| Freshwater prawns of the genus Macorbrachium (Crustacea: Decapoda: Caridea: Palaemonidae) constitute one of the most diverse, abundant and widespread cruatacean genera. They inhabit a wide variety of environments from mountain steams and lowland rivers to estuaries and coastal lagoons. The palaemonids have historically been a taxonomically difficult group because they appear to be highly conservative in morphology. The problems have been attributed to difficulties in the interpretation of the significance of morphological characteristics used to classify palaemonid shrimp and have hindered the development of stable classification systems. Until recently, all major systematic treatments of palaemonids have been based on morphological characteristics alone. A few allozyme-based and DNA-based studies have been undertaken. However, phylogenetic relationships within Macrobrachium species remain poorly studied. In this study, collected all available specimen of Chinese Macrobrachium species, using morphological characters, mitochrondrial DNA sequencing and Inter-simple sequence repeats marker, employing MP, ML, BI and NJ to generate phylogenetic hypothesis, we intent to interpret the phylogenetic relationships, classification of the genus and study the genetic diversity of Macrobrachium nipponense populations in order to provide preliminary genetic information for the development of management strategies for this species.This study focuses on four subjects using morphological and molecular characters:1. A cladistic analysis of morphological and ecological characters was preformed in which 36 characters exhibited by 60 species of 9 genera of Palaemoninae. Two species of Procaridae were selected as outgroup for the character analysis. The cladogram shown that (1) the Palaemoninae species formed a monophyletic clade by three main characters (telson usually with 2 pairs of dorsal spines, 2 or more feathered setae on telson, third maxilliped with two orthrobranchia). P. ascensionis and V. chaceorum cluster together as related taxa at the base of the tree; (2) the Macrobrachium species forming a monophyletic clade. They are charaterised by the presence of hepatic spine on carapace and absence of branchiostergal spine; (3) the relationships among the rest genera remaining unclear. The results suggested that Holthuis (1950) and Chace (1992) classification provided a frame of reference to sort out species and some natural groups but failed to clarify the relationships of the group.2. Based on mitochondrial DNA fragement of the large subunit (16S) rRNA gene, the monophyletic phylogeny of the genus Macrobrachium, including freshwater and estuarine species, was supported, although there are some difference on the topology. The 50% consensus tree of MP, NJ, ML and BI trees showed two distinct clades: one clade includes the species with equal second pereiopod, the other clade separately clustered with the species with unequal second pereiopod. Furthermore, we found that three easy-confused species, M. nipponense, M. inflatum and M. superbum, have closer relationship.3. In order to identify the relationship of M. nipponense, M. inflatum and M. superbum which have the similar morphological characters and share similar distribution ranges, we chosed to use three markers proposed as most informative in delimiting species relationship with DNA barcodes, namely cytochrome c oxidase I (CO I), 16S ribosomal DNA and D-loop PCR-RFLP. The sequence analysis results of CO I and 16S rRNA gene showed that the much lower divergent level found among the ingroup samples in this study is more typical of what is seen among populations within species. The result of RFLP reinforced the above conclusion. And the trees produced by NJ analyses were identical. Haplotypes representing M. nipponense, M. inflatum and M. superbum collected from different locations across inland China form a tight monophyletic group, with very short branch lengths compared with the much longer branch lengths observed in other Macrobrachium species. Therefore, M. nipponense, M. inflatum and M. superbum may be a single species.4. The oriental river prawn M. nipponense is one of the most important freshwater prawn s for aquaculture in China, especially in southern regions. In present work we investigate the genetic diversity among the 10 populations from the Yangtze and Lancang River by CO I gene region and ISSR marker. The dendrogram produced resulted in the formation of three major clusters (Lancang River and upriver reaches of Yangtze River, middle reaches of Yangtze River and lower reaches of Yangtze River). The genetic differentiations among most of the populations corresponded to the geographic distances among the populations. The results of the two molecular markers also showed Wuhan population exhibited the high level of variability, which means this population can effectively adapt to environmental changes. Genetic distance and dendrograms showed that compared with other populations, Huzhou (HZ), Suzhou (SZ) population and Shanghai (SH) population are closer. At the species level, M. nipponense showed relatively high level of polymorphism. Compared to other indirect methods, the results of DNA sequencing can directly reveal the genetic variation of the species, but much expensive. Therefore, if the species do not have prior genome sequence information, ISSR is a powerful marker of choice for the assessment of genetic variation among populations.
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