Jump to ContentJump to Main Navigation
Show Summary Details
More options …

DNA Barcodes

Ed. by Mitchell, Andrew

1 Issue per year


Emerging Science

Open Access
Online
ISSN
2299-1077
See all formats and pricing
More options …

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Nicolas Hubert
  • Corresponding author
  • Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Kadarusman
  • Akademi Perikanan Sorong (APSOR), Kementerian Kelautan dan Perikanan, Jl. Kapitan Pattimura, Tanjung Kasuari, Sorong 98401, Papua Barat, Indonesia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Arif Wibowo
  • Research Institute of Inland Fisheries, Agency for Marine and Fisheries Research – Ministry for Marine and Fisheries Affair, Jl. Beringin No. 308, Mariana, Palembang 30763, Sumatera Selatan, Indonesia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Frédéric Busson
  • Muséum National d’Histoire Naturelle (MNHN), UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD), CP 026, 57 rue Cuvier, 75231 Paris Cedex 05, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Domenico Caruso
  • Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Sri Sulandari
  • Museum Zoologicum Bogoriense (MZB), Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km46, Cibinong 16911, Java Barat, Indonesia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Nuna Nafiqoh
  • Research and Development Institute for Fish Health Control, Indonesian Agency for Marine & Fisheries Research and Development, Jalan perikanan 12A, Depok, Java Barat, Indonesia
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Laurent Pouyaud
  • Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Lukas Rüber / Jean-Christophe Avarre
  • Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Fabian Herder
  • Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Robert Hanner
  • Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
  • Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Philippe Keith
  • Muséum National d’Histoire Naturelle (MNHN), UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD), CP 026, 57 rue Cuvier, 75231 Paris Cedex 05, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Renny K. Hadiaty
  • Museum Zoologicum Bogoriense (MZB), Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km46, Cibinong 16911, Java Barat, Indonesia.
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2015-11-26 | DOI: https://doi.org/10.1515/dna-2015-0018

Abstract

With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.

This article offers supplementary material which is provided at the end of the article.

Keywords: DNA barcoding;Checklist;Southeast Asia

References

  • [1] Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., Kent J., Biodiversity hotspots for conservation priorities, Nature, 2000, 403, 853-858Google Scholar

  • [2] Lamoureux J.F., Morrison J.C., Ricketts T.H., Olson D.M., Dinerstein E., McKnight M., et al., Global tests of biodiversity concordance and the importance of endemism, Nature, 2006, 440, 212-214Google Scholar

  • [3] Hoffman M., Hilton-Taylor C., Angulo A., Böhm M., Brooks T.M., Butchart S.H.M., et al., The impact of conservation on the status of the world’s vertebrates, Science, 2010, 330, 1503-1509Google Scholar

  • [4] Clements R., Sodhi N.S., Schilthuizen M., Ng P.K.L., Limestone karsts of Southeast Asia: Imperiled arks of biodiversity, Bioscience, 2006, 56, 733-742CrossrefGoogle Scholar

  • [5] Schilthuizen M., Liew T.S., Bin Elehan B., Lackman-Ancrenaz I., Effects of karst forest degradation on pulmonate and prosobranch land snail communities in Sabah, Malaysian Borneo, Conserv. Biol., 2005, 19, 949-954Google Scholar

  • [6] Fraser S., Threats to biodiversity, In: Marshall A.J., Beehler B.M (Eds.), The ecology of Indonesian Papua, Periplus Editions, Singapore, 2006Google Scholar

  • [7] Normile D., Saving forests to save biodiversity, Science, 2010, 329, 1278-1280Google Scholar

  • [8] Sodhi N.S., Koh L.P., Clements R., Wanger T.C., Hill J.K., Hamer K.C., et al., Conserving southeast asian forest biodiversity in human-modified landscapes, Biol. Conserv., 2010, 143, 2375-2384CrossrefGoogle Scholar

  • [9] Woodruff D.S., Biogeography and conservation in southeast asia: How 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugium-phase biodiversity, Biodiv. Conserv., 2010, 19, 919-941Google Scholar

  • [10] Kottelat M., Whitten A.J., Kartikasari S.R., Wirjoatmodjo S., Freshwater fishes of Western Indonesia and Sulawesi, Periplus Editions, Singapore, 1993Google Scholar

  • [11] Kottelat M., The fishes of the inland waters of southeast asia: A catalog and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries, Raffles Bull. Zool., 2013, Supplement 27, 1-663Google Scholar

  • [12] Froese R., Pauly D., Fishbase in Worldwide web electronic publication, http://www.fishbase.org, version (06/2011), 2011Google Scholar

  • [13] Kadarusman, Hubert N., Hadiaty R.K., Sudarto, Paradis E., Pouyaud L., Cryptic diversity in indo-australian rainbowfishes revealed by DNA barcoding: Implications for conservation in a biodiversity hotspot candidate., PLoS One, 2012, 7, e40627Google Scholar

  • [14] Hebert P.D.N., Gregory T.R., The promise of DNA barcoding for taxonomy, Syst. Biol., 2005, 54, 852-859CrossrefGoogle Scholar

  • [15] Hebert P.D.N., Cywinska A., Ball S.L., de Waard J.R., Biological identifications through DNA barcodes, Proc. R. Soc. London B, 2003, 270, 313-321Google Scholar

  • [16] Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M., Identification of birds through DNA barcodes, PLoS Biol., 2004, 2, e312CrossrefGoogle Scholar

  • [17] April J., Mayden R., L., Hanner R.H., Bernatchez L., Genetic calibration of species diversity among north america’s freshwater fishes, Proc. Nat. Acad. Sci. USA, 2011, 108, 10602-10607CrossrefGoogle Scholar

  • [18] Blaxter M., Molecular systematics: Counting angels with DNA, Nature, 2003, 421, 122-124CrossrefGoogle Scholar

  • [19] Tautz D., Arctander P., Minelli A., Thomas R.H., Vogler A.P., DNA points the way ahead in taxonomy, Nature, 2002, 418, 479Google Scholar

  • [20] Tautz D., Arctander P., Minelli A., Thomas R.H., Vogler A.P., A plea for DNA taxonomy, Trends Ecol. Evol., 2003, 18, 70-74CrossrefGoogle Scholar

  • [21] Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W., Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly astraptes fulgerator, Proc. Nat. Acad. Sci. USA, 2004, 101, 14812-14817CrossrefGoogle Scholar

