Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

Implications of changes in trophic diversity and food webs on fisheries and the environment

Most of the earth's ecosystems are experiencing slight to catastrophic losses of biodiversity, caused by habitat destruction, alien species introduction, climate change and pollution (Wilcove et al., 1998). These human effects have led to the extinction of native fish species, the collapse of their populations and the loss of ecological integrity and ecosystem functioning (Ogutu-Ohwayo & Hecky, 1991; Witte et al. , 1992a; Mills et al., 1994; Vitousek et al., 1996). Food webs are macro-descriptors of community feeding interactions that can be used to map the flow of materials and nutrients in ecosystems (Jepsen & Winemiller, 2002). Comparative food web studies have been used to address theoretical questions such as 'does greater trophic connectivity increase stability?' (Cohen et al., 1990), and 'does the number of trophic levels increase with productivity?' (Briand & Cohen, 1987). Answers to such questions have obvious applications for natural resources management. From a multi-species fisheries standpoint, there is a need to understand consumer-resource dynamics within complex trophic networks.

The diversity and abundance of zooplankton in the Lake Victoria and Kyoga basins and their relationship to fish production

Biological diversity of an ecosystem is considered a reliable measure of the state of health of the ecosystem. In Uganda's large lakes, the Victoria and Kyoga, the past three decades have been characterized by profound changes in fish species composition following the introduction of the piscivorous Nile perch (Oguto-Ohwayo 1990). Over 300 haplochromine cichlid species comprising a wide range of trophic groups were lost along with a host of non-cichlid fishes which occupied virtually all available ecological niches and in the lakes (Witte 1992). A second major ecological event has been the gradual nutrient enrichment of the water bodies (eutrophication) from diffuse and point sources, while at the same time pollutants have also gained entrance into the water systems in pace with indusfrial development and human population increases in the lake basins. Eutrophication and pollution have drastically altered the physical and-chemical character of the water medium in which different fauna and flora thrive. In Lake Victoria these alterations have resulted in changes of algal species composition from pristine community dominated by chlorophytes and diatoms (Melosira etc) to one composed largely of blue-green algae or Cyanobacteria (Microcystis, Anabaena, Planktolyngbya etc) (Mugidde 1993, Hecky 1993).

Studies on distribution, diversity and production of macrobenthic fauna in the Chahbahar Bay

The population density, distribution, diversity and secondry production of macrobenthic fauna of the inner Chahbahar Bay were studied through bi-monthly sampling from April 1995 to March 1996. Samples were collected from water near the bottom and sediment at 14 stations inside the Bay and one reference station located outside at the entrance to the Bay. The environmental parameters Such as temperature, water depth, salinity, pH and dissolved oxygen as well as percentage silt-clay and total organic matter of the sediment were measured. The faunal population density and their distribution is discussed in relation to the environmental changes. results obtained indicated both spatial and temporal heterogeneity in faunal distribution of the Chahbahar Bay. The total of 18 groups of macrofauna were identified in all samples. Amphipods formed the dominant group (21%) followed by polychaetes (19%), gastropods (15.7%) bivalves (10.6%) and all other groups (33.7%). Seasonal changes in faunal density is shown in relation to Indian Ocean southwest monsoon,the result of which indicated lower population density during monsoon (June to September) than that of the premonsoon (February to May) and post monsoon (October to January) periods. The numerical abundance of macrobenthos varied from 10260.m2 before monsoon to 5190 m2 during monsoon season. Three dominant groups of macrofauna including polychaetes, gastropods, and bivalves were identified in all collected samples. Indices of diversity, richness and evenness were calculated for these three dominant groups. The Shannon-Weaver information index was used to describe the spatially and temporally variation in diversity of these three major faunal groups. The results exhibited lower faunal diversity during monsoon period. The annual production of two dominant macrofauna species including a species of bivalve, Nuculana acuta and a species of Cephalochordata, Branchiostoma lanceolatum were measured by using age group determination. Furthermore the mean biomass and total annual production of macrobenthic fauna were estimated for the whole studied area. The potential yield of demersal fishery resources (fish and crustacean) then estimated and worked out to be 15360 tons/year asuming 10% ecological efficiency of hypothetical pyramid from 3rd to 4th marine trophic level. Accordingly the annual exploitable demersal fishery resources for the entire Chahbahar Bay was estimated to be 7600 to 8500 tons/year by taking 50 to 55% of the total estimated potential in to account.

Preliminary estimates of cetacean abundance in the northern Gulf of Mexico, and of selected cetacean species in the U.S. Atlantic Exclusive Economic Zone from vessel surveys

The Southeast Fisheries Science Center (SEFSC) initiated annual, vessel-based visual sampling surveys of northern Gulf of Mexico marine mammals in 1990 and conducted a similar survey in U.S. Atlantic Exclusive Economic Zone (EEZ) waters from Miami, Florida, to Cape Hatteras, North Carolina, in 1992. The primary goal of these surveys was to meet Marine Mammal Protection Act requirements for estimating abundance and monitoring trends of marine mammal stocks in United States waters. The surveys were designed to collect: 1) marine mammal sighting data to estimate abundance and to determine distribution and diversity; and 2) environmental data to evaluate factors which may affect the distribution, abundance and diversity of marine mammals. The preliminary analyses for abundance estimation from the 1990-1993 surveys are presented in this report.

