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The oriental river prawn (Macrobrachium nipponense) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK). The nucleotide diversity (π) of all individuals was 0.01134, with values ranging from 0.0089 (BLJ, Japan) to 0.01425 (MTR, Taiwan). A total of 83 haplotypes were obtained, and the haplotypes were divided into 2 main lineages: lineage A included the specimens from BLJ, KLJ, CLR, MTR, TLC, MRC and JRC, and lineage B comprised the ones from HRK, SRC, SMR, MTR, TLC, MRC and JRC. Lineage A could be further divided two sub-lineages (A1 and A2). Individuals of lineage A2 were only from TLC. Demographic expansion was observed in each lineage, starting within the second-to-latest interglacial period for lineage A and within the last glacial period for lineage B. All FST values among the ten populations were significantly different, except for the values between MRC and JRC, and SMR and SRC. The phylogeography and genetic structure of M. nipponense in East Asia might be influenced by Pleistocene glacial cycles, lake isolation and human introduction. The possible dispersal routes of M. nipponense in the East Asia were also discussed.

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.

Toll-like receptors (TLRs) have been identified as key sensors of invading microbes by identifying pathogen-associated molecular patterns and activating innate immune responses. Whereas purifying selection has been suggested in mammalian TLR9, evolutionary features of TLR9 in teleosts have not been investigated in detail. We therefore analysed TLR9 DNA sequences of eight teleost species, including zebrafish (Danio rerio), Japanese flounder (Paralichthys olivaceus), pufferfish (Takifugu rubripes), and five seabreams. Eleven sites subjected to positive selection were identified using the codon-substitution models of PAML 3.15. Ten of these 11 sites were found to be associated with leucine-rich repeats (LRRs). Seven of these 10 positively selected sites were associated with the convex surface of the LRR solenoids, leading to variations of the structures of the LRRs possibly by the introduction of flexibility into the LRR solenoids. The positive selection of LRRs in TLR9 may indicate the adaptation of teleosts to different oligodeoxynucleotides present in different bacterial species.

Sequence analyses on the complete mitochondrial DNA (mtDNA) control region (992 bp) were conducted to elucidate the population structure of kuruma prawns (Penaeus japonicus) in East Asia. Five populations including 95 individuals were collected. They are separated into the Japan Sea (JS), the north and south of the East China Sea (NECS and SECS), the Taiwan Strait (TS), and the north of the South China Sea (NSCS) populations. There are 292 variable sites without any insertions and deletions. Nucleotide diversity in the total populations is 2.51 ± 0.07%, and the variations within populations ranged from 2.61 ± 0.93% (SECS) to 2.29 ± 0.16% (JS). FST values between the JS and the rest of the populations, between the NECS and NSCS populations, and between the SECS and NSCS populations show significant differences. The UPGMA tree of these five populations shows three distinct clusters; one includes the JS population; another includes the NECS population; the third includes populations from the rest of the areas. The analysis of molecular variance (AMOVA) shows clear genetic difference between the JS and the rest of the populations. Additional AMOVA analysis excluding the JS population indicates significant variation between the NECS population and the other three populations. We, therefore, conclude that three distinct populations exist in East Asia; one is in the JS; another is in the NECS; and the third is distributed in SECS, TS and NSCS.

The oriental river prawn (Macrobrachium nipponense) is a non-obligatory amphidromous prawn, and it has a wide distribution covering almost the entire Taiwan. Mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA were combined and used to elucidate the population structure and historical demography of oriental river prawn in Taiwan. A total of 202 individuals from six reservoirs and three estuaries were separately collected. Nucleotide diversity (π) of all populations was 0.01217, with values ranging from 0.00188 (Shihmen Reservoir, SMR, northern Taiwan) to 0.01425 (Mingte Reservoir, MTR, west-central Taiwan). All 76 haplotypes were divided into 2 lineages: lineage A included individuals from all sampling areas except SMR, and lineage B included specimens from all sampling locations except Chengching Lake Reservoir (CLR) and Liyu Lake Reservoir (LLR). All F ST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan). UPGMA tree of nine populations showed two main groups: the first group included the SMR and Tamsui River Estuary (TSE) (both located northern Taiwan), and the second one included the other seven populations (west-central, southern and eastern Taiwan). Demographic analyses implied a population expansion occurred during the recent history of the species. The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively. And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.

The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.

Multivariate allometric coefficients for kuruma shrimp ( Penaeus japonicus ) in five geographic locations (N27, N24, TAS, PUT, and TON) off Taiwan were estimated and compared by sex. Eight morphometric measurements were made for each individual. The 1st eigenvector obtained from the covariance matrix of log-transformed data was used to represent the multivariate allometric coefficients. The bootstrap method was used to assess the accuracy of estimates. A dendrogram of five sampling areas was constructed by unweighted pair-group method with arithmetic means (UPGMA) using the angles between five 1st eigenvectors, and a permutation test was used to test if the difference between two multivariate allometric coefficients obtained from different populations/groups was significant. Five areas were clustered into two distinct groups for each sex, the first group included N27, N24, and TAS; the second one included TON and PUT. For each sex, permutation tests indicated that the difference of each within group pairwised multivariate allometric coefficients is not significant and of each between groups pairwised multivariate allometric coefficients is significant. Because (1) five populations considered here are from the same stock and (2) the size of individuals in the second group is smaller than those in the first group, we concluded that the allometry in life stages differs for this species. The difference between multivariate allometric coefficients in both sexes was also tested based on the two second group data sets, and the result showed that the difference between sexes is significant.

Multivariate allometric coefficients and size-adjusted shape were estimated and compared to elucidate the stock structure of spotted mackerel (Scomber australasicus) off Taiwan. Five samples were collected separately from the south of the East China Sea (ECS), the coastal waters of Taiwan (Tashi, Taitung and Kaohsiung) and the north of the South China Sea (SCS). Fourteen morphometric measurements were made for each individual. The first eigenvector obtained from the covariance matrix of log-transformed data was used to represent the multivariate allometric coefficients. Allometric method was used to obtain size-adjusted shape data. The cluster analysis, discriminant analysis, canonical variate analysis and permutation test was used to discriminate among samples. Results indicated that (1) five areas were clustered into three distinct groups; the first group included ECS, Tashi, and Taitung; the second one included SCS; the third one included Kaohsiung, and (2) differences of allometric coefficients and size-adjusted shape in each pair of three groups are all significant. Therefore, we concluded that there are three morphologically distinguishable stocks of spotted mackerel off Taiwan. One stock is distributed in the south of the East China Sea and the coastal waters of eastern Taiwan, another is in the coastal waters off Kaohsiung, and the other is in the north of the South China Sea. The utility of morphometric measurements for discriminating stock of spotted mackerel is demonstrated, but further verification of the stock structure may be essential.