RNA interference shows that Spook, the precursor gene of 20-hydroxyecdysone (20E), regulates the molting of Macrobrachium nipponense.

The aim of this study was to explore the function of the Mn-Spook gene, which was found in the ovary transcriptome of the Oriental river prawn (Macrobrachium nipponense). The Spook gene, which is the precursor gene of 20-hydroxyecdysone (20E), plays an important role in the process of molting in many arthropods, but its function in M. nipponense is unclear. We cloned the full-length Mn-Spook gene from the ovary of M. nipponense and found that it had the same conserved domains as the P450 gene of the Halloween family of genes. The Mn-Spook gene was highly expressed in ovary and gill tissue during the breeding period. During ovarian development, Mn-spook gene expression was highest at the nearly-ripe stage, and it also was highly expressed in the zoea developmental stage. Cellular localization analysis showed that Mn-Spook signals accumulated in the cytoplasmic membrane and nucleus of oocytes. Finally, we used RNA interference to evaluate the function of the Mn-Spook gene. Compared with the control group, in vivo injection of Mn-Spook dsRNA effectively downregulated the expression of Mn-Spook and the content of 20E. The molting frequency of M. nipponense in the experimental group also was significantly inhibited. These results demonstrated that the Mn-Spook gene played an important role in the molting process of M. nipponense.

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches.

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

Morphology and molecular phylogeny of Macrobrachium prachuapense sp. nov. (Decapoda: Palaemonidae) from Southern Thailand.

A new species of small freshwater prawn in the Macrobrachium pilimanus species group was found in the upper southern peninsula of Thailand. The prawns in this group exhibit velvet setae on the telopodites of the second pereiopods. The new species, named M. prachuapense sp. nov., is endemic to Thailand. It has several characteristics that make it standing apart and different from closely related species in the group, e.g. M. naiyanetri, M. forcipatum, M. malayanum, M. dienbienphuense, M. eriocheirum, and M. pilosum. The distinguishing characteristic of the new species is the shape of carpus of the second pereiopod (sub-cylindrical and subequal to palm), similar only to that of M. dienbienphuense. However, a fully-grown male of the new species was less than two-third the size of a fully-grown male M. dienbienphuense. Phylogenetic analysis further enhanced its novel species status with respect to its position in the phylogenetic tree relative to other closely related species.

Evolution of protective symbiosis in palaemonid shrimps (Decapoda: Caridea) with emphases on host spectrum and morphological adaptations.

Palaemonidae is the most speciose caridean shrimp family, with its huge biodiversity partially generated via symbiosis with various marine invertebrates. Previous studies have provided insights into the evolution of protective symbiosis in this family with evidence for frequent inter-phyla host switches, but the comprehensiveness of evolutionary pathways is hampered by the resolution of the previous phylogenetic trees as well as the taxon coverage. Furthermore, several critical issues related to the evolution of a symbiotic lifestyle, including the change in host spectrum and corresponding morphological adaptations, remain largely unresolved. We therefore performed a much extended phylogenetic comparative study on Palaemonidae, rooted in a comprehensive phylogeny reconstructed by a supermatrix-supertree approach based on a total of three mitochondrial and five nuclear markers. Ancestral state reconstruction of host associations revealed at least three independent evolutions into symbiosis, with potentially a drive to seek protection fuelling incipient symbiosis. Yet, most of the observed symbiotic species diversity was radiated from a single cnidarian associate. The evolution of mandibles and ambulatory dactyli suggests a general lack of correlation with host affiliation (except sponge endosymbionts), implying limited morphological adaptations following host switching, despite being putatively a major adaptive consequence of symbiosis. Our analyses of host spectrum, in terms of basic and taxonomic specificity, revealed no apparent phylogenetic signal but instead resolved a dynamic pattern attributable to frequent host switching. Uncoupling between host spectrum and the degree of morphological specialisation is the norm in palaemonids, suggesting that morphological characters are not fully in tune with host spectrum, in addition to host affiliation. This study demonstrates the complexity in the evolution of symbiosis, pointing to the presence of cryptic adaptations determining host spectrum and governing host switch diversification, and provides a clear direction for the evolutionary study of symbiosis in other marine symbiotic groups involving host switching.

Two new species of emTypton/em Costa, 1844 from tropical American waters, with taxonomic notes on emT. tortugae/em McClendon, 1911 and a new record of br /emT. granulosus/em Ayón-Parente, Hendrickx amp; Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae).