  • [22] Packer L., Gibbs J., Sheffield C., Hanner R., DNA barcoding and the mediocrity of morphology, Mol. Ecol. Res., 2009, 9, 42-50CrossrefGoogle Scholar

  • [23] Hubert N., Delrieu-Trottin E., Irisson J.O., Meyer C., Planes S., Identifying early stages of coral reef fishes through DNA barcoding : A test case with the families Acanthuridae and Holocentridae, Mol. Phylogenet. Evol., 2010, 55, 1195-1203CrossrefGoogle Scholar

  • [24] Ko H.-L., Wang Y.-T., Chiu T.-S., Lee M.-A., Leu M.-Y., Chang K.-Z., et al., Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding, PLoS One, 2013, 8, e53451Google Scholar

  • [25] Wong E.H.-K., Hanner R.H., DNA barcoding detects market subtitution in north american seafood, Food Res. Int., 2008, 41, 828-837CrossrefGoogle Scholar

  • [26] Holmes B.H., Steinke D., Ward R.D., Identification of shark and ray fins using DNA barcoding, Fish. Res., 2009, 95, 280-288CrossrefGoogle Scholar

  • [27] Smith A.M., Rodriguez J.J., Whitfield J.B., Deans A.R., Janzen D.H., Hallwachs W., et al., Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections, Proc. Nat. Acad. Sci. USA, 2008, 105, 12359-12364CrossrefGoogle Scholar

  • [28] Smith M.A., Wood D.M., Janzen D.H., Hallwachs W., Hebert P.D.N., DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists, Proc. Nat. Acad. Sci. USA, 2007, 104, 4967-4972CrossrefGoogle Scholar

  • [29] Hubert N., Meyer C., Bruggemann J.H., Guérin F., Komeno R.J.L., Espiau B., et al., Cryptic diversity in indo-pacific coral reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis, PLoS One, 2012, 7, e28987Google Scholar

  • [30] Jaafar T.N.A.M., Taylor M.I., Mohd Nor S.A., De Bruyn M., Carvalho G.R., DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes), PLoS One, 2012, 7, e49623Google Scholar

  • [31] Janzen D.H., Hajibabaei M., Burns J.M., Hallwachs W., Remigio E., Hebert P.D.N., Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding, Phil. Trans. R. Soc. B, 2005, 360, 1835-1845Google Scholar

  • [32] Eschmeyer W.N., Fricke R., Catalog of fishes - electronic version (updated 6 October 2014) Sciences C.A.o., San Francisco, 2014Google Scholar

  • [33] Lohman K., De Bruyn M., Page T., Von Rintelen K., Hall R., Ng P.K.L., et al., Biogeography of the Indo-Australian archipelago, Ann. Rev. Ecol.Evol.Syst., 2011, 42, 205-226CrossrefGoogle Scholar

  • [34] De Bruyn M., Rüber L., Nylinder S., Stelbrink B., Lovejoy N.R., Lavoué S., et al., Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots., Syst. Biol., 2013, 62, 398-410CrossrefGoogle Scholar

  • [35] De Bruyn M., Stelbrink B., Morley R.J., Hall R., Carvalho G.R., Cannon C.H., et al., Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity, Syst. Biol., 2014, 63, 879-901 CrossrefGoogle Scholar

  • [36] Polhemus D.A., Allen G.R., Freshwater biogeography of Papua, In: Marshall A.J., Beehler B.M (Eds.), The ecology of Indonesian Papua, Periplus Editions, Singapore, 2006Google Scholar

  • [37] Abell R., Thieme M.L., Revenga C., Bryer M., Kottelat M., al. e., Freshwater ecoregions of the world: A new map of biogeographic units for freshwater biodiversity conservation, Bioscience, 2008, 58, 403-414CrossrefGoogle Scholar

  • [38] Wallace A.R., On the zoological geography of the Malay archipelago, J. Proc. Linnean Soc., 1859, 4, 172-189Google Scholar

  • [39] Weber M., Enkele resultaten der siboga-expeditie.Versl. Gewone vergad. Wis- en natuurk., Afd. K. Akad. Wet. Amsterdam, 1904b, 12, 910-914Google Scholar

  • [40] Mayr E., Wallace’s line in the light of recent zoogeographic studies, Quarterly Rev. Biol., 1944, 19, 1-14CrossrefGoogle Scholar

  • [41] Herder F., Nolte A.W., Pfaender J., Schwarzer J., Hadiaty R.K., Schliewen U.K., Adaptative radiation and hybridization in wallace’s dreamponds: Evidence from Sailfin silversides in the Malili Lakes of Sulawesi, Proc. R. Soc. London B, 2006, 273, 2209-2217.Google Scholar

  • [42] Kottelat M., Britz R., Hui T.H., Witte K.-E., Paedocypris, a new genus of Southeast Asian Cyprinid fish with a remarkable sexual dimorphism, comprises the world’s smallest vertebrate, Proc. R. Soc. London B, 2006, 273, 895-899Google Scholar

  • [43] Conway K.W., Chen W.-J., Mayden R.L., The “Celestial pearl danio” is a miniature Danio (s.S.) (Ostariophysi: Cyprinidae): Evidence from morphology and molecules, Zootaxa, 2008, 1686, 1-28Google Scholar

  • [44] Britz R., Kottelat M., Hui T.H., Fangfangia spinicleithralis, a new genus and species of miniature Cyprinid fish from the peat swamp forests of Borneo (Teleostei: Cyprinidae), Ichthyol. Expl. Freshwaters, 2011, 22, 327Google Scholar

  • [45] Britz R., Kottelat M., Paedocypris carbunculus, a new species of miniature fish from Borneo (Teleostei: Cypriniformes: Cyprinidae), Raffles Bull. Zool., 2008, 56, 415-422Google Scholar

  • [46] Voris H.K., Maps of pleistocene sea levels in southeast asia: Shorelines, river systems and time durations, J. Biogeography, 2000, 27, 1153-1167CrossrefGoogle Scholar

  • [47] Mayden R., Chen W.J., Bart H.L., Doosey M.H., Simons A.M., Tang, K.L., Wood R.M., Agnew M.K., Yang L., Hirt M.V., Clements M.D., Saitoh K., Sado T., Miya M., Nishida M., Reconstructing the phylogenetic relationships of earth’s most diverse clade of freshwater fishes - order Cypriniformes (Actynopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome, Mol. Phylogenet. Evol., 2009, 51, 500-514CrossrefGoogle Scholar

