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Gouramy (Osphronemus gouramy) has very high economic value and is easy to cultivate. Currently there are about six strains that have been successfully cultivated based on their reproductive ability to produce eggs, namely goose (soang, goose gouramy), jepun (japan, japonica), blue sapphire, paris, bastar (broiler) and porcelain. One of the reasons for these differences in ability is internal factors which can be seen through the identification and expression of the cGnRH gene that each of these gouramy strains have. The cGnRH gene functions in signaling the pituitary gland to secrete the hormone GtH. This study aims to identify sequences and gene expression values ​​resulting from three strains of gouramyat different age levels. The research method used was the exploration of three gouramy strains (soang, jepun, blue sapphire) at different age levels (4 months, 8 months, 12 months), and three gouramy strains were taken for each age level. This research was conducted through several stages, namely organ preparation, isolation, sequence identification and measurement of cGnRH gene expression. Sequence data was analyzed using phylogenetic trees and gene expression was analyzed using One Way ANOVA test. The sequence results showed that the soang strain had a sequence that was more similar to the jepun strain than the blue sapphire strain, and the resulting gene expression showed that the three gouramy strains with three different age levels did not give different results.

Pennahia anea is among of the demersal fish landed at Asemdoyong Fish Auction Centre, Pemalang. P. anea doesn't show sexual dimorphism, so that other characters are needed to differentiate male and female individuals, i.e. truss morphometric and meristic characters. Previous studies have shown that truss morphometric and meristic can differentiate between male and female individuals. This study aims to describe the morphometric and meristic truss characters and determine the truss morphometrically and meristic characters that distinguish between males and females of Pennahia anea. The research used a survey method with a purposive random sampling technique. Male and female individuals of P. anea were examined based on their meristic and truss morphometric characters. The data were analyzed statistically using Mann Whitney non-parametric test. The result proved that male and female were significantly different in seven out of the 31 truss distances. Male individuals had a larger size than female individuals in three truss distances. In contrast, the male had a smaller size than the female individuals in four out of seven truss distances that distinguish both sexualities. The soft fin radius of the ventral fin was significantly different between male and female of P. anea. It could be concluded that male and female individuals of Pennahia anea have different truss distances and meristic characters with seven truss distances and one meristic character are different

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software. The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations. Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

Marine ornamental trade has been developing for several years with Indonesia as one of the major exporter countries. Among the popular marine ornamental fish in the local and international markets belong to the family of Chaetodontidae. The existence of this family has been reported from several areas in Indonesia. However, no information is available in terms of their phylogenetic relationships of the fish from the south coast of West Java. The aim of this research was to asses the phylogenetic relationships among ornamental fish members of Chaetodontidae in the South Coast of West Java. Fish samples were collected from two trading sites Ujung Genteng and Taman Manalusu. Collected fish were identified using a previously published study. The evolutionary relationships among species were analyzed statistically through phylogenetic analysis based on maximum parsimony algorithm and Kimura 2- Parameter substitution model as implemented in PAUP 4.0 software. Tree branching pattern supported by 1000 bootstraps pseudo-replicates and out-group comparison. Daschyllus trimaculatus used as outgroup species. Based on the study, Chaetodontidae from the South Coast of West Java formed one monophyletic group compared to Dascylus trimaculatus with Chelmon rostratus was the basal species. All the remaining species were the derived species. There are CI and RI value gained. The consistency index (CI) value of this family is 0.5833, and the retention index (RI) is 0.5082.

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java. This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.