Two new species of the palaemonid shrimp genus Typton Costa, 1844 are described based on material from Panama and Mexico. Both species are closely related to T. tortugae McClendon, 1911, a species originally described from the Dry Tortugas, off southern Florida, USA, and later scarcely recorded from other western Atlantic localities, from Bermuda to Mexico and Brazil. Some clarification and additional illustrations are provided for the type material of T. tortugae. Typton jonkayei sp. nov., is described based on material from fouling-encrusting communities dominated by sponges, growing on submerged roots of the red mangrove, Rhizhophora mangle L., in Bocas del Toro, Caribbean coast of Panama. This new species differs from T. tortugae in several morphological details, for instance, on the minor and major chelipeds (second pereiopods), telson, uropod, frontal margin and ambulatory pereiopods. Typton cousteaui sp. nov. is described based on a single ovigerous female dredged in the southern Gulf of California off Baja California Sur, Mexico, previously reported as T. tortugae. This new taxon seems to represent a true cryptic species with no significant morphological divergence from the allopatrically isolated T. tortugae, except for slight morphometric differences. In addition, T. granulosus Ayón-Parente, Hendrickx Galvan-Villa, 2015 is recorded from the Pacific coast of Panama, based on material collected in the Coiba Archipelago. Some taxonomic, distributional and ecological remarks are provided for T. granulosus and the closely related T. serratus Holthuis, 1951.

Macrobrachium/ Spence Bate, 1868 (Decapoda: Palaemonidae): New records, range extension and geographic distribution in the Northeastern Caatinga amp; Coastal Drainages, and São Francisco hydrographic ecoregions, Northeast of Brazil.

This study constitutes the most comprehensive effort ever done to assess the faunal diversity of the Macrobrachium genus within two ecoregions that encompass part of the northeastern Brazil: the Northeastern Caatinga Coastal Drainages, and the São Francisco (Lower-middle and Lower portions). Through sampling in several of their hydrographic basins, bibliographic research, and consulting scientific collections, our results reveal the occurrence of five species along these ecoregions: Macrobrachium acanthurus, M. amazonicum, M. carcinus, M. jelskii and M. olfersii. We also provide the first record of these species for several river basins in both ecoregions. Additionally, we confirm the occurrence of M. carcinus from Rio Grande do Norte State and provide updated distribution maps for each species in the studied area. This carcinofauna survey may form the basis for future evaluations of eventual anthropic impacts on biological diversity resulting from projects being implemented in these regions, which involve the São Francisco interbasin water transfer.

A new species of palaemonid prawn emMacrobrachium/em emramae/em sp.nov. (Malacostraca:Decapoda:Palaemonidae) from Rupnarayana River, West Bengal, India with its molecular profiles.

A new species Macrobrachium ramae is described from Rupnarayana river, West Bengal, India along with its molecular characterization and Scanning electron microscopy. The species shares certain characters with M.gurudeve, M.jayasreei, M.kunjuramani and M.saengphani but differs remarkably from these species in the structure and shape of rostrum, telson, appendix masculina and in the size of the proximal segment of the antennular peduncle. Molecular characterization and phylogenetic analysis of M.ramae with mitochondrial COI and 16S rRNA genes reinforce the morphological conclusion and supports the view that it is a new species.

New data on Beurlenia araripensis Martins-Neto & Mezzalira, 1991, a lacustrine shrimp from Crato Formation, and its morphological variations based on the shape and the number of rostral spines.

Fossil freshwater carideans are very rare worldwide. Here, we present new taxonomic remarks about Beurlenia araripensis from the Early Cretaceous laminated limestones of the Crato Formation, Araripe Basin, northeastern Brazil. We analyzed five fossil samples, testing the morphological variations such as, rostrum with 5 to 14 supra-rostral spines and 2 to 3 sub-rostral spines, which appears as serrate for Caridea. This variation demonstrates a morphologic plasticity also seen in extant species of the group, such as those of the genera Macrobrachium and Palaemon.

Do plasticity in gene expression and physiological responses in Palaemonid prawns facilitate adaptive response to different osmotic challenges?

Integrating physiological and genomic approaches in a comparative framework offers excellent opportunity to investigate the underlying mechanisms for acclimation to specific challenges. The present study was conducted on three different prawn species (inhabitants of different salinity environments) of the genus Macrobrachium (M. australiense, M. tolmerum and M. novaehollandiae) to investigate the salinity induced changes in expression patterns of 10 candidate genes in the gill tissue (that previously had been inferred to play important functional roles in acclimation and adaptation to freshwater environments), and hemolymph osmolality. The prawn individuals were maintained in laboratory condition under three different salinity levels (0‰, 6‰ and 12‰) for 28 days using 6‰ as the control. All of the genes studied, showed salinity induced differential expression patterns. Genes with more important functional roles under low ionic conditions (i.e. Claudin, Na+/H+exchanger, V-type H+-ATPase and UNT2) showed 2.5 to 6 fold higher expression at 0‰ compared with at higher salinities (6‰ and 12‰) but no significant differences (p > 0.05) were observed between 6‰ and 12‰ for the same genes. In contrast, 1.5 to 4 fold higher expression levels were observed at 6‰ and 12‰ for genes that have important roles in mediating salinity tolerance (i.e., Na+/K+-ATPase, Na+/K+/2Cl-Co-transporter, Diuretic Hormone, Crustacean Hyperglycaemic Hormone and UNT1). The osmotic stress response gene, Calreticulin, showed significant differences (p < 0.05) in expression between different salinity comparisons. Hemolymph osmolality also was impacted in all three species with a strong correlation evident between hemolymph osmolality and expression of genes influencing this trait. Findings indicate an important role of plasticity that facilitates rapid acclimation to changing salinity levels.

Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications.

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

Molecular Cytogenetic Analysis in Freshwater Prawns of the Genus Macrobrachium (Crustacea: Decapoda: Palaemonidae).

Freshwater prawns of the genus Macrobrachium are one of the important components of circumtropical marine, estuarine, and freshwater environments. They have been extensively exploited for human consumption for many years. More than 250 species reflect the evolutionary success of this highly diversified group, with a complex and challenging taxonomy due to morphological variations and vast geographical distribution. Although genetic approaches have been used to clarify phylogenetic and taxonomic aspects of Macrobrachium species, cytogenetic information is still very scarce and mostly focused on chromosome number and morphology. Here, we present chromosome data for three species from the Neotropical region, M. carcinus, M. acanthurus, and M. amazonicum, and one species from the Oriental region, M. rosenbergii. Using conventional cytogenetic approaches and chromosome mapping of repetitive DNAs by fluorescence in situ hybridization (FISH), we identified numerical diversification of the diploid set, within and between both zoogeographic regions. These included M. acanthurus and M. amazonicum sharing diploid chromosomes of 98, while M. carcinus has 94, and M. rosenbergii has 118 chromosomes. Argentophilic sites are also variable in number, but they occur in a much higher number than 18S rDNA, representing two to 10 sites within the study species. Microsatellites repeat motifs are also abundant in the chromosomes, with a co-localization and uniform distribution along the chromosome arms, but completely absent in the AT-rich centromeric regions. As a whole, our study suggests that the 2n divergence was followed by a considerable rDNA diversification. The abundance of the exceptional amount of microsatellite sequences in the chromosomes also suggests that they are essential components of the Macrobrachium genome and, therefore, maintained as a shared feature by the species, the reason for which is yet unknown.

Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species.

The mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T-. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.

Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers.

BACKGROUND: The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. RESULTS: Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. CONCLUSION: This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

Evolutionary history of genus Macrobrachium inferred from mitochondrial markers: a molecular clock approach.

Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers. Previous studies on Macrobrachium relied on the highly variable morphological characters which were insufficient for accurate diagnosis of natural species groups. Present study focuses on the utility of molecular markers (viz. COI and 16S rRNA) for resolving the evolutionary history of genus Macrobrachium using a combination of phylogeny and timescale components. It is for the first time a molecular clock approach had been carried out towards genus Macrobrachium in a broad aspect with the incorporation of congeners inhabiting diverse geographical realms including endemic species M. striatum from South West coast of India. Molecular results obtained revealed the phylogenetic relationships between congeners of genus Macrobrachium at intra/inter-continental level along with the corresponding evolutionary time estimates.

Isolation and characterization of 21 polymorphic microsatellite loci for the rockpool shrimp Palaemon elegans using Illumina MiSeq sequencing.

The rockpool shrimp Palaemon elegans is considered an important crustacean species within the European coastline fauna. This species is experiencing an ongoing geographical expansion beyond its native distribution range due to unintentional human introductions. A better knowledge of the genetic diversity, geographic structure and connectivity of its populations is necessary. In the present study, microsatellite loci were isolated using the Illumina MiSeq platform. The microsatellite-enriched library sequencing produced 3.9 million raw reads. Reads were processed and primer pairs were designed for microsatellite sequences amplification. Ninety-six microsatellite loci were preliminary screened in individuals from Atlantic and Mediterranean localities. From them, 21 loci exhibited reliable polymorphism and were thoroughly characterized in 30 individuals from a Cantabrian locality (Spain). No linkage disequilibrium between pairs of loci was detected. Number of alleles per locus ranged from 2 to 12. Observed and expected heterozygosities ranged from 0.033 to 0.833 and from 0.033 to 0.869 respectively. No significant departure from the Hardy-Weinberg equilibrium was detected in most of loci. This is the first time that microsatellite markers have been developed for P. elegans. This characterized microsatellite suite provides new suitable tools for further analyses, facilitating the understanding of population genetics both in natural and introduced populations.