  • [48] Chen W.-J., Mayden R.L., Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes, Mol. Phylogenet. Evol., 2009, 52, 544-549CrossrefGoogle Scholar

  • [49] Mayden R., Chen W.J., The world’s smallest vertebrate species of the genus Paedocypris: A new family of freshwater fishes and the sister group of the world’s most diverse clade of freshwater fishes (Teleostei: Cypriniformes), Mol. Phylogenet. Evol., 2010, 57, 152-175CrossrefGoogle Scholar

  • [50] Britz R., Conway K.W., Rüber L., Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes), Zool. J. Linnean Soc., 2014, 172, 556-615CrossrefGoogle Scholar

  • [51] Slechtova V., Bohlen J., Tan H.H., Families of Cobitoidea (Teleostei; Cypriniformes) as revealed from nuclear genetic data and the position of the mysterious genera Barbucca, Psilorhynchus, Serpenticobitis and Vaillantella, Mol. Phylogenet. Evol., 2007, 44, 1358-1365CrossrefGoogle Scholar

  • [52] Chen W.-J., Lheknim V., Mayden R.L., Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: Position of enigmatic Loach ellopostoma resolved with six nuclear genes, J. Fish Biol., 2009, 75, 2197-2208CrossrefGoogle Scholar

  • [53] Slechtova V., Bohlen J., Freyhof J., Rab P., Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution, Mol. Phylogenet. Evol., 2006, 39, 529-541CrossrefGoogle Scholar

  • [54] Slechtova V., Bohlen J., Perdices A., Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): Delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism, Mol. Phylogenet. Evol., 2008, 47, 812-831CrossrefGoogle Scholar

  • [55] Bohlen J.R., Šlechtová V., Tan H.H., Britz R., Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes; Cobitidae), Mol. Phylogenet. Evol., 2011, 61, 854-865CrossrefGoogle Scholar

  • [56] Mayden R.L., Tang K.L., Conway K.W., Freyhof J., Chamberlain S., Haskins M., et al., Phylogenetic relationships of Danio within the order Cypriniformes: A framework for comparative and evolutionary studies of a model species, J. Exp. Zool., 2007, 308B, 642-654Google Scholar

  • [57] Yang L., Mayden R.L., Sado T., He S., Saitoh K., Miya M., Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes), Zoologica Scripta, 2010, 39, 527-550CrossrefGoogle Scholar

  • [58] Tang K.L., Agnew M.K., Chen W.-J., Hirt M.V., Raley M.E., Sado T., et al., Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae), Mol. Phylogenet. Evol., 2011, 61, 103-124CrossrefGoogle Scholar

  • [59] Saitoh K., Sado T., Doosey M.H., Bart Jr. H.L., Inoue J.G., Nishida M., et al., Evidence from mitochondrial genomics supports the lower mesozoic of South Asia as the time and place of basal divergence of Cypriniform fishes (Actinopterygii: Ostariophysi), Zool. J. Linnean Soc. London, 2011, 161, 633-632Google Scholar

  • [60] Yang L., Arunachalam M., Sado T., Levin B.A., Golubtsov A.S., Freyhof J., et al., Molecular phylogeny of the Cyprinid tribe Labeonini (Teleostei: Cypriniformes), Mol. Phylogenet. Evol., 2012, 1-29Google Scholar

  • [61] Tang K.L., Agnew M.K., Hirt M.V., Lumbantobing D.N., Raley M.E., Sado T., et al., Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae), Zootaxa, 2013, 3681, 101Google Scholar

  • [62] Rüber L., Kottelat, M, Tan, HH, Ng, PKL, Britz, R, Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world’s smallest vertebrate, BMC Evol. Biol., 2007, 7Google Scholar

  • [63] Fang F., Norïn M., Liao T.Y., Källersjö M., Kullander S.O., Molecular phylogenetic interrelationships of the South Asian Cyprinid genera Danio, Devario and Microrasbora (Teleostei, Cyprinidae, Danioninae), Zoologica Scripta, 2009, 38, 237-256CrossrefGoogle Scholar

  • [64] Tang K., Agnew, MK, Hirt, MV, Sado, T, Schneider, LM, Freyhof, J, Sulaiman, Z, Swartz, E, Vidthayanon, C, Miya, M, Saitoh, K, Simons, AM, Wood, RM, Mayden, RL, Systematics of the subfamily Danioniae (Teleostei: Cypriniformes: Cyprinidae), Mol. Phylogenet. Evol., 2010, 57, 189-214CrossrefGoogle Scholar

  • [65] Rüber L., Britz R., Zardoya R., Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei), Syst. Biol., 2006, 55, 374-397 CrossrefGoogle Scholar

  • [66] Rüber L., Britz R., Tan H.H., Ng P.K.L., Zardoya R., Evolution of mouthbrooding and life-history correlates in the fighting fish genus Betta, Evolution, 2004, 58, 799-813CrossrefGoogle Scholar

  • [67] Nguyen T.T.T., Na-Nakorn U., Sukmanomon S., ZiMing C., A study on phylogeny and biogeography of mahseer species (Pisces: Cyprinidae) using sequences of three mitochondrial DNA gene regions, Mol. Phylogenet. Evol., 2008, 48, 1223-1231CrossrefGoogle Scholar

  • [68] Pouyaud L., Sudarto, Paradis E., The phylogenetic structure of habitat shift and morphological convergence in Asian Clarias (Teleostei, Siluriformes: Clariidae), J. Zool. Syst. Evol. Res., 2009, 47, 344-356CrossrefGoogle Scholar

  • [69] von Rintelen T., von Rintelen K., Glaubrecht M., Schubart C.D., Herder F., Aquatic biodiversity hotspots in Wallacea - the species flocks in the ancient lakes of Sulawesi, Indonesia, In: Gower G.W., Johnson K.G., Richardson J.E., Rosen B.R., Rüber L., Williams S.T. (Eds.), Biotic evolution and environmental change in Southeast Asia, Cambridge University Press, Cambridge, 2012Google Scholar

  • [70] Kottelat M., Sailfin silversides (Pisces: Telmatherinidae) of lakes Towuti, Mahalona and Wawontoa (Sulawesi, Indonesia) with descriptions of two new genera and two new species, Ichthyol. Expl. Freshwaters 1990, 1, 35-54Google Scholar

  • [71] Kottelat M., Sailfin silversides (Pisces: Telmatherinidae) of lake Matano, Sulawesi, Indonesia, with descriptions of six new species, Ichthyol. Expl. Freshwaters, 1991, 1, 321-344Google Scholar