Rhacophorus margaritifer is an endemic species of arboreal frog in Java. Previous studies found this frog in several locations of Baturraden, namely in primary forest of Ketenger area, along Pancuran Pitu tourism track, and Baturraden Botanical Garden. There were still limited studies of molecular diversity of R. margaritifer and no prior data from population in the southern slope of Mount Slamet. This study aimed to look at the genetic polymorphism and determine the locus diversity of R.margaritifer population in Baturraden by using the PCR-RAPD technique. Frog tissue samples were taken from three populations in Kalipagu hiking trail (HPK 01), Baturraden hiking trail (HPK 02), and Baturraden Botanical Garden (KRB). DNA was extracted using the Chelex method. Molecular characterization was performed based on RAPD markers. The RAPD marker band pattern was changed to binary data 0-1 and analysed using Arlequin software ver.3.5. A total of 19 frog individuals were obtained during sampling at three locations. High genetic diversity had been observed in all populations with gene diversity range from 0.9643 in HPK 01 population to 1.0000 in both KRB and HPK 02 populations. A high locus variation was also observed for all populations with values of 0.159524 in KRB; 0.165816 in HPK 01; 0.192857 in HPK 02, respectively. AMOVA indicated no genetic difference among populations of R. margaritifer (p=0.50244).

Abstract. Pomacentridae has a wide distribution in Indonesia waters. Research on species richness of Pomacentridae has been carried out in some areas in Indonesia. However, there are no data about the relationships of Pomacentridae on the southern coast of West Java. This research aims to know the evolutionary kinship of Pomacentridae ornamental fish in Ujung Genteng and Taman Manalusu Beach, West Java. This research used a survey method with a judgment sampling technique. The parameters measured were the consistency index (CI) and character evolution of the resulting phylogenetic tree. Cladogram reconstructed based on maximum parsimony algorithm with 1000 bootstrap replicates in PAUP software. The result showed that the tree had a CI value of 0.6000 which indicated low homoplasy. Pomacentridae formed a monophyletic group when they compared with Chaetodon collare as outgroup. The Pomacentridae clade divided into two subclades. The first subclade consisted of Abudefduf indicus as a basal species, then Neoglypydodon bonang and Plectroglyphidodon lacrymatus have a closed kinship and diverged after Dascyllus trimaculatus, and then Abudefduf notatus and Abudefduf sexfaciatus have a close kinship and diverged after Abudefduf vaigiensis. The second subclade referred to as a basal group, and within this subclade, Chrysiptera brownriggii has a closely related to Chrysiptera unimaculata and diverged after Chromis opercularis. Keywords: Cladistics, damselfish, meristic, morphometric, Pomacentridae

Captive population of Mandiangin giant gourami (Osphronemus goramy Lac.) is a new strain developed from wild pop-ulations in Riam Kanan Dam. No much is known about the genetic constituent of this strain compared to the parental population. This re-search was done to obtain information whether genetic alteration has occurred in captive population compared to their wild parental pop-ulation. Wild population was caught from Riam Kanan Dam, while captive population was collected from Balai Perikanan Budidaya Air Tawar (BPBAT) “Freshwater Aquaculture Centre” Mandiangin, South Kalimantan. The captive population of Batanghari strain from BPBAT Sungai Gelam, Jambi was also analyzed. Molecular assess-ment was done using CO1 PCR-RFLP which was developed by digest-ing the amplicon of the CO1 gene from all populations using two re-striction enzymes, namely HindIII and TaqI and resulted CO1-HindIII and CO1-TaqI RFLP markers. All tested populations showed uniform patterns of those CO1-RFLP markers but with different fragment sizes among populations. This means all resulted RFLP markers were mono-morphic in each populations but polymorphic among giant gourami populations. In other words, no genetic diversity within population but substantial genetic differences was observed between wild and cap-tive Mandiangin populations. This proved that genetic alteration has occurred in Mandiangin captive populations compared to the wild pa-rental giant gourami population. In conclusion, captive and wild pop-ulations of Mandiangin giant gourami were genetically different. This result is vital as scientific base for future development of inland fish-eries, especially for breeding strategy of Mandiangin giant gourami.

