The complete nucleotide sequence of the mitochondrial genome was determined for a harpacticoid copepod, Tigriopus japonicus (Crustacea), using an approach that employs a long polymerase chain reaction technique and primer walking. Although the genome (14,628 bp) contained the same set of 37 genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other metazoan animals, none of the previously reported gene orders were comparable to that of T. japonicus. Furthermore, all genes were encoded on one strand, unlike the mitochondrial genomes of most metazoan animals. Size reductions were notable for tRNA and rRNA genes, resulting in one of the smallest mitochondrial genomes in the arthropod lineage. Although it appears that such large-scale gene rearrangements have occurred in the ancestral species of T. japonicus, none of the proposed mechanisms parsimoniously account for this eccentric gene arrangement.

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To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness), the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan's marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans.

Background: Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla. Here we present the results of single-gene zooplankton community analysis using a method that determines a large number of mitochondrial COI gene sequences from a bulk zooplankton sample. This approach will enable us to estimate the species richness of almost the entire zooplankton community.

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IntroductionThe animals that drift with ocean currents throughout their lives (that is, the holozooplankton) include approximately 7,000 described species in 15 phyla. The holozooplankton assemblage is the focus of the Census of Marine Zooplankton (CMarZ; www.CMarZ.org ), which has produced comprehensive new information on species diversity, distribution, abundance, biomass, and genetic diversity. Our realm among Census of Marine Life projects is the open ocean; we have sampled biodiversity hot spots throughout the world ' s oceans: little -known seas of Southeast Asia, deep -sea zones below 5,000 m, and polar seas. We have used traditional plankton nets and newer sensing systems deployed from ships and submersibles. Our analysis has included traditional microscopic and morphological examination, as well as molecular genetic analysis of zooplankton populations and species. CMarZ has contributed to Census legacies in data and information for the Ocean Biogeographic Information System (see Chapter 17 ) and proven technologies of DNA barcoding. Our photograph galleries of living plankton have captured public interest, and our training workshops have enhanced taxonomic expertise in many countries. The knowledge gained will provide a new baseline for detection of impacts of climate change, and will contribute to our fundamental understanding of biogeochemical transports, fl uxes and sinks, productivity of living marine resources, and marine ecosystem health. Historical PerspectiveDespite more than a century of sampling the oceans, comprehensive understanding of zooplankton biodiversity has eluded oceanographers because of the fragility, rarity, small size, and/or systematic complexity of many taxa. For many zooplankton groups, there are long -standing and unresolved questions of species identifi cation, systematic relationships, genetic diversity and structure, and biogeography.There has never been a taxonomically comprehensive, global -scale summary of the current status of our knowledge of biodiversity of marine zooplankton. Although studies of the taxonomy, distribution, and abundance of zooplankton date back as far as the middle of the nineteenth century, worldwide distribution patterns have not been mapped for all described species. The cosmopolitan or circumglobal distributions characteristic of holozooplankton species of many groups have created special Life in the W orld's Oceans: Diversity, Distribution, and Abundance Edited