in native and introduced populations. Main Conclusions Historical records and inferences from genetics agree that both Northeastern and Mid‐Atlantic regions were sources for Gemma in California. Only complex genetic hypotheses reconcile the strong segregation of haplotypes in California to the historical evidence of mixing in their proximate source (New York). These hypotheses include sorting of mixtures of haplotypes or selection in non‐native areas. Haplotype turnover in San Francisco and Massachusetts samples over time suggests that the sorting hypothesis is plausible. We suggest, however, that Gemma was introduced independently and recently to Tomales Bay and Bodega Harbor.     

BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity

Aim We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results Phylogenetic inference indicates that inaccurate species‐level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north‐eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north‐eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera.     

Cryptic genetic diversity in Rattus of the San Francisco Bay region, California

Invasive species can have complex invasion histories, harbor cryptic levels of diversity, and pose taxonomic problems for pest management authorities. Roof rats, Rattus rattus sensu lato, are common invasive pests of the San Francisco Bay Area in California, USA. They are a significant health risk and pest management efforts impose a large financial investment from public institutions and private individuals. Recent molecular genetic and taxonomic studies of black rats in their native range in Asia have shown that the species is a complex of two karyotypic forms and four mitochondrial genetic lineages that may represent four distinct species. We used mtDNA sequences and nuclear microsatellite variation to identify which mitochondrial lineages of the R. rattus group are present in the San Francisco Bay Area and to test for gene flow among them. We recovered specimens with mtDNA sequences representing two of the major mtDNA lineages of the R. rattus group. Microsatellite variation, however, was not structured in concordance with mtDNA lineages, suggesting a more complex history involving hybridization and introgression between these lineages. Although Aplin et al. (2011) and Lack et al. (2012) reported R. rattus Lineage II in North America, this is the first detailed examination of possible gene flow amongst lineages in this region.     

Slipping through the Cracks: The Taxonomic Impediment Conceals the Origin and Dispersal of Haminoea japonica,an Invasive Species with Impacts to Human Health

Haminoea japonica is a species of opisthobranch sea slug native to Japan and Korea. Non-native populations have spread unnoticed for decades due to difficulties in the taxonomy of Haminoea species. Haminoea japonica is associated with a schistosome parasite in San Francisco Bay, thus further spread could have consequence to human health and economies. Anecdotal evidence suggests that H. japonica has displaced native species of Haminoea in North America and Europe, becoming locally dominant in estuaries and coastal lagoons. In this paper we study the population genetics of native and non-native populations of H. japonica based on mt-DNA data including newly discovered populations in Italy and France. The conclusions of this study further corroborate a Northeastern Japan origin for the non-native populations and suggest possible independent introductions into North America and Europe. Additionally, the data obtained revealed possible secondary introductions within Japan. Although non-native populations have experienced severe genetic bottlenecks they have colonized different regions with a broad range of water temperatures and other environmental conditions. The environmental tolerance of this species, along with its ability to become dominant in invaded areas and its association with a schistosome parasite, suggest H. japonica could be a dangerous invasive species.     

European green crabs (Carcinus maenas) in the northeastern Pacific: genetic evidence for high population connectivity and current-mediated expansion from a single introduced source population

Aim The European green crab (Carcinus maenas) expanded dramatically after its introduction to the west coast of North America, spreading over 1000 km in < 10 years. We use samples of Carcinus maenas collected over time and space to investigate the genetic patterns underlying the species’ initial establishment and spread, and discuss our findings in the context of the species’ life history characteristics and demography. Location The central west coast of North America, encompassing California, Oregon, and Washington (USA) and British Columbia (Canada). Methods We collected 1040 total samples from 21 sites representing the major episodes of population establishment and expansion along the west coast of North America. Microsatellite markers were used to assess genetic diversity and structure at different time points in the species’ spread, to investigate connectivity between embayments and to estimate both short‐term effective population sizes and the number of original founders. Assignment testing was performed to determine the likely source of the introduction. Results Carcinus maenas in western North America likely derived from a single introduction of a small number of founders to San Francisco Bay, CA from the east coast of North America. Throughout its western North American range, the species experiences periodic migration between embayments, resulting in a minor loss of genetic diversity in more recently established populations versus the populations in the area of initial establishment. Main conclusions Low genetic diversity has not precluded the ability of C. maenas to successfully establish and spread on the west coast of North America. An efficient oceanographic transport mechanism combined with highly conducive life history traits are likely the major drivers of C. maenas spread. Evidence for a single introduction underscores the potential utility of early detection and eradication of high‐risk invasive species.     

