Ocean-going ships carry, as ballast, seawater that is taken on in port and released at subsequent ports of call. Plankton samples from Japanese ballast water released in Oregon contained 367 taxa. Most taxa with a planktonic phase in their life cycle were found in ballast water, as were all major marine habitat and trophic groups. Transport of entire coastal planktonic assemblages across oceanic barriers to similar habitats renders bays, estuaries, and inland waters among the most threatened ecosystems in the world. Presence of taxonomically difficult or inconspicuous taxa in these samples suggests that ballast water invasions are already pervasive.

DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 ('Folmer primers') designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all-taxon surveys and metazoan metagenomics.

The European green crab Carcinus maenas is one of the world's most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non-native populations. The global data set includes sequences from the mitochondrial cytochrome c oxidase subunit I gene, as well as multilocus genotype data from nine polymorphic nuclear microsatellite loci. Combined phylogeographic and population genetic analyses clarify the global colonization history of C. maenas, providing evidence of multiple invasions to Atlantic North America and South Africa, secondary invasions to the northeastern Pacific, Tasmania, and Argentina, and a strong likelihood of C. maenas x C. aestuarii hybrids in South Africa and Japan. Successful C. maenas invasions vary broadly in the degree to which they retain genetic diversity, although populations with the least variation typically derive from secondary invasions or from introductions that occurred more than 100 years ago.

The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved our ability to make inferences regarding invasion histories. Genetic methods have helped to resolve longstanding questions regarding the cryptogenic status of marine species, facilitated recognition of cryptic marine biodiversity, and provided means to determine the sources of introduced marine populations and to begin to recover the patterns of anthropogenic reshuffling of the ocean's biota. These approaches stand to aid materially in the development of effective management strategies and sustainable science-based policies. Continued advancements in the statistical analysis of genetic data promise to overcome some existing limitations of current approaches. Still other limitations will be best addressed by concerted collaborative and multidisciplinary efforts that recognize the important synergy between understanding the extent of biological invasions and coming to a more complete picture of both modern-day and historical marine biogeography.

The perceived wide geographic range of organisms in the sea, facilitated by ready dispersal of waterborne dispersal stages, is a challenge for hypotheses of marine speciation but a boon to efforts of marine conservation. Wide species ranges are especially striking in the reef-rich Indo-west Pacific, the largest and most diverse marine biogeographic region, extending across half the planet. The insular marine biota of the tropical Pacific is characterized by wide-ranging species and provides the most striking examples of long distance dispersal, with endemism largely confined to the most remote island groups. Here we show that the gastropod Astralium "rhodostomum" has developed endemic clades on almost every Pacific archipelago sampled, a pattern unprecedented in marine biogeography, and reminiscent of the terrestrial biota of oceanic islands. Mitochondrial DNA sequences indicate that this species-complex is comprised of at least 30 geographically isolated clades, separated by as little as 180 km. Evidence suggests that such fine scale endemism and high diversity is not exceptional, but likely characterizes a substantial fraction of the reef biota. These results imply that (1) marine speciation can regularly occur over much finer spatial scales than generally accepted, (2) the diversity of coral reefs is even higher than suggested by morphology-based estimates, and (3) conservation efforts need to focus at the archipelagic level in the sea as on land.