title: Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.
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. This 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 this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific 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.
authors.affiliation: LIPI, Research Center for Biology, Zoology Division, MZB, Gedung Widyasatwaloka, Jl. Raya Jakarta Bogor Km. 46, Cibinong- Bogor, 16911, Indonesia.
authors.forename: Hadi
authors.initials: H
authors.lastname: Dahruddin
authors.affiliation: Faculty of Mathematics and Natural Science, Animal Bioscience, Bogor Agricultural University, Jl. Raya Darmaga, Bogor, 16680, Indonesia.
authors.forename: Aditya
authors.initials: A
authors.lastname: Hutama
authors.affiliation: Muséum national d'Histoire naturelle, UMR 7208 (MNHN-CNRS-UPMC-IRD-UCBN), CP 026, 43, rue Cuvier, Paris Cedex 05, F-75231, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Busson
authors.affiliation: LIPI, Research Center for Biology, Zoology Division, MZB, Gedung Widyasatwaloka, Jl. Raya Jakarta Bogor Km. 46, Cibinong- Bogor, 16911, Indonesia.
authors.forename: Sopian
authors.initials: S
authors.lastname: Sauri
authors.affiliation: Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Hanner
authors.affiliation: Muséum national d'Histoire naturelle, UMR 7208 (MNHN-CNRS-UPMC-IRD-UCBN), CP 026, 43, rue Cuvier, Paris Cedex 05, F-75231, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Keith
authors.affiliation: LIPI, Research Center for Biology, Zoology Division, MZB, Gedung Widyasatwaloka, Jl. Raya Jakarta Bogor Km. 46, Cibinong- Bogor, 16911, Indonesia.
authors.forename: Renny
authors.initials: R
authors.lastname: Hadiaty
authors.affiliation: Institut de Recherche pour le Développement, UMR 226 ISEM (UM2-CNRS-IRD), Place Eugène Bataillon, CC 065, F-34095, Montpellier cedex 05, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Hubert
mesh_terms: D000818:Animals; D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic; D017753:Ecosystem; D005399:Fishes / Q000145:classification* / Q000235:genetics*; D005618:Fresh Water; D007214:Indonesia
keywords: DNA barcoding; fish; fisheries management; habitat degradation; wildlife management