Spermonde Archipelago in South Sulawesi is among groupers sources in Indonesia for International Marine Live Trade. It was not much known which species are mostly exploited in those areas during the study because only fin clip samples could be obtained. Here we performed DNA forensic analysis to groupers fin clips collected from Spermonde Archipelago using barcode marker to know what species were exploited and which ones was the most exploited species. A total of 110 fin clip samples were obtained during the field trips. Sequencing of the cytochrome c oxidase 1 gene was successful for only 36 samples. Species determination was based on sequences similarity to conspecific sequence available in barcoding of life database (BOLD). BOLD similarity test placed the 36 fin clip samples into four different species, namely Cromileptes altivelis, Epinephelus ongus, Plectropomus leopardus, and Plectropomus maculatus. The K-2P taxonomic tree showed clear separation among species which was supported by high K2P genetic distances among species. Most of fin clips were identified as Plectropomus leopardus indicates that this species was the most exploited in Spermonde Archipelago. This proved that molecular identification not only can be used to biodiversity study in certain area but also in forensic analysis of a threatened wildlife. This study has important contribution for conservation effort of those groupers species, especially P. leopradus and provides new approach for taxonomist and conservation managers to identify samples, especially when only incomplete specimens are available.

Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB – rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB – rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB – rbcL sequences.

Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and Φst-value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to Osphronemus goramy sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise Φst-comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.

The cultivation of giant gourami is constrained by its high mortality due to low resistance to diseases. Resistance is an inherited character from the parental to their seeds. High resistance seeds can be selected using molecular marker, such as Major Histocompatibility complex (MHC) gene. Resistance character is assumed to be different among individual from different broodstocks and is suggested related to their genetic constituent. This research aims to analyze the resistance of sowang gouramy seeds from different broodstocks and describe genetic character of seeds from different broodstocks. An explorative survey was perfomed. One hundred individuals were taken purposively from Balai Benih Ikan Sikamaju Ciamis West Java and hundred individuals were bought from fish farmer in Ciamis West Java. Sampling was performed in 2015 for the first seed group and in 2016 for the second seed group. Samples were subjected to Aeromonas hydrophila and Pseudomonas aeruginosa infection. The fragments of MHC gene were amplified using PCR technique from eight individual of first group and six individuals of second group. The resistance characteristic was analyzed using simple mathematics based on the number of living seeds compared total infected seeds and molecular characteristics was analyzed descriptively based on DNA band pattern. Different resistance to A. hydrophila was observed between seed groups from different broodstocks. The seeds group from the first broodstocks showed lower resistance level with the value of 29% than that from the second broodstocks with the resistance value reached of 100%. Both seed groups also showed resistance differences to P.aeruginosa, although not as high as A.hydrophila infection. The differencies were also reflected in their MHC gene between seed groups from two different broodstocks. The amplication of MHC gene of the seeds from the first broodstacks resulted of 585 bp and 400 bp length fragments, while from those second broodstocks was only resulted of 400 bp frament. The differences on DNA band pattern between seed groups indicate a different molecular characteristics among seeds from different broodstocks. Usaha budidaya ikan gurami terhambat oleh tingginya mortalitas benih karena rendahnya resistensi terhadap penyakit. Resistensi merupakan sifat yang diwariskan dari tetua ke anakan. Benih yang resisten dapat diseleksimenggunakan marka molekuler seperti gen Major Histocompatibility complex (MHC). Sifat resisten diduga berbeda diantara benih yang beraasal dari induk berbeda dan diduga terkait dengan kompenen genetik yang dimiliki. Tujuan penelitian ini adalah untuk mengetahui sifat reisten dan karakter molekuler benih gurami sowang asal induk berbeda. Fragmen gen MHC diamplifikasimenggunakan teknik PCR. Sifat resistensi dianalisis menggunakan perhitungan matematika sederhana berdasarkan jumlah benih hidup dibagi jumlah total benih yang diinfeksi, sedangkan karakter molekuler dianalisis secara deskritif berdasakan pola pita yang dihasilkan. Kedua kelompok benih memiliki sifat resistensi berbeda terhadap Aeromonas hydrophila. Benih dari induk pertama memiliki sifat resistensi lebih rendah dengan nilai kelangsungan hidup sebesar 29% daripada kelompok benih dari induk kedua yang memiliki kelangsungan hidup mencapai 100%. Kedua kelompok benih juga memperlihatkan perbedaan sifat resisten terhadap P. aeruginosa, meskipun perbedaannya tidak sebesar terhadap A.hydrophila. Perbedaan tersebut juga tercermin pada gen MHC kedua kelompok benih. Pada kelompok benih pertama dihasilkan dua fragmen gen MHC dengan ukuran 585 pb dan 400 pb, sedangkan dari kelompok benih kedua hanya dihasilkan fragmen berukeuran 400 pb. Perbedaan pola pita diantara kedua kelompok benih tersebut merupakan idikasi adanya perbedaan karakter molekuler pada benih yang berasal dari dua induk berbeda