Fishery methods and fish diversity in the Kilombero River in south-eastern Tanzania

Assessment of common fishery methods and of fish diversity was undertaken in two fishing camps on the Kilombero River in south-eastern Tanzania in surveys towards the end of the dry season, 1994. Fishermen identified 23 different types of fish that they caught on a regular basis. Only 19 species of fish, belonging to 17 genera and 11 families were, however, identified according to Linnean taxonomy. Hooks, nets, traps and spears were used to catch fish. Fish were either sold fresh. or preserved for storage and long-distance tranport by smoking or frying. based un frequency distributions of the numbers of fish landed over a 4 day period at one of the camps, a Shannon-diversity index of 1.95 was calculted. The fork (or total) length of 480 fish and the weight of 413 fish were measured and length frequency distributions as well as length-weight relationships determined for the six most common species. It is concluded that local fishing methods applied in the Kilombero River allow for sustainable fish production.

Bacterial diversity in activated sludge from a consecutively aerated submerged membrane bioreactor treating domestic wastewater

The bacterial diversity of activated sludge from submerged membrane bioreactor (SMBR) was investigated. A 16S rDNA clone library was generated, and 150 clones were screened using restriction fragment length polymorphism (RFLP). Of the screened clones, almost full-length 16S rDNA sequences of 64 clones were sequenced. Phylogenetic tree was constructed with a database containing clone sequences from this study and bacterial rDNA sequences from NCB1 for identification purposes. The 90.6% of the clones were affiliated with the two phyla Bacteroidetes (50%) and Proteobacteria (40%), and beta-, -gamma-, and delta-Proteobacteria accounted for 7.8%, 28.1%, and 4.7%, respectively. Minor portions were affiliated with the Actinobacteria and Firmicutes (both 3.1%). Only 6 out of 64 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species, which indicated that a substantial fraction of the clone sequences were derived from unknown taxa. Rarefaction analysis of operational taxonomic units (orrUs) clusters demonstrated that 150 clones screened were still insufficient to describe the whole bacterial diversity. Measurement of water quality parameter demonstrated that performance of the SMBR maintained high level, and the SMBR system remained stable during this study.

Characterization of novel microsatellite loci in rare minnow (Gobiocypris rarus) and amplification in closely related species in Gobioninae

Rare minnow (Gobiocypris rarus) is an endangered small fish endemic to upper reach of the Yangtze River. From a (GT)n enriched genomic library, 32 microsatellites were isolated and characterized. Nineteen of these loci were polymorphic in a test population with alleles ranging from 2-7, and observed and expected heterozygosities from zero to 0.8438, and 0.2679 to 0.8264, respectively. In the cross-species amplifications, 13 out of 19 polymorphic loci were found to be also polymorphic in at least one of the 7 closely related species of the subfamily Gobioninae. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the fine-scale population structure in rare minnow and its closely related species for the conservation purpose.

Utility of ITS1-5.8S-ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea : Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected.

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

DNA polymorphism of the plankton community and its relationships to species composition in the Three Gorges Reservoir Region of the Yangtze River

We examined DNA polymorphism of the plankton community in the Three Gorges Reservoir Region of Yangtze River and studied its relationships to species composition. Samples of the plankton community were collected from nine sampling sites and analyzed by random amplified polymorphic DNA (RAPD). Nine of 60 screened primers generated a total of 88 observable 180 to 1400 by bands, all of which were polymorphic. Cluster analysis of the resulting binary format from DNA banding patterns grouped the target communities into three clusters. The topology of the constructed diagram from species composition data was generally similar to that based on RAPD markers.

Ex situ conservation status of an endangered Yangtze finless porpoise population (Neophocaena phocaenoides asiaeorientalis) as measured from microsatellites and mtDNA diversity

The Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis, is all endangered small cetacean that occurs only in the middle and lower reaches of the Yangtze River of China. The establishment of a breeding population of the porpoise in Tian-e-Zhou Baiji National Natural Reserve represents the first attempt at ex situ conservation efforts for a cetacean species. With the goal of effective protection, management, and monitoring of this preserved population, we examined its genetic diversity using 930 bp of mtDNA control region sequences and 13 polymorphic microsatellite loci. A very low level of genetic variation (h = 0.6010 +/- 0.0029 s.d.; pi = 0.0007 +/- 0.0000002 s.d.) in the mtDNA control region sequences and a moderate genetic diversity (Ho = 0.5740 +/- 0.2575 s.d.) in the microsatellites were detected in the population. It is necessary to introduce more individuals with representative genetic variations into the reserve ill order to foml a larger and healthier group structure for long-term survival of the population. Successful establishment of the Yangtze finless porpoise population in the Reserve also provides a useful model for an ex situ conservation programme for other rare and endangered species. (c) 2005 International Council for the Exploration ofthe Sea. Published by Elsevier Ltd. All rights reserved.