  • [72] Herder F., Schwarzer J., Pfaender J., Hadiaty R.K., Schliewen U.K., Preliminary checklist of Sailfin silversides (Pisces: Telmatherinidae) in the Malili Lakes of Sulawesi (Indonesia), with a synopsis of systematics and threats, Verh Ges Ichthyol., 2006, 5, 139-163Google Scholar

  • [73] Herder F., Schliewen U.K., Beyond sympatric speciation: Radiation of Sailfin silverside fishes in the Malili Lakes (Sulawesi), In: Glaubrecht M. (Ed.), Evolution in action - adaptive radiations and the origins of biodiversity, Springer, Heidelberg, 2010Google Scholar

  • [74] Gray S.M., Dill L.M., Tantu F.Y., Loew E.R., Herder F., McKinnon J.S., Environment-contingent sexual selection in a colour polymorphic fish, Proc. R. Soc. London B, 2008, 275, 1785-1791Google Scholar

  • [75] Pfaender J., Gray S.M., Rick I.P., Chapuis S., Hadiaty R.K., Herder F., Spectral data reveal unexpected cryptic colour polymorphism in female Sailfin silverside fish, Hydrobiologia, 2014, 739, 155-161Google Scholar

  • [76] Roy D., Docker M.F., Hehanussa P.E., Heath D.D., Haffner G.D., Genetic and morphological data supporting the hypothesis of adaptive radiation in the endemic fish of Lake Matano, J. Evol. Biol., 2004, 17, 1268-1276Google Scholar

  • [77] Stelbrink B., Ströger I., Hadiaty R.K., Schliewen U.K., Herder F., Age estimates for an adaptive lake fish radiation, its mitochondrial introgression, and an unexpected sister group: Sailfin silversides of the Malili Lakes system in Sulawesi, BMC Evol. Biol., 2014, 14, 94CrossrefGoogle Scholar

  • [78] Schwarzer J., Herder F., Misof B., Hadiaty R.K., Schliewen U.K., Gene flow at the margin of Lake Matano’s adaptive Sailfin silverside radiation: Telmatherinidae of River Petea in Sulawesi, Hydrobiologia, 2008, 615, 201-213Google Scholar

  • [79] Roy D., Paterson, G., Hamilton, P. B., Heath, D. D., Haffner, G. D., Resource-based adaptive divergence in the freshwater fish Telmatherina from Lake Matano, Indonesia, Mol. Ecol., 2007, 16, 35-48 Google Scholar

  • [80] Herder F., Pfaender J., Schliewen U.K., Adaptive sympatric speciation of polychromatic “roundfin” Sailfin silverside fish in Lake Matano (Sulawesi), Evolution, 2008, 62, 2178-2195CrossrefGoogle Scholar

  • [81] Pfaender J., Schliewen U.K., Herder F., Phenotypic traits meet patterns of resource use in the radiation of “sharpfin” Sailfin silverside fish in Lake Matano, Evol. Ecol., 2010, 24, 957-974CrossrefGoogle Scholar

  • [82] Takehana Y., Naruse K., Sakaizumi M., Molecular phylogeny of the medaka fishes genus Oryzias (Beloniformes: Adrianichthyidae) based on nuclear and mitochondrial DNA sequences, Mol. Phylogenet. Evol., 2005, 36, 417-428CrossrefGoogle Scholar

  • [83] Herder F., Hadiaty R.K., Nolte A.W., Pelvic-fin brooding in a new species of riverine ricefish (Atherinomorpha: Beloniformes: Adryanichthyidae) from Tara Toraja, Central Sulawesi, Indonesia, Raffles Bull. Zool., 2012, 60, 267-276Google Scholar

  • [84] Parenti L.R., Hadiaty R.K., Lumbantobing D., Herder F., Discovery and description of two new ricefishes of the genus Oryzias (Atherinomorpha, Beloniformes, Adrianichthyidae) augments the endemic freshwater fish fauna of Southeastern Sulawesi, Indonesia, Copeia, 2013, 3, 403-414CrossrefGoogle Scholar

  • [85] Larson A., Geiger M.F., Hadiaty R.K., Herder F., Mugilogobius hitam, a new species of freshwater Goby (Teleostei: Gobioidei: Gobiidae) from Lake Towuti, Central Sulawesi, Indonesia, Raffles Bull. Zool., 2014, 62, 718-725Google Scholar

  • [86] Allen G.R., Rainbowfishes in nature and the aquarium, Tetra Publications, Melle, Germany, 1995Google Scholar

  • [87] Allen G.R., Renyaan S.J., Three new species of rainbowfishes (Melanotaeniidae) from Irian Jaya, Indoensia, Aqua, Int. J. Ichthyol., 1998, 32, 69-80Google Scholar

  • [88] Allen A.P., Renyaan S.J., Three new species of rainbowfishes (Melanotaeniidae) from the Triton Lakes, Irian Jaya, New Guinea, Aqua, Int. J. Ichthyol., 1996, 2, 13-24Google Scholar

  • [89] Allen A.P., Unmack P., Hadiaty R.K., Two new species of rainbowfishes (Melanotaenia: Melanotaeniidae), from Western New Guinea (Papua Barat Province, Indonesia), Aqua, Int. J. Ichthyol., 2008, 14, 209-224Google Scholar

  • [90] Nugraha M.F.I., Kadarusman, Hubert N., Avarre J.C., Hadiaty R.K., Slembrouck J., et al., Eight new species of rainbowfishes (Melanotaeniidae) from the bird’s head region, West Papua, Indonesia, Cybium, 2015, 39, 99-130Google Scholar

  • [91] Unmack P., Allen G.R., Johnson J.B., Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea, Mol. Phylogenet. Evol., 2013, 67, 15-27CrossrefGoogle Scholar

  • [92] Allen G.R., Renyaan S.J., Eleotrid fishes of the Triton lakes, Irian Jaya, with descriptions of four new species, Revue Française d’Aquariologie, 1996, 23, 47-56Google Scholar

  • [93] Allen G.R., Field guide to the freshwater fishes of New Guinea, Christensen Research Institute Publication, Madang, Papua New Guinea, 1991Google Scholar

  • [94] Allen G.R., Jenkins A.P., Two new species of Mogurnda (Osteichthyes: Eleotrididae) from the Etna Bay region, Irian Jaya, Jndonesia, Ichthyol. Expl. Freshwaters, 1999, 10, 237-246Google Scholar

