@article {8404, title = {Eleotris (Teleostei: Eleotridae) from Indonesia with description of three news species}, journal = {Pacific Science}, volume = {75}, year = {2021}, month = {11/2021}, pages = {469-496}, abstract = {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 {\textquoteleft}melanosoma{\textquoteright} 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 {\textquoteleft}melanosoma{\textquoteright} group, Eleotris melanosoma Bleeker, 1853 and Eleotris macrolepis (Bleeker, 1875), both belonging to this group, are given for comparison. A key for Eleotris species from Indonesia is provided.}, doi = {https://doi.org/10.2984/75.4.2}, author = {Marion Mennesson and Philippe Keith and Hubert, Nicolas} } @article {7047, title = {Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods}, journal = {Evolutionary Applications}, year = {2020}, month = {Nov-02-2020}, abstract = {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.}, keywords = {Coral Triangle, Cryptic diversity, DNA barcoding, reference library, taxonomic gap}, issn = {1752-4571}, doi = {10.1111/eva.12926}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12926}, author = {Delrieu-Trottin, Erwan and Durand, Jean-Dominique and Limmon, Gino and Sukmono, Tedjo and Kadarusman and Sugeha, Hagi Yulia and Chen, Wei-Jen and Busson, Frederic and Borsa, Philippe and Dahruddin, Hadi and Sauri, Sopian and Fitriana, Yuli and Zein, Mochamad Syamsul Arifin and Hocd{\'e}, R{\'e}gis and Pouyaud, Laurent and Philippe Keith and Wowor, Daisy and Steinke, Dirk and Hanner, Robert and Hubert, Nicolas} } @article {7046, title = {Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes}, journal = {Scientific Reports}, volume = {10}, year = {2020}, month = {Jan-12-2020}, abstract = {iodiversity 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.}, keywords = {Conservation genetics, Cryptic diversity, Population fragmentation, Southeast Asia, taxonomy}, doi = {10.1038/s41598-020-59544-9}, url = {http://www.nature.com/articles/s41598-020-59544-9}, author = {Sholihah, Arni and Delrieu-Trottin, Erwan and Sukmono, Tedjo and Dahruddin, Hadi and Risdawati, Renny and Elvyra, Roza and Wibowo, Arif and Kustiati, Kustiati and Busson, Frederic and Sauri, Sopian and Nurhaman, Ujang and Dounias, Edmond and Zein, Muhamad Syamsul Arifin and Fitriana, Yuli and Utama, Ilham Vemendra and Muchlisin, Zainal Abidin and Agn{\`e}se, Jean-Fran{\c c}ois and Hanner, Robert and Wowor, Daisy and Steinke, Dirk and Philippe Keith and R{\"u}ber, Lukas and Hubert, Nicolas} } @article {7042, title = {Exploring community assembly among Javanese and Balinese freshwater shrimps (Atyidae, Palaemonidae) through DNA barcodes}, journal = {Hydrobiologia}, volume = {847}, year = {2020}, month = {Jan-01-2020}, pages = {647 - 663}, abstract = {Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the relative contribution of evolutionary and ecological dynamics might be a difficult task, particularly so for the tropical biotas due to their extreme diversity and large knowledge gaps. Here, we explore genetic diversity and distribution of 23 freshwater shrimp species of the genera Caridina and Macrobrachium in Sundaland to examine patterns of species co-occurrence based on 1583 observations across 19 sites in Java and Bali islands. DNA-based species delimitation methods applied to 204 cytochrome oxidase I sequences detected 30 operational taxonomic units and a few cases of deep intraspecific divergence. Species co-occurrence and phylogenetic community structure show no departure from expectations under a random distribution of species in landscapes and support a lottery model of community assembly. Species age estimates expand beyond the geological settlement of Sundaland, suggesting that species proliferation and community assembly are driven by mechanisms acting at distinct spatial and temporal scales.}, keywords = {Caridina, Dispersa, Lottery model, Macrobrachium, Phylogenetic community structure, Species delimitation}, issn = {0018-8158}, doi = {10.1007/s10750-019-04127-7}, url = {http://link.springer.com/10.1007/s10750-019-04127-7}, author = {Hernawati, Rena and Nurhaman, Ujang and Busson, Frederic and Suryobroto, Bambang and Hanner, Robert and Philippe Keith and Wowor, Daisy and Hubert, Nicolas} } @article {8285, title = {Giuris (Teleostei: Eleotridae) from Indonesia, with description of a new species}, journal = {Cybium}, volume = {44}, year = {2020}, pages = {331-349}, author = {Philippe Keith and Marion Mennesson and Sauri, S and Fr{\'e}d{\'e}ric Busson and Delrieu-Trottin, Erwan and Limmon, G and Sukomono, T and Jiran and Risdawati, Renny and Dahruddin, Hadi and Hubert, Nicolas} } @article {7041, title = {Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot}, journal = {Conservation Genetics}, volume = {20}, year = {2019}, month = {Jan-06-2019}, pages = {517 - 529}, abstract = {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.}, keywords = {Conservation genetics, Cryptic diversity, Population fragmentation, Southeast Asia, taxonomy}, issn = {1566-0621}, doi = {10.1007/s10592-019-01152-w}, url = {http://link.springer.com/10.1007/s10592-019-01152-w}, author = {Hubert, Nicolas and Lumbantobing, Daniel and Sholihah, Arni and Dahruddin, Hadi and Delrieu-Trottin, Erwan and Busson, Frederic and Sauri, Sopian and Hadiaty, Renny and Philippe Keith} } @article {5908, title = {Geography and life history traits account for the accumulation of cryptic diversity among {Indo}-{West} {Pacific} coral reef fishes}, journal = {Marine Ecology Progress Series}, volume = {583}, year = {2017}, pages = {179{\textendash}193}, author = {Hubert, Nicolas and Dettai, Agn{\`e}s and Patrice Pruvost and Cruaud, Corinne and Kulbicki, Michel and Myers, Robert F. and Borsa, Philippe} } @article {5024, title = {Schismatogobius (Gobiidae) from Indonesia, with description of four new species}, journal = {Cybium}, volume = {41}, year = {2017}, month = {06/2017}, pages = {195-211}, abstract = {

