Freshwater habitats in the Indo-Pacific Islands are colonised by amphidromous fish, which undergo a marine larval phase while the rest of the life cycle takes place in the riverine habitat. These fish are mainly represented by Gobiiformes. Among these, Stenogobius genivittatus (Valenciennes, 1837) is widely distributed in the Indo-Pacific Region, from South Africa to French Polynesia. We studied elements of the life history of S. genivittatus to better understand the processes contributing to its vast distribution: we analysed population genetic structure based on partial mitochondrial DNA sequences ( COI and ND6 ) and we used otolith microstructural analysis to estimate the duration of the marine pelagic larval phase (PLD). The analysis indicates the presence of a unique population broadly distributed across the Indo-Pacific Ocean, from South Africa to French Polynesia, while individuals from Hawaii appear to constitute a potentially distinct population. Also, our results show a homogeneous PLD in the West Indo-Pacific Region, except for Hawaii where it is longer and the Central Pacific Ocean (French Polynesia and the Marquesas) where it is shorter.

Tropical insular systems have long attracted biologists, stimulating some important controversies in ecology and evolution. Eustatic fluctuations during the Pleistocene have been invoked to explain species dispersal and proliferation in these fragmented systems by controlling the extent of landmasses and their temporary connections. In ancient archipelagos, the Pleistocene represents only a small slice of their history, so long-standing configurations might better explain insular diversity patterns. With a geological history of ca. 30 million years, the Sunda Shelf is old. Upon entering the Pleistocene, islands of the Sunda Shelf repeatedly separated and merged; however, recent reappraisals of its paleoenvironments and evolutionary dynamics have questioned their biogeographic significance. Based on the molecular inventory of 6 common freshwater fish families, we explored population fragmentation and demographic history of the most common species using mitochondrial DNA sequences. Species delimitation methods, applied to 1062 sequences belonging to 37 species from 188 sites, detected 95 Molecular Operational Taxonomic Units (MOTUs). Among the 9 most widespread species, the number of MOTUs ranged from 1 to 11, and correlated with time to the most recent common ancestor. Extended Bayesian Skyline Plots applied to mitogenomes and cytochrome c oxidase I sequences detected no variation in past effective population size within MOTUs, while hierarchical Approximate Bayesian Computation provided no evidence of congruent changes in effective population sizes. Fragmentation of an ancestral range is the most likely explanation for the rampant cryptic diversity observed, but demographic inferences do not support MOTUs as being refugial from an evolutionary perspective.

Ikan lepu batu genus Synanceia adalah kelompok ikan berbisa yang umum dijumpai di perairan tropis Indo-Pasifik. Tujuan penelitian ini adalah untuk melakukan identifikasi berdasarkan karakter morfologi pada spesimen ikan lepu batu genus Synanceia koleksi Museum Zoologicum Bogoriense. Karakter morfologi yang meliputi karakter meristik dan morfometrik dari 22 spesimen diperiksa dengan teliti. Hasil penelitian menunjukkan adanya dua spesies yang teridentifikasi, yaitu Synanceia horrida dan Synanceia verrucosa. Kedua spesies ini dapat dibedakan berdasarkan beberapa karakter, seperti jumlah jari-jari sirip dada, kondisi tulang di atas mata, kondisi membran di antara duri kedua dan ketiga sirip dorsal, panjang duri sirip dubur, dan diameter orbit. Informasi mengenai kandungan bisa dari ikan lepu batu dibahas dalam artikel ini.

Syngnathidae are a charismatic family of teleost fishes, represented by seahorses, seadragons, and pipefishes. Syngnathidae are mainly composed of marine species, but about 30 species of pipefishes inhabit freshwater insular environments of the Indo-Pacific realm. Recent research has shown that some freshwater pipefish species are amphidromous and exhibit high intraspecific divergences across their distribution range, like Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia and Microphis retzii (Bleeker, 1856) distributed from Taiwan to Indonesia. In this study, we used the mitochondrial cytochrome oxidase I (COI) partial gene of 91 specimens of M. brachyurus and 30 specimens of M. retzii from localities representative of their respective distribution area to improve knowledge on the population structure of these two widespread species. Genetic species delimitation and phylogeographic analyses were combined to explore spatial patterns of genetic diversity across the distribution ranges of the two species. We have highlighted deep genetic structuring within the two species and relate these results to various biotic and abiotic factors. For M. brachyurus, the population in Polynesia is distinct from those in the West Pacific, suggesting its distinctiveness and recognition as an evolutionary significant unit (ESU). For M. retzii, three lineages are delimited in its range distribution, suggesting the existence of two distinct species in Southeast Asia (Bali/Java/Lombok and China/Taiwan). Pipefish species are particularly vulnerable to anthropogenic pressures (inherent to Syngnathidae and insular environments). The present results, revising species delimitation and geographic distribution, will help implement effective conservation and management measures.