  • [95] Allen G.R., Jenkins A.P., Renyaan S.J., Morgurnda wapoga, a new species of freshwater Gudgeon (Eleotridae) from Irian Jaya, Revue Française d’Aquariologie, 1999, 26, 63-66Google Scholar

  • [96] Adams M., Page T.J., Hurwood D.A., Hughes J.M., A molecular assessment of species boundaries and phylogenetic affinities in Mogurnda (Eleotridae): A case study of cryptic biodiversity in the Australian freshwater fishes, Marine Freshwater Res., 2013, 64, 920-931 Google Scholar

  • [97] Taillebois L., Maeda K., Vigne S., Keith P., Pelagic larval duration of three amphidromous Sicydiinae gobies (Teleostei: Gobioidei) including widespread and endemic species, Ecol. Freshwater Fish, 2012, 21, 552-559Google Scholar

  • [98] Lord C., Brun C., Hautecoeur M., Keith P., Insights on endemism: Comparison of the duration of the marine larval phase estimated by otolith microstructural analysis of three amphidromous Sicyopterus species (Gobioidei: Sicydiinae) from vanuatu and new caledonia, Ecol. Freshwater Fish, 2010, 19, 26-38Google Scholar

  • [99] Sale P.F., Maintenance of high diversity in coral reef fish communities, Am. Natural., 1977, 111, 337-359CrossrefGoogle Scholar

  • [100] Chesson P.L., Warner R.R., Environmental variability promotes coexistence in lottery competitive systems, Am. Natural., 1981, 117, 923-943CrossrefGoogle Scholar

  • [101] Warner R.R., Chesson P.L., Coexistence mediated by recruitment fluctuations: A field guide to the storage effect, Am. Natural., 1985, 125, 769-787CrossrefGoogle Scholar

  • [102] Briggs J.C., Marine zoogeograhy, McGraw Hill, New York, 1974Google Scholar

  • [103] Briggs J.C., Centrifugal speciation and centres of origin, J. Biogeography, 2000, 27, 1183-1188CrossrefGoogle Scholar

  • [104] Briggs J.C., The marine East Indies: Diversity and speciation, J. Biogeography, 2005, 32, 1517-1522CrossrefGoogle Scholar

  • [105] Bellwood D.R., Hughes T., Regional-scale assembly rules and biodiversity of coral reefs, Science, 2001, 292, 1532-1534Google Scholar

  • [106] Mora C., Chittaro P.M., Sale P.F., Kritzer J.P., Ludsin S.A., Patterns and processes in reef fish diversity, Nature, 2003, 421, 933-936Google Scholar

  • [107] Hubert N., Paradis E., Bruggemann J.H., Planes S., Community assembly and diversification in indo-pacific coral reef fishes, Ecol. Evol., 2011, 1, 229-250Google Scholar

  • [108] Gaither M.R., Rocha L.A., Origins of species richness in the Indo-Malay-Philippine biodiversity hotspot: Evidence for the centre of overlap hypothesis, J. Biogeography, 2013, 40, 1638-1648CrossrefGoogle Scholar

  • [109] Pellissier L., Leprieur F., Parravicini V., Cowman P.F., Kulbicki M., Litsios G., et al., Quaternary coral ree frefugia preserved fish diversity, Science, 2014, 344, 1015-1019Google Scholar

  • [110] Bellwood D.R., Hughes T.P., Connolly S.R., Tanner J., Environmental and geometric constraints on Indo-Pacific coral reef biodiversity, Ecol. Lett., 2005, 8, 643-651CrossrefGoogle Scholar

  • [111] Colwell R., Lees, DC, The mid-domain effect: Geometric constraints on the geography of species richness, Trends Ecol.Evol., 2000, 15, 70-76 CrossrefGoogle Scholar

  • [112] Taillebois L., Castelin M., Lord C., Chabarria R., Dettaï A., Keith P., New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: Insights on systematics and ancestral areas, Mol. Phylogenet. Evol., 2014, 70, 260-271CrossrefGoogle Scholar

  • [113] Keith P., Biology and ecology of amphidromous Gobiidae of the Indo-Pacific and the Caribbean regions, J. Fish Biol., 2003, 63, 831-847CrossrefGoogle Scholar

  • [114] Keith P., Lord C., Systematics of Sicydiinae, In: Patzner R.A., Van Tassell J.L., Kovacic M., Kapoor B.G. (Eds.), The biology of Gobies, Science Publisher Inc., New York, 2011Google Scholar

  • [115] Keith P., Lord C., Lorion J., Watanabe S., Tsukamoto K., Couloux A., et al., Phylogeny and biogeography of Sicydiinae (Teleostei: Gobiidae) inferred from mitochondrial and nuclear genes, Marine Biol., 2011, 158, 311-326 Google Scholar

  • [116] Keith P., Taillebois L., Status and distribution of Smilosicyopus species (Teleostei, Gobioidei), Cybium, 2014, 38, 69-73Google Scholar

  • [117] Keith P., Hadiaty R.K., Hubert N., Busson F., Lord C., Three new species of Lentipes from Indonesia (Gobiidae), Cybium, 2014, 38, 133-146Google Scholar

  • [118] Keith P., Hadiaty R.K., Busson F., Hubert N., A new species of Sicyopus (Gobiidae) from Java and Bali, Cybium, 2014, 38, 173-178Google Scholar

  • [119] Wibowo A., Bioecology study to determine the course of the giant featherback (Chitala Lopis Bleeker 1851) management in Kampar River, Riau province, Bogor Agricultural University, Bogor, 2011Google Scholar

  • [120] Rachmatika I., Haryono, Ichthyofauna and fisheries development in Bentuang Karimum National Park (BKNP), West Borneo, Management plan of the BKNP proceeding, ed Herwasono H., WWF-IP, PHPA and ITTO, Jakarta, 1999Google Scholar

  • [121] Inoue J.G., Kumazawa Y., Miya M., Nishida M., The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A mesozoic origin of the Asian Notopterids (Actinopterygii: Osteoglossomorpha), Mol. Phylogenet. Evol., 2009, 51, 486-499CrossrefGoogle Scholar

  • [122] Sunarno M.T.D., Save giant featherback plasma nuftah, Indonesian Fish. Bull., 2001, 8, 2-6Google Scholar

  • [123] Fisheries A.f.M.A.a., Statistic of capture by the fisheries of the Riau province, Pekan Baru, Palembang, 2008Google Scholar

