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

  • Nicolas HubertEmail author
  • Daniel Lumbantobing
  • Arni Sholihah
  • Hadi Dahruddin
  • Erwan Delrieu-Trottin
  • Frédéric Busson
  • Sopian Sauri
  • Renny Hadiaty
  • Philippe Keith
Research Article


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.


Conservation genetics Taxonomy Southeast Asia Cryptic diversity Population fragmentation 



The authors wish to thank Siti Nuramaliati Prijono, Bambang Sunarko, Witjaksono, Mohammad Irham, Marlina Adriyani, Ruliyana Susanti, Rosichon Ubaidillah, Hari Sutrisno and Muhamad Syamsul Arifin Zein at Research Centre for Biology (RCB-LIPI); Jean-Paul Toutain, Robert Arfi, Valérie Verdier and Jean-François Agnèse from the ‘Institut de Recherche pour le Développement’; Joel Le Bail and Nicolas Gascoin at the French embassy in Jakarta for their continuous support. We are thankful Sumanta at IRD Jakarta for his help during the field sampling. Part of the present study was funded by the Institut de Recherche pour le Développement (UMR226 ISE-M and IRD through incentive funds), the MNHN (UMR BOREA), the RCB-LIPI, the French Ichthyological Society (SFI), the Foundation de France and the French embassy in Jakarta. The Indonesian Ministry of Research and Technology approved this study and field sampling was conducted according to the research permits 097/SIP/FRP/SM/IV/2014 for Philippe Keith, 60/EXT/SIP/FRP/SM/XI/2014 for Frédéric Busson and 41/EXT/SIP/FRP/SM/VIII/2014 for Nicolas Hubert. Sequence analysis was aided by funding from the government of Canada through Genome Canada and the Ontario Genomics Institute in support of the International Barcode of Life project. We thank Paul Hebert, Robert Hanner and Evgeny Zakharov as well as BOLD and CCDB staffs at the University of Guelph for their valuable support. Finally, we thank Anti Vasemägi and the three anonymous reviewers for providing constructive comments of earlier versions of the manuscript. This publication has ISEM Number 2018-279-SUD.

Supplementary material

10592_2019_1152_MOESM1_ESM.jpg (69 kb)
Illustration of Nemacheilus chrysolaimos in its original description (JPG 68 KB)
10592_2019_1152_MOESM2_ESM.xlsx (24 kb)
Collection information (XLSX 23 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Nicolas Hubert
    • 1
    Email author
  • Daniel Lumbantobing
    • 2
  • Arni Sholihah
    • 1
    • 3
  • Hadi Dahruddin
    • 1
    • 2
  • Erwan Delrieu-Trottin
    • 1
    • 4
  • Frédéric Busson
    • 1
    • 5
  • Sopian Sauri
    • 2
  • Renny Hadiaty
    • 2
  • Philippe Keith
    • 5
  1. 1.Institut de Recherche pour le Développement, UMR 226 ISEM (UM, CNRS, IRD, EPHE)Université de MontpellierMontpellier cedex 05France
  2. 2.Division of Zoology, Research Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
  3. 3.Instut Teknologi Bandung, School of Life Science and TechnologyBandungIndonesia
  4. 4.Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu BerlinBerlinGermany
  5. 5.UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN)Muséum National d’Histoire NaturelleParis cedex 05France

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