Background: The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.Results: We present the complete mitochondrial genome sequences of five mud shrimps,Austinogebia edulis,Upogebia major,Thalassina kelanang(Gebiidea),Nihonotrypaea thermophilusandNeaxius glyptocercus(Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except forT.kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A.edulisandU.major) and two Axiidea species (N.glyptocercusandN.thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis.Conclusions: Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Nihonotrypaea thermophila, new species, is described on the basis of 26 specimens from a hydrothermally influenced field off northeastern Taiwan at depths of 128–320 m. This is the first callianassid shrimp to be reported from deep-water hydrothermal vents, and available data seems to suggest that the new species is vent-endemic. The new species is assigned to Nihonotrypaea Manning & Tamaki, 1998, a genus including three previously described species inhabiting coastal mud or sand flat areas in Japan and its adjacent waters. The new species is unique in the genus in having the antennal peduncle distinctly longer than the antennular peduncle.

The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species.

We determined the complete mitochondrial genome (mitogenome) sequence of Metzia formosae, which is known as an endangered freshwater species in Taiwan and mainland China, with a long polymerase chain reaction (PCR) method. The total length of M. formosae mitogenome is 16,614 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The overall base composition of M. formosae is 31.39% for A, 25.56% for T, 16.23% for G and 26.82% for C, with a slight AT bias of 56.95%. The molecular data here we presented could play a useful role not only for studying the evolutionary relationships and population genetics of Metzia species, but for practicing conservation on endangered fishes.

Recent discovery of a specimen of Oxyrhynchaxius Parisi, 1917, from Taiwan led to a survey of the material of this rare and monotypic axiid genus deposited at various museums. Other than the type, five specimens of this genus from Japan, Taiwan, Hong Kong, and Australia were found and can be separated into two forms. Those from Japan to Hong Kong are large in size, have slender eyes and bear a dorsal carina on the posterior carapace but lack a median carina on the abdomen. The Australian specimens are small, have stout eyestalks and bear a median carina on the abdomen but lack a middorsal carina on the posterior carapace. The specimens from Japan to Hong Kong probably all belong to O. japonicus Parisi, 1917. The Australian material, though probably juvenile, represents a distinct species and is described as new.