Molecular Cloning and Expression of MnGST-1 and MnGST-2 from Oriental River Prawn, Macrobrachium nipponense, in Response to Hypoxia and Reoxygenation.

The glutathione-S-transferase (GST) superfamily includes seven classes, and different classes have different functions. GST superfamily members function in various processes including detoxification of xenobiotics, protection against oxidative damage, and intracellular transport of hormones, endogenous metabolites, and exogenous chemicals. Herein, to elucidate the tissue-specific expression pattern of GSTs in response to hypoxia stress, which induces cell death, we investigated the expression of GSTs in response to hypoxia and reoxygenation in oriental river prawn, Macrobrachium nipponense. Full-length cDNAs of two δ class GSTs were cloned from the hepatopancreas, and named MnGST-1 and MnGST-2 based on the established GST nomenclature system. Expression profiles of both GSTs in various tissues were different under acute and chronic experimental hypoxia stress conditions, suggesting that both respond strongly to hypoxia-induced oxidative stress. However, the intensity of responses to hypoxia and reoxygenation were different in different tissues. During acute hypoxia stress, MnGST-1 responds earlier than MnGST-2 in the hepatopancreas and gill, but more slowly in muscle. By contrast, during chronic hypoxia stress, MnGST-2 plays a more important role in the hepatopancreas and gill than MnGST-1.

Identification of Peptide Biomarkers for Discrimination of Shrimp Species through SWATH-MS-Based Proteomics and Chemometrics.

Incorrect labeling and adulteration of shrimp occurs due to interspecies similarities and carapace removal during processing. This study attempted to identify three related commercial shrimp species of the order Decapoda: Marsupenaeus japonicus, Fenneropenaeus chinensis, and Litopenaeus vannamei. All measurable trypsin-digested peptides in the individual shrimp were detected using ultrahigh-performance liquid chromatography quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition. Further analysis of peptide biomarkers was carried out with an orthogonal partial least-squares discriminant analysis (OPLS-DA) model. BLAST was used for species-specific analysis. Subsequently, multiple reaction monitoring (MRM) methods were developed for sensitivity and selectivity screening of the selected peptides, and 27 were identified as biomarkers allowing rapid and accurate discrimination of shrimp species without high-resolution mass spectrometry or statistical model building. These strategies could be applied in authentication of other products containing highly homologous proteomes.

Isolation and identification of the main carotenoid pigment from a new variety of the ridgetail white prawn Exopalaemon carinicauda.

The ridgetail white prawn (Exopalaemon carinicauda) is an important economic species in China. In order to know the molecular basis and evaluate the potential nutrition value of a new variety of this species with orange-red color, the main carotenoid pigments were extracted and identified through high performance liquid chromatography. It showed that higher concentration of free astaxanthin existed in the new variety which might cause the color variation. The concentration of total astaxanthin in muscle and waste of the new variety was 3.3 and 1.9 fold higher than that in natural prawn under the same culture condition (P < 0.05). The predominant geometric and optical isomers of astaxanthin in muscle of the new variety were identified as all-trans and 3S,3'S astaxanthin. This is the first report of astaxanthin-enriched E. carinicauda, which also provides an alternative source of natural astaxanthin and the possibility for improving the nutrition value in this species.

Phylogeographic patterning among two codistributed shrimp species (Crustacea: Decapoda: Palaemonidae) reveals high levels of connectivity across biogeographic regions along the South African coast.

We compare the genetic structuring and demographic history of two sympatric caridean shrimp species with distinct life history traits, one amphidromous species Palaemon capensis and one marine/estuarine species Palaemon peringueyi, in the historical biogeographical context of South Africa. A total of 103 specimens of P. capensis collected from 12 localities and 217 specimens of P. peringueyi collected from 24 localities were sequenced for the mitochondrial cytochrome oxidase one (CO1) locus. Results from analyses of molecular variance (AMOVA), pairwise ΦST comparisons and haplotype networks demonstrate weak to moderate genetic differentiation in P. capensis and P. peringueyi respectively. P. peringueyi exhibits partial isolation between populations associated with distinct biogeographic regions, likely driven by the region's oceanography. However, there is minimal evidence for the occurrence of discrete regional evolutionary lineages. This demonstrated lack of genetic differentiation is consistent with a marine, highly dispersive planktonic phase in both the amphidromous P. capensis and the marine/estuarine P. peringueyi. Bayesian skyline plots, mismatch expansions and time since expansion indicate that both species maintained stable populations during the Last Glacial Maximum (LGM), unlike other southern African aquatic species.

Phylogeography and genetic structure of the oriental river prawn Macrobrachium nipponense (Crustacea: Decapoda: Palaemonidae) in East Asia.

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.