  • [124] Khan M.A., Sinha M., Status of mahseer fisheries in north and north-eastern india with a note on their conservation, J. Inland Fish. Soc. India, 2000, 32, 28-36Google Scholar

  • [125] Wibowo A., Husna, Genetic structure of the white cyprinid (tor tambroides) from the manna and semanka rivers, inferred from coi gene sequence, Indonesian Fish. Res. J., 2012, 18, 13-17Google Scholar

  • [126] Ingram B., Sungan G., Gooley S.Y., Sim D., De Silva S.S., Induced spawning, larval development and rearing of two indigenous Malaysian mahseer, Tor tambroides and T. douronensis, Aquaculture Res., 2005, 36, 984-995Google Scholar

  • [127] Keith P., Hoareau T.B., Lord C., Ah-Yane O., Gimmoneau G., Robinet T., et al., Characterisation of post-larval to juvenile stages, metamorphosis, and recruitment of an amphidromous goby, Sicyopterus lagocephalus (Pallas, 1767) (Teleostei: Gobiidae: Sicydiinae), Marine Freshwater Res., 2008, 59, 876-889Google Scholar

  • [128] Manacop P.R., The life history and habits of the goby Sicyopterus extraneus herre (Anga) Gobiidae, with an account of the goby-fry fishery of Cagayan River, oriental misamis, Philippine J. Fish., 1953, 2, 1-57Google Scholar

  • [129] Walter R.P., Hogan J.D., Blum M.J., Gagner R.B., Hain E.F., Gilliam J.F., et al., Climate change and conservation of endemic amphidromous fishes in Hawaiian streams, Endangered Species Res., 2012, 16, 261-272Google Scholar

  • [130] Olivier K., The ornamental fish market in FAO/Globefish Research Programme, United Nations Food and Agriculture Organisation, Rome, Italy, 2001Google Scholar

  • [131] Bartley D., Reponsible ornamental fisheries, FAO Aquaculture Newsletter, 2000, 24, 10Google Scholar

  • [132] Ng P.K.L., Tan H.H., Freshwater fishes of Southeast Asia: Potential for the aquarium fish trade and conservation issues, Aquarium Sci. Conserv., 1997, 1, 79-90Google Scholar

  • [133] Ng P.K.L., Native southeast asian freshwater fishes - conservation of a precarious resource, Role of ASAIHL Universities in Promoting Preservation of the Environment, ASAIHL, 373-381, 1991Google Scholar

  • [134] Ling K.H., Lim L.Y., The status of ornamental fish industry in Singapore, Singapore J. Pri. Ind., 2005, 32, 59-69Google Scholar

  • [135] Ng P.K.L., Tay J.B., Lim B.K., Diversity and conservation of blackwater fishes in peninsular Malaysia, particularly in the North Selangor peat swamp forest, Hydrobiologia, 1994, 285, 203-218Google Scholar

  • [136] Hansen M.C., Stehman S.V., Potapov P.V., Arunarwati B., Stolle F., Pittman K., Quantifying changes in the rates of forest clearing in Indonesia from 1990 to 2005 using remotely sensed data sets, Environ. Res. Lett., 4, 2009, doi:10.1088/1748-9326/4/3/034001CrossrefGoogle Scholar

  • [137] Giam X., Koh L.P., Tan H.H., Miettinen J., Tan H.T.W., Ng P.K.L., Global extinctions of freshwater fishes follow peatland conversion in Sundaland, Front. Ecol. Environ., 2012, 10, 465-470CrossrefGoogle Scholar

  • [138] Goh W., Chua J., The Asian Arowana, Industry D.F., Singapore, 1999Google Scholar

  • [139] Pouyaud L., Sudarto, Teugels, G., G., The different colour varieties of the Asian arowana Scleropages formosus (Osteoglossidae) are distinct species: Morphologic and genetic evidences, Cybium, 2003, 27, 287-305Google Scholar

  • [140] Legendre M., Satyani D., Subandiyah S., Sudarto, Pouyaud L., Baras E., et al., Biology and culture of the clown loach Chromobotia macracanthus (Cypriniformes, Cobitidae). 1 - hormonal induced breeding, unusual latency response and egg production in two populations from Sumatra and Borneo islands, Aquatic Living Resour., 2012, 25, 95-108Google Scholar

  • [141] Ebner B., Theusen H., Larson A., Keith P., Partially known range and precautionary conservation requirements of Sicydiine gobies in Australia, Cybium, 2012, 35, 397-414Google Scholar

  • [142] Theusen P.B., Ebner B., Larson A., Keith P., Silcock R., Prince J., et al., Amphidromy links a newly documented fish community of continental Australian streams, to oceanic islands of the West Pacific, PLoS One, 2011, 6, e26685Google Scholar

  • [143] Maeda K., H. H.T., Review of Stiphodon (Gobiidae: Sicydiinae) from Western Sumatra, with description of a new species, Raffles Bull. Zool., 2013, 61, 749-761Google Scholar

  • [144] Maeda K., Tachihara K., Diel and seasonal occurrence patterns of drifting fish larvae in the Teima stream, Okinawa Island, Pacific Sci., 2010, 64, 161-176Google Scholar

  • [145] Talde C.M., Mamaril A.C., Palomares M.L.D., The diet composition of some economically important fishes in the three floodplain lakes in Agusan marsh wildlife sanctuary in the Philippines, Sri Lanka J. Aquatic Sci., 2004, 9, 45-56Google Scholar

  • [146] Huet M., Aperçu de la pisciculture en indonésie in Bulletin d’Agriculture du Congo Belge, 55, 1956Google Scholar

  • [147] Setijaningsih L., Zenaiarifin O., Gustiano R., Characterization of three strains of giant gouramy (Osphronemus gouramy Lac) based on truss morphometries method, Jurnal Iktiologi Indonesia, 2007, 7, 23-30Google Scholar

  • [148] Nuryanto A., Wijayanti G.E., Susilo U., Darsono, Suharno, The failure of partial sequences of cytocrhome c oxidase i sequences on the giant gouramy strains differentiation, Jurnal Iktiologi Indonesia, 2015, in pressGoogle Scholar

  • [149] Roberts T.R., Vidthayanon C., Systematic revision of the Asian catfish family Pangasiidae, with biological observations and descriptions of three new species, Proc. Acad. Nat. Sci. Philadelphia, 1991, 143, 97-144 Google Scholar