Since the integration of LIPI into BRIN in 2021, the Museum Zoologicum Bogoriense (MZB), which is managed by the coordinator of the zoological collection assisted by 20 collection technician staffs, has been transferred to the Directorate of Scientific Collections Management. The process of integration and management transfer does not change the main duties and functions of MZB as the national depository for zoological specimen collections. In addition to managing collections, researchers frequently ask MZB staff for assistance during field research and teaching collection management courses to students, teaching staff, and regional museum directors. The management of the MZB collection is described in a scientific publication for the first time. We hope that this documentation will continue so that museum management science can advance and assist the scientific community, particularly in Indonesia.

Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective of estimating intraspecific genetic diversity and inferring past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods, and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and 5 genera. Two cases of discordance between morphology and mitochondrial sequence are observed, suggesting ongoing speciation and/or introgression in 2 genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which correspond to observations of a few individuals far from the range distribution of their conspecifics. Among the 10 species or species groups whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima’s D tests and Bayesian Skyline Plot reconstructions. Together, these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males’ coloration among diverging species pairs seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea.

Freshwater habitats in Indo-Pacific tropical islands are mainly inhabited by amphidromous fish, which display a marine larval phase while the rest of their life cycle takes place in rivers. Gobiiformes are the most diversified fish component in these ecosystems. In this study, we focused on the status of the widespread Stenogobius genus (Gobioidei). This genus is distributed from the Indian Ocean to French Polynesia. Recently, a first revision of Stenogobius was undertaken leading to the redescription of S. genivittatus (Valenciennes, 1837) and the placement of 12 species names as synonyms of this species. This paper focuses on the status of nine Stenogobius species supposedly present in Indonesia, a country well known as one of the freshwater hotspots of biodiversity. The present study is based on 95 specimens, and includes morphomeristic data and partial mito-chondrial COI sequences. Our results show that, at least four species occur in Indonesia, including the wide-spread species S. genivittat

A new species of freshwater pipefish, Microphis arrakisae sp. nov., is described from the West Indonesian Islands (Java, Bali and Lombok). This species is morphologically very close to Microphis retzii (Bleeker, 1856), which is found in the eastern Indonesian Islands (Sulawesi, Ceram, Ambon and Papua). However, it can be distinguished by its in vivo coloration. Furthermore, genetic analysis of the partial COI gene (barcoding) indicates that it represents a distinct genetic lineage in the Indonesian region.

Inland water ecosystems in Indonesia face an increasing threat of alien and invasive alien fish species. Their existence have been found in Indonesian waters since before 1900, and their introduction is rapid and ongoing. In this review, we mapped the distribution of alien and invasive alien fish in different inland waters ecosystem types and islands in Indonesia, based on available literature indexed by Google Scholar. Impacts of invasive alien fish and how to control them are also discussed. This data mining exercise resulted in the successful mapping of alien and invasive alien fish in 72 lakes and 57 river systems, covering 28 provinces. A total of 50 species have spread with different compositions in each type of ecosystem and island. Oreochromis niloticus is the most commonly encountered alien species. Moreover, invasive cichlid fish are most frequently found in lakes, while Pterygoplichthys spp. are more frequently found in rivers although they can also inhabit many lakes. Java Island is a hotspot of alien and invasive alien fish distribution, with 39 species reported. Invasive alien fish harm native and endemic fish in Indonesia through competition for food, space and direct predation. The gradual reduction of established populations of invasive alien species is necessary to protect Indonesia’s freshwater ecosystems.

Balashark, Balantiocheilus melanopterus (Bleeker, 1850), has been discovered for the first time in the swamp inside Muara Angke Wildlife Reserve, Jakarta, Indonesia. Balashark in Indonesia is originally distributed in Sumatra and Kalimantan. However, the fish was collected in the public waters of Java which is not its distribution areas. Fishing gear used was gill net with a diameter of 2 inches".The characteristics, morphometric and meristic records are supplemented with water quality information to supplement existing data.