Gurami (Osphronemus gouramy Lac.) is a popular fish species among Indonesian people. Several Gurami strains have been cultivated by fish farmer, one of which is Gurami Soang. This strain is belived to have a faster growth rate compared to other strains. However, like other strains, the fingerling of Soang strain have also a low survival and suceptible to disease, especially that caused by Aeromonas hydrophila infection. It has been proved that seeds from a single spawning event show varibale disease resistance. The difference in resistance among individuals is suggested related to the difference in their genetic component. One of the genes responsible for resistance is Major Histocompatibility Complex (MHC) class II B gene. Variability in resistance can be analyzed by using PCR - RFLP technique. PCR-RFLP is a technique that can produce a specific DNA fragments by PCR, followed by cutting the PCR product using restriction enzymes to describe the presence or absence of restriction sites in DNA fragments. This research aims to determine genetic marker to differiantiate between resitant and irresistant individual of Gurami Soang infected by A. hydrophila which die at a different time priod based on PCR-RFLP MHC class IIB gene. The study used survey method with purposive random sampling. The Data of PCR-RFLP band patterns were analyzed descriptively. The result indicated that cutting of the MHC class II B gene using HinfI produce two RFLP bands with 300 bp and 100 bp length in all samples. Meanwhile, the MHC IIB gene was not cuted by PstI, HindIII, BamHI and EcoRI enzymes forall samples. These mean that MHC II gene in all individuals were monomorphic. Therefore,it can be concluded that there is no specific genetic marker to differentiate gurami soang individulas which was dying in different time periods.

Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. The result showed that PCR-RFLP markers of Cytochrome b-HinfI of 315 bp, and 210 bp, and also Cytochrome b-AluI of 334 bp and 189 bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b- HinfI 366 bp, and 159 bp and Cytochrome b-AluI 525 bp fragments. It is observed that genetic variation of Cytochrome b-HinfI and -AluI markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-HinfI and -AluI gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries.

Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using Basic Local Alignment Search Tool (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination.

Gourami (Osprhronemus goramy Lac.) is a freshwater fish that is widely cultivated in Indonesia, particularly by fish farmer in Java. Soang strain has a faster growth rate than other strains. However, the fry that derived from a single cohort (generated from a single spawning) shows various sizes even in the same age because they have different growth rate. Differences in growth rate may occur due to differences in metabolic capabilities especially cellular respiration. Different rate of respiration can be assumed to be due to differences in the genetic component, especially on their cytochrome c oxidase 1 gene (CO1). Therefore this study aimed to determine whether there are differences in PCR-RFLP marker CO1 gene among different sizes of gourami soang strain from the same cohort so that can be used to analyze genetic diversity. This study used survey method by applying purposive random sampling. Four restriction enzymes were used during the research. Molecular characters were defined descriptively based on the appearance of restriction fragment on agarose gel. The result showed that soang strain which used in this study had monomorphics allele on their CO1-HindIII. PstI, BamHI, and EcoRI, could not cut the PCR products and results no RFLP markers. So that genetic variation in the used CO1 gene fragment could not be detected using HindIII, Pst1, BamH1 and EcoR1 enzymes. The three different sizes of soang strain had similar alleles or homozygous, meaning that heterozigocity value was 0 (zero). Therefore, the CO1 gene in this study could not be used as molecular character to differentiate different sizes of gourami soang strain from the same cohort.