  • [150] Pouyaud L., Teugels G.C., Description of a new pangasiid catfish from east kalimantan, indonesia (siluriformes: Pangasiidae), Ichthyol. Expl. Freshwaters, 2000, 11, 193-200Google Scholar

  • [151] Pouyaud L., Gustiano R., Teugels G.C., Systematic revision of Pangasius polyuranodon (Siluriformes, Pangasiidae) with description of two new species, Cybium, 2002, 26, 243-252Google Scholar

  • [152] Pouyaud L., Teugels G.C., Legendre M., Description of a new Pangasiid catfish from South-East asia (siluriformes), Cybium, 1999, 23, 247-258Google Scholar

  • [153] Gustiano R., Teugels G.C., Pouyaud L., Revision of the Pangasius kunyit catfish complex, with description of two new species from South-East Asia (Siluriformes; Pangasiidae), J. Nat. History, 2003, 37, 357-376Google Scholar

  • [154] Pouyaud L., Gustiano R., Teugels G.C., Contribution to the phylogeny of the Pangasiidae based on mitochondrial 12s rDNA, Indonesian J. Agricult. Sci., 2004, 5, 45-62Google Scholar

  • [155] Kristanto A.H., Slembrouck J., Legendre M., First sexual maturation and breeding cycle of Pangasius hypophthalmus (Siluriformes, Pangasiidae) reared in pond, Indonesian Fish. Res. J., 2005, 11, 53-57Google Scholar

  • [156] Slembrouck J., Komarudin O., Maskur, Legendre M., Petunjuk teknis pembenihan ikan patin Indonesia, Pangasius djambal, IRD-PRPB Edisi, Karya Pratama, 2005Google Scholar

  • [157] Gustiano R., Biometric analysis of the artificial hybridization between Pangasius djambal Bleeker, 1846 and Pangasianodon hypothtalmus Sauvage, 1878, Indonesian J. Agr. Sci., 2004, 5, 70-74Google Scholar

  • [158] Leprieur F., Beauchard, O, Blanchet, S, Oberdorff, T, Brosse, S, Fish invasions in the world’s river systems: When natural processes are blurred by human activites, PLoS Biol. 2007, 6, 404-410Google Scholar

  • [159] Lever C., Naturalized fishes of the world, Academic Press, London, 1996Google Scholar

  • [160] Blanchet S., Grenouillet G., Beauchard O., Tedesco P.A., Leprieur F., Dürr H.H., et al., Non-native species disrupt the worldwide patterns of freshwater fish body size: Implications for Bergmann’s rule, Ecol. Lett., 2010, 13, 421-431CrossrefGoogle Scholar

  • [161] Gozlan R.E., Biodiversity crisis and the introduction of nonnative fish: Solutions, not scapegoats, Fish Fish., 2009, 10, 109-110Google Scholar

  • [162] Vitule J.R.S., Freire C.A., Simberloff D., Introduction of nonnative freshwater fish can certainly be bad, Fish Fish., 2009, 10Google Scholar

  • [163] Ng H.H., Clarias insolitus, a new species of Clariid catfish (Teleostei: Siluriformes) from Southern Borneo, Zootaxa, 2003, 284, 1-8Google Scholar

  • [164] Teugels G.C., Sudarto, Pouyaud L., Description of a new clarias species from Southeast Asia based on morphological and genetical evidence (Siluriformes, Clariidae), Cybium, 2001, 25, 81-92Google Scholar

  • [165] Sudarto, Teugels G.C., Pouyaud L., Description of two new Clarias species from Borneo (Siluriformes, Clariidae), Cybium, 2003, 27, 153-161Google Scholar

  • [166] Ng H.H., Hadiaty R.K., Clarias microspilus, a new walking catfish (Teleostei: Clariidae) from Northern Sumatra, Indonesia, J. Threatened Taxa, 2011, 3, 1577-1584Google Scholar

  • [167] Ng H.H., Clarias microstomus, a new species of Clariid catfish from Eastern Borneo (Teleostei: Siluriformes), Zool. Stud., 2001, 40, 158-162 Google Scholar

  • [168] Ng H.H., Clarias nigricans, a new species of Clariid catfish (Teleostei: Siluriformes) from Eastern Borneo, Raffles Bull. Zool., 2003, 51, 393-398Google Scholar

  • [169] Sudarto, Teugels G.C., Pouyaud L., Description of a new Clariid catfish, Clarias pseudonieuhofii from West Borneo (Siluriformes: Clariidae), Zool. Stud., 2004, 43, 8-19Google Scholar

  • [170] Collins R.A., Armstrong K.F., Meier R., Yi Y., Brown S.D.J., Cruickshank R.H., et al., Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade, PLoS One, 2012, 7, e28381Google Scholar

  • [171] Liao T.Y., Tan H.H., Brevibora exilis, a new rasborin fish from borneo (teleostei: Cyprinidae), Ichthyol. Expl. Freshwaters, 2014, 24, 209-125Google Scholar

  • [172] Tweedley J.R., Bird D.J., Potter I.C., Gill H.S., Miller P.J., Donovan G.O., et al., Species compositions and ecology of the riverine ichthyofaunas in two Sulawesian islands in the biodiversity hotspot of Wallacea, J. Fish Biol., 2013, 82, 1916-1950CrossrefGoogle Scholar

  • [173] Herder F., Schliewen U.K., Geiger M.F., Hadiaty R.K., Gray S.M., McKinnon J.S., et al., Alien invasion in wallace’s dreamponds: Records of the hybridogenic flowerhorn Cichlid in lake Matano, with an annotated checklist of fish species introduced to the Malili lakes system in Central Sulawesi, Aquatic Inv., 2012, 7, 521-535Google Scholar

  • [174] Herborg L.-M., Mandrak N.E., Cudmore B.C., MacIsaac H.J., Comparative distribution and invasion risk of snakehead (Channidae) and Asian carp (Cyprinidae) species in North America, 2011, J. Can. Sci. Halieutiques Aquatiques, 12Google Scholar

  • [175] Roberts T., The freshwater fishes of Western Borneo (Kalimantan Barat, Indonesia), California Academy of Sciences, 1989Google Scholar

  • [176] Courtenay W.R., Williams J.D., Snakeheads (Pisces, Channidae): A biological synopsis and risk assessment, US Geological Survey, Denver, Colorado, 2004Google Scholar

