%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 Cybium %D 2017 %T Schismatogobius (Gobiidae) from Indonesia, with description of four new species %A Philippe Keith %A Clara Lord %A Darhuddin, H. %A Limmon, G %A Sukmono, T %A Hadiaty, Renny %A Hubert, Nicolas %K Gobiidae %K Indonesia %K New species %K Schismatogobius %X

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.

%B Cybium %V 41 %P 195-211 %8 06/2017 %G eng %N 2 %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 %0 Journal Article %J Genome %D 2015 %T Comparative phylogeography of Javanese and Balinese freshwater fishes: DNA barcodes shed light on Quaternary range expansion dynamic in a biodiversity hotspot. %A Hutama, A. %A Darhuddin, H. %A Frédéric Busson %A Sauri, S %A Hanner, R %A Philippe Keith %A Hadiaty, Renny %A Hubert, N %B Genome %V 58 %P 230 %G eng %0 Journal Article %J DNA barcode %D 2015 %T DNA Barcoding Indonesian freshwater fishes: challenges and prospects. %A Hubert, Nicolas %A Kadarusman %A Wibowo, A %A Frédéric Busson %A Caruso, D. %A Sulandari, S. %A Nafiqoh, N %A Rüber, L %A Pouyaud, L %A Avarre, JC %A Herder, F %A Hanner, R %A Philippe Keith %A Hadiaty, Renny %K Checklist %K DNA barcoding %K Southeast Asia %B DNA barcode %V 3 %P 144-169 %G eng %0 Journal Article %J Genome %D 2015 %T DNA barcoding of Javanese and Balinese freshwater fishes: molecular insights into a poorly known ichthyofauna. %A Darhuddin, H. %A Hutama, A. %A Frédéric Busson %A Sauri, S %A Philippe Keith %A Hanner, R %A Hadiaty, Renny %A Hubert, Nicolas %B Genome %V 58 %P 209 %G eng %0 Journal Article %J Cybium %D 2015 %T A new species of Sicyopterus (Teleostei: Gobiidae) from Indonesia. %A Philippe Keith %A Clara Lord %A Sauri, S %A Frédéric Busson %A Hubert, Nicolas %A Hadiaty, Renny %B Cybium %V 39 %P 243-248 %G eng %N 4 %0 Journal Article %J Cybium %D 2015 %T A new Stiphodon from Indonesia (Teleostei: Gobiidae) %A Philippe Keith %A Clara Lord %A Frédéric Busson %A Sauri, S %A Hubert, Nicolas %A Hadiaty, Renny %K Indonesia %K New species %K Stiphodon %B Cybium %V 39 %P 219-225 %G eng %N 3 %0 Journal Article %J Cybium %D 2015 %T A new Stiphodon from Indonesia (Teleostei: Gobiidae) %A Philippe Keith %A Frédéric Busson %A Sauri, S %A Hubert, N %A Hadiaty, Renny %K Freshwater %K Gobiidae %K Indonesia %K New species %K Stiphodon aureofuscus %B Cybium %V 39. %P 219-225 %G eng %N 3 %0 Journal Article %J Cybium %D 2015 %T Stiphodon annieae, a new species of freshwater goby from Indonesia (Teleostei: Gobiidae). %A Philippe Keith %A Hadiaty, Renny %K Freshwater %K Halmahera %K Indonesia %K New species %K Stiphodon annieae %B Cybium %V 38 %P 267-272 %G eng %N 4 %0 Journal Article %J Cybium %D 2014 %T A new species of Sicyopus (Gobioidei) from Java and Bali %A Philippe Keith %A Hadiaty, Renny %A Frédéric Busson %A Hubert, Nicolas %K Freshwater %K Gobiidae %K Indonesia %K New species %K Sicyopus rubicundus %X

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.

%B Cybium %V 38 %P 173-178 %G eng %N 3 %0 Journal Article %J Cybium %D 2014 %T Three new species of Lentipes (Teleostei: Gobiidae) from Indonesia. %A Philippe Keith %A Hadiaty, Renny %A Hubert, Nicolas %A Frédéric Busson %A Clara Lord %K Bali %K Freshwater %K Gobiidae %K Java %K Lentipes %K New species %K Sulawesi %K Sumatra %X

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.

%B Cybium %V 38 %P 133-146 %G eng %N 2