Giant gouramy, Osphronemus gouramy Lac. is a popular fish species in Indonesia, especially in Java and Sumatera as this freshwater fish species has a high economic value of stable price. Fish farmers in Bogor divide giant gouramy into six strains based on egg productivity, growth rate, and maximum weight of the adult. They are soang, jepang, blue saphire, paris, bastar, and porselin. These various strains lead to the need of study on the genetic relationship among them, which can be performed by the use of RAPD (Random Amplified Polymorphic DNA) marker. This study aims to determine primers producing consistent and polymorphic RAPD markers, determine specific RAPD markers, and know the genetic relationship among several giant gouramy strains. The strains used in this study are soang, jepang, and blue saphire. Survey method was applied employing purposive random sampling technique. Total genomic DNA was isolated using Genjettm genomic DNA purification kit (Fermentas), which was then used as template to amplify RAPD markers with primers OPA-07, OPA-09, OPA-11, OPA-20, OPAH-01, OPAH-08, OPAH-09, and OPAC-14. The variables examined were patterns and numbers of specific DNA fragments as the PCR amplification products. Selected primers were determined descriptively on the basis of specific DNA bands appearing on the agarose gel. Genetic diversity was predetermined by changing qualitative band pattern into quantitative binnary data. Genetic relationship was analyzed using cladistic method with PAUP software. The results showed that only five of the eight primers produce consistent and polymorphic RAPD markers, i.e. OPA-11, OPA-20, OPAH-1, OPAH-8, and OPAH-9. Specific RAPD markers which can be used to distinguish several gouramy strains are those amplified with OPA-20 of 786 bp, OPA-20 of 1,176 bp, OPAH-8 of 1,000 bp and OPAC-14 of 1,607 bp. Nervertheless, it was found that RAPD markers cannot be used to clearly determine genetic relationship among gouramy strains.

Cijalu River is located in Western Cilacap Regency of Central Java Province. The river runs through forestry, housing and farming areas. This condition leads to a prediction that the river has been altered on its physico-chemical characteristics causing the river to be inhabited by a variety of fish species. This study aimed to collect data about fish species inhabiting Cijalu River and its distribution. A survey method has been done with clustered random sampling technique. The river was divided into three different areas, i.e. upper-, middle- and downstreams. Species diversitywas measured as the number of species, while distribution was measured as the presentation of fish species in each site. Nineteen fish species of 10 families were identified from Cijalu River. The 10 families were Anabantidae, Bagridae, Balitoridae, Channidae, Cichlidae, Cyprinidae, Loricariidae, Osphronemidae, Poecilidae and Sisoridae. Cyprinidae was the family having the highest number of species (6 species), followed by Bagridae (3 species), Channidae (2 species) and Osphronemidae (2 species). The remaining respective families were represented by one species. A complex pattern of fish distribution was observed during the study. Glyptothorax platypogon and Channa gacua were only found at the upper-streams, while Anabas testudineus was obtained in downstreams. The other remaining species could be observed either from the middle-to downstreams, or even from upper- to downstreams. Different pattern of species distribution could be caused by physico-chemical characteristics variation from upper to lower parts of the river, especiallywater velocity and substrate types. Keywords: Cijalu River, distribution, diversity, fish

Mud clams, Polymesoda erosa, in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD). Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The results proved that the use of RAPD marker has high polymorphisms. The mud clam population also showed a high level of heterozygosity and genetic diversity. This has important implication for the management plan towards sustainable use of P. erosa in the Segara Anakan Cilacap.

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA.