Cryptic diversity of Melanochlamys sea slugs (Gastropoda,Aglajidae) in the North Pacific

North Pacific specimens of Melanochlamys sea slugs were examined morphologically (including the male reproductive morphology, shell and external coloration) and were sequenced for three genes (mitochondrial COI and 16S and nuclear H3). Phylogenetic and species delimitation analyses were used to determine the evolutionary relationships and species diversity among the specimens examined. Both molecular and morphological data revealed an unexpected high level of cryptic diversity. At least four distinct species occur on the Northwestern Pacific. Melanochlamys ezoensis occurs in Russia and temperate and cold areas in Japan. Three additional undescribed species occur in Japan and/or South Korea. One of the undescribed species occurs both in South Korea and in Japan, but only in Tokyo Bay, suggesting that it could be non‐native in Japan. Two distinct species occur on the Northeastern Pacific coast; Melanochlamys diomedea is widespread from Southern California to Alaska, whereas M. ezoensis was found only in San Francisco Bay, suggesting a human‐mediated introduction. This is further supported by the absence of records of M. ezoensis in San Francisco prior to 2001. The species diversity of Melanochlamys in the Northwestern Pacific is much greater than in the Northeastern Pacific; it is hypothesized that differences in geographic and ocean current system complexity might account for different responses to glacial extinction and postglacial expansion.     

Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America

Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.     

Invasion by a Japanese marine microorganism in western North America

The earliest record in western North America of Trochammina hadai Uchio, a benthic foraminifer common in Japanese estuaries, is from sediment collected in Puget Sound in 1971. It was first found in San Francisco Bay in sediment samples taken in 1983, and since 1986 has been collected at 91% of the sampled sites in the Bay, constituting up to 93% of the foraminiferal assemblage at individual sites. The species is also present in recent sediment samples from 12 other sites along the west coast of North America. The evidence indicates that T. hadai is a recent introduction to San Francisco Bay, and is probably also not native to the other North American sites. Trochammina hadai was probably transported from Japan in ships' ballast tanks, in mud associated with anchors, or in sediments associated with oysters imported for mariculture. Its remarkable invasion of San Francisco Bay suggests the potential for massive, rapid invasions by other marine microorganisms.     

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (<Emphasis Type="Italic">Rallus obsoletus obsoletus</Emphasis>)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.     

Biological tags for stock separation in Pacific herring Clupea harengus pallasi in California.

A survey of the parasites of Pacific herring (Clupea harengus pallasi) off northern California identified 1 species of Acanthocephala, 1 species of Cestoda, 2 species of Copepoda, 1 species and 1 family of Digenea, 3 species of Nematoda, and 3 species of Protozoa. From this survey, Lacistorhynchus dollfusi (Cestoda), Parahemiurus merus (Digenea), and Anisakis simplex, Contracaecum sp., Hysterothylacium sp. (Nematoda) were selected as potential tags. Herring were collected in Tomales, San Francisco, and Monterey bays for the following 9 yr and examined for these select parasites. The results suggest that these parasites can be used to distinguish the spawning stocks of San Francisco and Tomales bays. The distribution of the definitive hosts of the respective parasites suggests that the Tomales Bay fish are offshore during the nonbreeding season and the San Francisco Bay fish onshore. The similarity in parasitism between San Francisco Bay and the nonspawning population in Monterey Bay suggests that these 2 populations represent a single stock.     

Preliminary Observations of Population Genetics and Relatedness of the Broadnose Sevengill Shark,Notorynchus cepedianus,in Two Northeast Pacific Estuaries

The broadnose sevengill shark, Notorynchus cepedianus, a common coastal species in the eastern North Pacific, was sampled during routine capture and tagging operations conducted from 2005–2012. One hundred and thirty three biopsy samples were taken during these research operations in Willapa Bay, Washington and in San Francisco Bay, California. Genotypic data from seven polymorphic microsatellites (derived from the related sixgill shark, Hexanchus griseus) were used to describe N. cepedianus genetic diversity, population structure and relatedness. Diversity within N. cepedianus was found to be low to moderate with an average observed heterozygosity of 0.41, expected heterozygosity of 0.53, and an average of 5.1 alleles per microsatellite locus. There was no evidence of a recent population bottleneck based on genetic data. Analyses of genetic differences between the two sampled estuaries suggest two distinct populations with some genetic mixing of sharks sampled during 2005–2006. Relatedness within sampled populations was high, with percent relatedness among sharks caught in the same area indicating 42.30% first-order relative relationships (full or half siblings). Estuary-specific familial relationships suggest that management of N. cepedianus on the U.S. West Coast should incorporate stock-specific management goals to conserve this ecologically important predator.     

Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus)

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.     

Low genetic diversity contrasts with high phenotypic variability in heptaploid Spartina densiflora populations invading the Pacific coast of North America

Species can respond to environmental pressures through genetic and epigenetic changes and through phenotypic plasticity, but few studies have evaluated the relationships between genetic differentiation and phenotypic plasticity of plant species along changing environmental conditions throughout wide latitudinal ranges. We studied inter‐ and intrapopulation genetic diversity (using simple sequence repeats and chloroplast DNA sequencing) and inter‐ and intrapopulation phenotypic variability of 33 plant traits (using field and common‐garden measurements) for five populations of the invasive cordgrass Spartina densiflora Brongn. along the Pacific coast of North America from San Francisco Bay to Vancouver Island. Studied populations showed very low genetic diversity, high levels of phenotypic variability when growing in contrasted environments and high intrapopulation phenotypic variability for many plant traits. This intrapopulation phenotypic variability was especially high, irrespective of environmental conditions, for those traits showing also high phenotypic plasticity. Within‐population variation represented 84% of the total genetic variation coinciding with certain individual plants keeping consistent responses for three plant traits (chlorophyll b and carotenoid contents, and dead shoot biomass) in the field and in common‐garden conditions. These populations have most likely undergone genetic bottleneck since their introduction from South America; multiple introductions are unknown but possible as the population from Vancouver Island was the most recent and one of the most genetically diverse. S. densiflora appears as a species that would not be very affected itself by climate change and sea‐level rise as it can disperse, establish, and acclimate to contrasted environments along wide latitudinal ranges.     

A genetic reconstruction of the invasion of the calanoid copepod <Emphasis Type="Italic">Pseudodiaptomus inopinus</Emphasis> across the North American Pacific Coast

The rate of aquatic invasions by planktonic organisms has increased considerably in recent decades. In order to effectively direct funding and resources to control the spread of such invasions, a methodological framework for identifying high-risk transport vectors, as well as ruling out vectors of lesser concern will be necessary. A number of estuarine ecosystems on the North American Pacific Northwest coast have experienced a series of high impact planktonic invasions that have slowly unfolded across the region in recent decades, most notably, that of the planktonic copepod crustacean Pseudodiaptomus inopinus. Although introduction of P. inopinus to the United States almost certainly occurred through the discharge of ballast water from commercial vessels originating in Asia (the species’ native range), the mechanisms and patterns of subsequent spread remain unknown. In order to elucidate the migration events shaping this invasion, we sampled the genomes of copepods from seven invasive and two native populations using restriction-site associated DNA sequencing. This genetic data was evaluated against spatially-explicit genetic simulation models to evaluate competing scenarios of invasion spread. Our results indicate that invasive populations of P. inopinus exhibit a geographically unstructured genetic composition, likely arising from infrequent and large migration events. This pattern of genetic patchiness was unexpected given the linear geographic structure of the sampled populations, and strongly contrasts with the clear invasion corridors observed in many aquatic systems.     

Big changes to a small bay: introduced species and long-term compositional shifts to the fouling community of Morro Bay (CA)

Invasive species are cited as being a threat to communities and ecosystems worldwide, yet few studies have demonstrated invader impacts at these scales. Lack of historic data makes capturing large-scale community shifts problematic. We assessed long-term changes in invertebrate composition to the fouling community of a small estuary with relatively little boat traffic and no ballast water input (Morro Bay, CA). We also compared relative invasiveness of Morro Bay to international harbors (San Francisco Bay and Los Angeles/San Diego harbors). While the proportion of introduced species has not significantly changed from historic records, introduced species now occupy 86.00 % of the primary substrate. Other community shifts include; (1) a state shift to an invasive bryozoan (Watersipora subtorquata) dominated community, (2) a decrease in Mollusc richness and, (3) substantial shifts in abundance of certain species. Compared to larger more actively used harbors, Morro Bay has proportionally fewer introduced species (12.00 %) than San Francisco Bay (50.79 %) or Los Angeles/San Diego Harbors (26.23 %). Our study documents changes to a small relatively isolated estuary with little boat traffic and no ballast water input. We discuss the potential role of invasive species and other natural and anthropogenic factors as drivers of these community wide shifts. Specifically, we discuss how reintroduction of the Southern Sea Otter (Enhydra lutris nereis), an increase in sea stars (Pisaster spp.), climate change and interaction amongst potential drivers support the patterns of shifts in the Morro Bay community.     