The species of Schismatogobius from Indonesia are reviewed and compared to the known species described from the area. Eight species are recognized including four new species. These are described using genetic and morphomeristic approaches. The 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 pattern of the ventral surface of the head in males and/or females, the pectoral fin colour pattern, the jaw length/head length ratio or the jaw length of male and/or female.

}, keywords = {Gobiidae, Indonesia, New species, Schismatogobius}, author = {Philippe Keith and Clara Lord and Darhuddin, H. and Limmon, G and Sukmono, T and Hadiaty, Renny and Hubert, Nicolas} } @article {4365, title = {Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.}, journal = {Mol Ecol Resour}, year = {2016}, month = {2016 Mar 22}, abstract = {

Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50\% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous and the taxonomic knowledge is scattered in the literature. The present study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of the present study, a checklist was compiled based on online catalogs. A total of 95 sites were visited and a library including 1,046 DNA barcodes for 159 species was assembled. Nearest neighbor distance was 28-fold higher than maximum intra-specific distance on average and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36\% (i.e. 77 species) and 60\% (i.e.24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. This article is protected by copyright. All rights reserved.

}, issn = {1755-0998}, doi = {10.1111/1755-0998.12528}, author = {Dahruddin, Hadi and Hutama, Aditya and Fr{\'e}d{\'e}ric Busson and Sauri, Sopian and Hanner, Robert and Philippe Keith and Hadiaty, Renny and Hubert, Nicolas} } @article {4102, title = {DNA Barcoding Indonesian freshwater fishes: challenges and prospects.}, journal = {DNA barcode}, volume = {3}, year = {2015}, pages = {144-169}, keywords = {Checklist, DNA barcoding, Southeast Asia}, author = {Hubert, Nicolas and Kadarusman and Wibowo, A and Fr{\'e}d{\'e}ric Busson and Caruso, D. and Sulandari, S. and Nafiqoh, N and R{\"u}ber, L and Pouyaud, L and Avarre, JC and Herder, F and Hanner, R and Philippe Keith and Hadiaty, Renny} } @article {4356, title = {DNA barcoding of Javanese and Balinese freshwater fishes: molecular insights into a poorly known ichthyofauna.}, journal = {Genome}, volume = {58}, year = {2015}, pages = {209}, author = {Darhuddin, H. and Hutama, A. and Fr{\'e}d{\'e}ric Busson and Sauri, S and Philippe Keith and Hanner, R and Hadiaty, Renny and Hubert, Nicolas} } @article {4363, title = {A new species of Sicyopterus (Teleostei: Gobiidae) from Indonesia. }, journal = {Cybium}, volume = {39}, year = {2015}, pages = {243-248}, author = {Philippe Keith and Clara Lord and Sauri, S and Fr{\'e}d{\'e}ric Busson and Hubert, Nicolas and Hadiaty, Renny} } @article {4360, title = {A new Stiphodon from Indonesia (Teleostei: Gobiidae)}, journal = {Cybium}, volume = {39}, year = {2015}, pages = {219-225}, keywords = {Indonesia, New species, Stiphodon}, author = {Philippe Keith and Clara Lord and Fr{\'e}d{\'e}ric Busson and Sauri, S and Hubert, Nicolas and Hadiaty, Renny} } @article {3724, title = {A new species of Sicyopus (Gobioidei) from Java and Bali}, journal = {Cybium}, volume = {38}, year = {2014}, pages = {173-178}, abstract = {

Sicyopus rubicundus n. sp., a sicydiine goby, is described from specimens collected in streams of\ Java and Bali (Indonesia). It differs from other species of this amphidromous genus by a combination of characters\ including a first dorsal fin with five spines in both sexes, a second dorsal fin with one spine and nine segmented\ rays, an anal fin with one spine and nine segmented rays, and a distinctive body colour in male.

}, keywords = {Freshwater, Gobiidae, Indonesia, New species, Sicyopus rubicundus}, author = {Philippe Keith and Hadiaty, Renny and Fr{\'e}d{\'e}ric Busson and Hubert, Nicolas} } @article {3723, title = {Three new species of Lentipes (Teleostei: Gobiidae) from Indonesia. }, journal = {Cybium}, volume = {38}, year = {2014}, pages = {133-146}, abstract = {

Three new species of Lentipes (L. argenteus, L. ikeae and L. mekonggaensis), freshwater gobies, are
described from streams of Sumatra, Java, Bali and Sulawesi (Indonesia). They differ from other species of the
genus by a combination of characters including an urogenital papilla lacking lateral lobes and retractable into a
sheath-like groove, the number of pectoral fin rays, the number of scales, tricuspid teeth in the upper jaw, and a
specific body colour in males.

}, keywords = {Bali, Freshwater, Gobiidae, Java, Lentipes, New species, Sulawesi, Sumatra}, author = {Philippe Keith and Hadiaty, Renny and Hubert, Nicolas and Fr{\'e}d{\'e}ric Busson and Clara Lord} }