Rasbora is a genus of freshwater fish of the family Cyprinidae. Three species belonging to this genus were found in Java Island; R. aprotaenia, R. lateristriata, and R. argyrotaenia. Rasbora inhabits clear running water with sandy and gravel bottom. This study aimed to determine the longitudinal distribution of Rasbora spp. based on their species richness and abundance at Banjaran River; to determine the population structure of Rasbora spp based on their body weight, standard and total length; and to identify interactions between physical-chemical factors with species richness and abundance of Rasbora spp. This research was a survey, with purposive random sampling technique applied to collect samples. The research divided the study sites into five stations based on their altitude and topography. The Cluster Analysis was calculated based on species richness and relative abundance of Rasbora spp., while the longitudinal distribution and the population structure were presented descriptively. The interaction between the physical-chemical factors and the species richness and abundance of Rasbora were analyzed using Principal Component Analysis (PCA). Thi study found two species of Rasbora, namely Rasbora argyrotaenia and Rasbora lateristriata with 80 and 2 individuals respectively. R. argyrotaenia was distributed longitudinally along Banjaran River. Meanwhile, R. latestriata was only found at the upstream. Based on the body weight, the population of R. argyrotaenia at the station three were found highest by the average body weight of 1–6 gr of a total 31 individuals. The maximum measurements of the standard length were observed at the station 3 with a range of diameter 4.0–5.9 cm of 30 individuals. The total length were also found at the station 3 with a range of measuremtnt 5.0–7.9 cm of 33 individuals. R. latestriata was found only two individual with body weights measured were 9 gr and 10 gr, the standard lengths were 7.6 and 8.5 cm, and the total lengths were 9.5 and 10.5 cm. The distribution of R. argyrotaenia was influenced mostly by pH, the speed of the water, and DO. The presence of R. lateristriata was influenced primarily by BOD and depth.

Fish is one of the aquatic commodities with significant economic value, and Segara Anakan areas is a habitat for valuable fishes for local fisherman. Segara Anakan is a eutrophic waters and serves as nursery and spawning ground and also provide an optimal environment for several species fish larvae to grow, either sedentary or migratory species. Therefore it is suggested that diverse species inhabit Segara Anakan and different part of those areas has different species because different species commonly exhibit different habitat preferences. The objectives of this research were to determine the diversity and spatial distribution of fish species in Segara Anakan Cilacap. This research was a survey with the Cluster Random Sampling was implemented as sampling technique. Species diversity was analyzed descriptively, as well as the spatial distribution. The relationships between environmental parameters and spatial distribution were analyzed using Principal Component Analysis. Environmental factors such as temperature, pH, salinity, and water DO were measured. The result showed that Stolephorus indicus was the most dominant species in Segara Anakan. The spatial distribution of fishes in every sampling station was found fluctuated. The environmental factors and fish were found highly correlated.

Catfish species are commercially cultivated freshwater fish by fish farmer. Formerly, only one species of catfish had been cultivated, namely local catfish (walking catfish) Clarias batrachus. However, since 1985, local catfish was replaced by a new commodity from Africa called African catfish (C. gariepinus). In 2004, BBPBAT Sukabumi had introduced a new strain of catfish, namely Sangkuriang catfish. Taxonomic analysis needed, especially for Sangkuriang catfish using molecular marker, in order to get a clearer picture about its genetics departure from their parental, so their taxonomic status and relationships with local and African catfish is clearer.  One of the molecular markers is randomly amplified polymorphic DNA (RAPD) markers. Species status defined based on the presence and absence of specific band on each catfish. Phylogenetics relationships was inferred from phylogenetic tree which was built using UPGMA tool as implemented in NTSYS software based on the similarity of RAPD band pattern. The result showed that Sangkuriang and local catfish had specific RAPD markers, while African catfish was not. This means that all RAPD markers of African catfish were shared with those of two others catfish. Local catfish phylogenetically distantly related to African and Sakuriang catfish. Only one individual of African catfish (D4) genetically close related to Sangkuriang catfish while the rest individuals of African catfish genetically closed related to green catfish. This means that African catfish showed very divergence genetic constituent.  Key words: catfish, molecular identification, phylogenetic relationships, RAPD

Phylogenetic assessment of the giant clams need to be improved using various genetic markers since their relaionships are plagued by inconsistency result of several studies. This is especially true for the species under sub-genus Chametrachea. Here we studied the phylogeny of the giant clams using amino acid sequence of the mitochondrial COI gene. This study is aimed to assess and better understand the relationships of the giant clams, especially for three species under subgenus Chametrachea. The result showed close proximity between T. crocea and T. squamosa and between T. maxima and T. gigas. However, amino acids sequences of cytochrome c oxidase I gene was not strong enough to discriminate between T. crocea and T. squamosa. The majority of mutations were hydrophobic to hydrophilic amino acids.