%0 Journal Article %J Pacific Science %D 2021 %T Eleotris (Teleostei: Eleotridae) from Indonesia with description of three news species %A Marion Mennesson %A Philippe Keith %A Hubert, Nicolas %Y Frédéric Busson %Y Delrieu-Trottin, Erwan %Y Limmon, Gino %Y Sukmono, Tedjo %Y Jiran %Y Risdawati, Renny %Y Dahruddin, Hadi %X 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 Eleotris macrolepis (Bleeker, 1875), both belonging to this group, are given for comparison. A key for Eleotris species from Indonesia is provided. %B Pacific Science %V 75 %P 469-496 %8 11/2021 %G eng %N 4 %R https://doi.org/10.2984/75.4.2 %0 Journal Article %J Evolutionary Applications %D 2020 %T 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 %A Delrieu‐Trottin, Erwan %A Durand, Jean‐Dominique %A Limmon, Gino %A Sukmono, Tedjo %A Kadarusman %A Sugeha, Hagi Yulia %A Chen, Wei‐Jen %A Busson, Frederic %A Borsa, Philippe %A Dahruddin, Hadi %A Sauri, Sopian %A Fitriana, Yuli %A Zein, Mochamad Syamsul Arifin %A Hocdé, Régis %A Pouyaud, Laurent %A Philippe Keith %A Wowor, Daisy %A Steinke, Dirk %A Hanner, Robert %A Hubert, Nicolas %K Coral Triangle %K Cryptic diversity %K DNA barcoding %K reference library %K taxonomic gap %X 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. %B Evolutionary Applications %8 Nov-02-2020 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12926 %! Evol Appl %R 10.1111/eva.12926 %0 Journal Article %J Scientific Reports %D 2020 %T Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes %A Sholihah, Arni %A Delrieu-Trottin, Erwan %A Sukmono, Tedjo %A Dahruddin, Hadi %A Risdawati, Renny %A Elvyra, Roza %A Wibowo, Arif %A Kustiati, Kustiati %A Busson, Frederic %A Sauri, Sopian %A Nurhaman, Ujang %A Dounias, Edmond %A Zein, Muhamad Syamsul Arifin %A Fitriana, Yuli %A Utama, Ilham Vemendra %A Muchlisin, Zainal Abidin %A Agnèse, Jean-François %A Hanner, Robert %A Wowor, Daisy %A Steinke, Dirk %A Philippe Keith %A Rüber, Lukas %A Hubert, Nicolas %K Conservation genetics %K Cryptic diversity %K Population fragmentation %K Southeast Asia %K taxonomy %X 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. %B Scientific Reports %V 10 %8 Jan-12-2020 %G eng %U http://www.nature.com/articles/s41598-020-59544-9 %N 1 %! Sci Rep %R 10.1038/s41598-020-59544-9 %0 Journal Article %J Cybium %D 2020 %T Giuris (Teleostei: Eleotridae) from Indonesia, with description of a new species %A Philippe Keith %A Marion Mennesson %A Sauri, S %A Frédéric Busson %A Delrieu-Trottin, Erwan %A Limmon, G %A Sukomono, T %A Jiran %A Risdawati, Renny %A Dahruddin, Hadi %A Hubert, Nicolas %B Cybium %V 44 %P 331-349 %G eng %N 4 %0 Journal Article %J Conservation Genetics %D 2019 %T 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 %A Hubert, Nicolas %A Lumbantobing, Daniel %A Sholihah, Arni %A Dahruddin, Hadi %A Delrieu-Trottin, Erwan %A Busson, Frederic %A Sauri, Sopian %A Hadiaty, Renny %A Philippe Keith %K Conservation genetics %K Cryptic diversity %K Population fragmentation %K Southeast Asia %K taxonomy %X 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. %B Conservation Genetics %V 20 %P 517 - 529 %8 Jan-06-2019 %G eng %U http://link.springer.com/10.1007/s10592-019-01152-w %N 3 %! Conserv Genet %R 10.1007/s10592-019-01152-w %0 Journal Article %J Mol Ecol Resour %D 2016 %T Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. %A Dahruddin, Hadi %A Hutama, Aditya %A Frédéric Busson %A Sauri, Sopian %A Hanner, Robert %A Philippe Keith %A Hadiaty, Renny %A Hubert, Nicolas %X

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.

%B Mol Ecol Resour %8 2016 Mar 22 %G eng %R 10.1111/1755-0998.12528