Reconstructing the range expansion and subsequent invasion of introduced European green crab along the west coast of the United States

The European green crab, Carcinus maenas, was first documented in San Francisco Bay in 1989, and has since spread north along the west coast of North America. The spread of this invasion has not been a smooth expansion, which has raised questions about the underlying causes of variation in recruitment. We modeled larval development and transport along the West Coast by employing an individual-based model that incorporated oceanographic model output of water temperature and ocean currents at fine spatial and temporal scales. The distance that larvae were advected depended primarily on the timing of larval release. However, the effect of seasonal ocean currents varied across latitude and years. Our results imply that the furthest northern transport from California occurs when larvae are released from Humboldt Bay during the fall of an El Niño year, making this a particularly risky time for invasion to Oregon and Washington estuaries. To precisely predict future spread and potential impacts of green crab, we recommend further empirical research to determine the precise timing of larval release and seasonal abundance of green crab larvae from North American west coast populations.     

Possible Ballast Water Transfer of Lionfish to the Eastern Pacific Ocean

The Indo-Pacific Red Lionfish was first reported off the Florida coast in 1985, following which it has spread across much of the SE USA, Gulf of Mexico, and Caribbean Sea. Lionfish negatively impact fish and invertebrate assemblages and abundances, thus further spread is cause for concern. To date, the fish has not been reported on the Pacific coast of North or Central America. Here we examine the possibility of ballast water transfer of lionfish from colonized areas in the Atlantic Ocean to USA ports on the Pacific coast. Over an eight-year period, we documented 27 commercial vessel-trips in which ballast water was loaded in colonized sites and later discharged untreated into Pacific coast ports in the USA. California had the highest number of discharges including San Francisco Bay and Los Angeles-Long Beach. A species distribution model suggests that the probability of lionfish establishment is low for the western USA, Colombia and Panama, low to medium for Costa Rica, Nicaragua, El Salvador and Guatemala, medium to high for mainland Ecuador, and very high for western Mexico, Peru and the Galapagos Islands. Given the species’ intolerance of freshwater conditions, we propose that ballast water exchange be conducted in Gatún Lake, Panama for western-bound vessels carrying ‘risky’ ballast water to prevent invasion of the eastern Pacific Ocean.     

Introduced or glacial relict? Phylogeography of the cryptogenic tunicate Molgula manhattensis (Ascidiacea,Pleurogona)

Aim The tunicate Molgula manhattensis has a disjunct amphi‐Atlantic distribution and a recent history of world‐wide introductions. Its distribution could be the result of regional extinctions followed by post‐glacial recolonization, or anthropogenic dispersal. To determine whether the North Atlantic distribution of M. manhattensis is natural or human‐mediated, we analysed mtDNA cytochrome c oxidase subunit I (COI) sequence variation in individuals from cryptogenic and introduced ranges. Location North Atlantic Europe and America; Black Sea; San Francisco Bay; Osaka Bay. Methods Nuclear 18S rDNA sequences were used to resolve phylogenetic relationships and mtDNA COI sequences for phylogeographic analyses. Results Phylogenetic analyses confirmed that M. manhattensis and M. socialis, which are frequently confused, are distinct species. MtDNA haplotype diversity was nearly three times higher with deeper relationships among haplotypes on the North‐east American coast than in Europe. Diversity declined from south to north in America but not in Europe. In areas of known introductions (Black Sea, Japan, San Francisco Bay), M. manhattensis showed variable levels of haplotype diversity. Medium‐to‐high‐frequency haplotypes originating from the North‐west Atlantic were present in two locations of known introductions, but not in Europe. Private haplotypes were found on both sides of the Atlantic and in introduced populations. The mismatch distribution for the North‐east Atlantic coast indicates a recent expansion. Main conclusions Molgula manhattensis is native in North‐east America. However, whether it was introduced or is native to Europe remains equivocal. Additional sampling might or might not reveal the presence of putative private European haplotypes in America. The low European diversity may be explained by low effective population size and a recent expansion, or by low propagule pressure of anthropogenic introduction. Absence of medium‐to‐high‐frequency American haplotypes in Europe may be the result of exclusive transport from southern ports, or long‐term residence. These arguments are ambiguous, and M. manhattensis remains cryptogenic in Europe.