ABSTRACT TNBNW is included in the Wallacea Region which is a transitional zone between Oriental and Australian zoogeography which is estimated to have many unique and endemic flora and fauna species, including fish species that have not been fully disclosed. This study aims to inventory the diversity of ichthyofauna that live in the fresh waters of the TNBNW area and its surroundings. Sampling was carried out by making 11 research stations from the waters that flow from the Matabulawa peak to the Bone River. Samples were collected by electrofishing then identified and preserved using formalin solution. The species of fish obtained were analyzed on the index of diversity, evenness, and species richness. To complete the data, tabulation of data on fish species in the TNBNW area from previous studies as well as specimens that already have catalog numbers deposited in MZB was carried out. This study found 13 species of fish consisting of 6 families and 10 genera. The total ichthyofauna in the TNBNW area and its surroundings is 32 species consisting of 15 families. Stiphodon sp. is the species that has the highest relative abundance (48.80), followed by Poecilia reticulata (11.00). The species with the highest local distribution was Belobranchus belobranchs (90.91%). The rivers that have the highest index of species diversity, evenness, and species richness are Pilolode River, Pilohampaa River, and Loji River, respectively. Two species are classified as introduced fish, namely Poecilia reticulata and Oreochromis niloticus . Several species of fish have potential as ornamental fish as well as consumption fish. Key words: Species diversity, ichthyofauna, TNBNW ABSTRAK TNBNW termasuk ke dalam Kawasan Wallacea yang merupakan zona peralihan antara zoogeografi Oriental dan Australia yang diperkirakan memiliki banyak jenis flora dan fauna yang unik dan endemik, termasuk jenis-jenis ikan yang belum semua dapat diungkapkan. Penelitian ini bertujuan untuk menginventarisasi keragaman iktiofauna yang hidup di perairan tawar kawasan TNBNW dan sekitarnya. Sampling dilakukan dengan membuat 11 stasiun penelitian dari perairan yang mengalir dari puncak Matabulawa menuju Sungai Bone. Sampel dikoleksi dengan elektrofishing kemudian diidentifikasi dan dipreservasi menggunakan larutan formalin. Jenis ikan yang diperoleh dianalisis indeks keanekaragaman, kemerataan dan kekayaan jenisnya. Untuk melengkapi data, dilakukan tabulasi data jenis-jenis ikan di kawasan TNBNW dari penelitian-penelitian sebelumnya serta spesimen yang telah terkatalog yang terdeposit di MZB. Penelitian ini menemukan 13 jenis ikan yang terdiri dari 6 famili dan 10 genus. Total iktiofauna di kawasan TNBNW dan sekitarnya adalah 32 jenis, terdiri dari 15 famili. Stiphodon sp. merupakan jenis yang memiliki kelimpahan relatif tertinggi (48,80) diikuti Poecilia reticulata (11,00). Jenis yang memiliki distribusi lokal tertinggi adalah Belobranchus belobranchus (90,91%). Sungai yang memiliki indeks keanekaragaman jenis, kemerataan dan kekayaan jenis paling tinggi masing-masing adalah Sungai Pilolode, Sungai Pilohampaa dan Sungai Loji. Dua jenis ikan tergolong ikan introduksi yaitu Poecilia reticulata dan Oreochromis niloticus . Beberapa jenis ikan memiliki potensi sebagai ikan hias dan juga ikan konsumsi. Kata Kunci: Keragaman jenis, iktiofauna, TNBNW

The species of Eleotris from Indonesia are reviewed and compared to the known species described from the area. Nine species are recognized including three new species in the 'melanosoma' neuromast pattern group. These are described using genetic and morpho-meristic approaches. The new species differ by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the number of scales in lateral, predorsal, forward and zigzag series. The main characteristics of the other known species in the area in the 'melanosoma' group, Eleotris melanosoma Bleeker, 1853 and Eleotrismacrolepis (Bleeker, 1875), both belonging to this group, are given for comparison. A key for Eleotris species from Indonesia is provided.

A new species of Schismatogobius, a freshwater goby, is described from Sulawesi (Indonesia). It differs from other species belonging to the genus by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters, including the number of pectoral fin rays, the pectoral fin colour pattern, the jaw length/head length ratio and the preanal length.

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of mediumto large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

ten-Abstract . – a new species of Schismatogobius, a freshwater goby, is described from Sulawesi (indonesia). it differs from other species belonging to the genus by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters, including the number of pectoral fin rays, the pectoral fin colour pattern, the jaw length/head length ratio and the preanal length. résumé . – une nouvelle espèce

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

Indonesia merupakan negara dengan kekayaan jenis ikan yang tinggi, namun belum terdata dengan lengkap. Salah satunya adalah komunitas ikan air tawar di wilayah Kabupaten Banggai Kepulauan. Tujuan dari penelitian ini untuk mengkaji keanekaragaman jenis ikan, kelimpahan, sebaran, dan potensinya. Penelitian ini menggunakan metode survey pada tujuh stasiun berbasis CPUE (catch per unit of effort). Pengambilan sampel ikan menggunakan electrofishing yang dioperasikan selama 1-2 jam per stasiun. Ikan yang tertangkap dicatat jumlah jenis dan jumlah individu setiap jenisnya. Hasil penelitian ditemukan 22 spesies yang tergabung ke dalam 9 famili, Gobiidae merupakan famili yang paling dominan dengan anggota sebanyak 9 spesies diikuti Eleotrididae 6 spesies. Kelimpahan jenis ikan yang ditemukan bervariasi dengan kisaran 1-14,60 ind./st., jenis ikan yang paling melimpah adalah Ophieleotris aporos (14,60 ind./st.); kisaran sebaran antara 14,29-85,71% dan yang tersebar paling luas adalah Kuhlia marginata. Berdasarkan potensinya sebagian besar jenis ikan yang ditemukan dapat dikembangkan sebagai ikan hias.

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.

Indonesian Giuris species are reviewed and compared to the known species described from the area. Three species are recognized including one new species, which is described in this paper using genetic and morphomeristic approaches. The three species differ by a high percentage of divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the scales in transverse forward series, the scales around the eye and the interorbital length.

Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.