  • [177] Li X., Musikasinthorn P., Kumazawa Y., Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences, Ichthyol. Res., 2006, 53, 148-159CrossrefGoogle Scholar

  • [178] Adamson E.A.S., Hurwood D.A., Mather P.B., A reappraisal of the evolution of Asian snakehead fishes (Pisces, Channidae) using molecular data from multiple genes and fossil calibration, Mol. Phylogenet. Evol., 2010, 56, 707-717CrossrefGoogle Scholar

  • [179] Serrao N.R., Steinke D., Hanner R., Calibrating snakehead diversity with DNA barcodes: Expanding taxonomic coverage to enable identification of potential and established invasive species, PLoS One, 2014, 9, e99546Google Scholar

  • [180] Hubert N., Hanner R., DNA barcoding, species delineation and taxonomy: A historical perspective, DNA Barcodes, 2015, 3, 44-58Google Scholar

  • [181] Hajibabaei M., Singer G.A.C., Hebert P.D.N., Hickey D.A., DNA barcoding: How it complements taxonomy, molecular phylogenetics and population genetics, Trends Ecol. Evol., 2007, Google Scholar

  • [182] Hubert N., Hanner R.H., Holm E., Mandrak N.E., Taylor E.B., Burridge M., et al., Identifying canadian freshwater fishes through DNA barcodes, PLoS One, 2008, 3, e2490Google Scholar

  • [183] Steinke D., Zemlak T.S., Hebert P.D.N., Barcoding nemo: DNA-based identifications for the ornamental fish trade, PLoS One, 2009, 4, e6300 Google Scholar

  • [184] Hubert N., Espiau B., Meyer C., Planes S., Identifying the ichthyoplankton of a coral reef using DNA barcodes, Mol. Ecol. Res., 2015, 15, 57-67CrossrefGoogle Scholar

  • [185] Tittensor D.P., Mora C., Jetz W., Lotze H.K., Ricard D., Vanden Berghe E., et al., Global patterns and predictors of marine biodiversity across taxa, Nature, 2010, 466, 1098-1103CrossrefGoogle Scholar

  • [186] Hebert P.D.N., deWaard J.R., Zakharov E., Prosser S.W.J., Sones J.E., McKeown J.T.A., et al., A DNA ‘barcode blitz’: Rapid digitization and sequencing of a natural history collection, PLoS One, 2013, 8, e68535Google Scholar

  • [187] Butcher B.A., Smith M.A., Sharkey M.J., Quicke D.L.J., A turbotaxonomic study of thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadiniae) based largely on coi barcoded specimens, with rapid descriptions of 179 new species, Zootaxa, 2012, 3457, 1-232Google Scholar

  • [188] Riedel A., Sagata K., Suhardjono Y.R., Tänzler R., Balke M., Integrative taxonomy on the fast track - towards more sustainability in biodiversity research, Front. Ecol., 2013, 10, 15Google Scholar

  • [189] Collins R.A., Cruickshank R.H., The seven deadly sins of DNA barcoding, Mol. Ecol. Res., 2013, 13, 969-975Google Scholar

  • [190] Bohmann K., Evans A., Gilbert M.T.P., Carvalho G.R., Creer S., Knapp M., et al., Environmental DNA for wildlife biology and biodiversity monitoring, Trends Ecol. Evol., 2014, 29, 358-367CrossrefGoogle Scholar

  • [191] Andersen K., Bird K.L., Rasmussen M., Haile J., Breuning- Madsen H., Kjaer K.H., et al., Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity, Mol. Ecol., 2012, 21, 1966-1979CrossrefGoogle Scholar

  • [192] Gibson J., Shokralla S., Porter T.M., King I., van Konynenburg S., Janzen D.H., et al., Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics, Proc. Nat. Acad. Sci., 2014, 111, 8007-8012CrossrefGoogle Scholar

  • [193] Hajibabaei M., Shokralla S., Zhou X., Singer G.A.C., Baird D.J., Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos, PLoS One, 2011, 6, e17497Google Scholar

  • [194] Meusnier I., Singer G., Landry J.-F., Hickey D., Hebert P., Hajibabaei M., A universal DNA mini-barcode for biodiversity analysis, BMC Genomics, 2008, 9, 214CrossrefGoogle Scholar

  • [195] Hajibabaei M., Smith M.A., Janzen D.H., Rodriguez J.J., Whitfield J.B., Hebert P.D.N., A minimalist barcode can identify a specimen whose DNA is degraded, Mol. Ecol. Notes, 2006, 6, 959-964CrossrefGoogle Scholar

  • [196] Leray M., Yang J.Y., Meyer C., Mills S.C., Agudelo N., Ranwez V., et al., A new versatile primer set targeting a short fragment of the mitochondrial coi region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents., Front. Zool., 2013, 10, 34CrossrefGoogle Scholar

  • [197] Bhattacharjee M.J., Ghosh S.K., Design of mini-barcode for catfishes for assessment of archival biodiversity, Mol. Ecol. Res., 2014, 14, 469-477CrossrefGoogle Scholar

  • [198] Leray M., Agudelo N., Mills S.C., Meyer C., Effectiveness of annealing blocking primers versus restriction enzymes for characterization of generalist diets: Unexpected prey revealed in the gut contents of two coral reef fish species, PLoS One, 2013, 8, e58076Google Scholar

  • [199] Zhan A., He S., Brown E.A., Chain F.J.J., Therriault T.W., Abbott C.L., et al., Reproducibility of pyrosequencing data for biodiversity assessment in complex communities, Meth. Ecol. Evol., 2014, 5, 881-890 CrossrefGoogle Scholar

  • [200] Brown S.D.J., Collins R.A., Boyer S., Lefort C., Malumbres- Olarte J., Vink C.J., et al., Spider: An r package for the analysis of species identity and evolution, with particular reference to DNA barcoding, Mol. Ecol. Res., 2012, 12, 562-565CrossrefGoogle Scholar

  • [201] Taberlet P., Coissac E., Pompanon F., Brochmann C., Willerslev E., Towards next-generation biodiversity assessment using DNA metabarcoding, Mol. Ecol., 2012, 21, 2045 - 2050CrossrefGoogle Scholar

  • [202] Hajibabaei M., De Waard J.R., Ivanova N.V., Ratnasingham S., Dooh R.T., Kirk S.L., et al., Critical factors for assembling a high volume of DNA barcodes, Phil. Trans. R. Soc. B, 2005, 360, 1959-1967Google Scholar

  • [203] Thomsen P.F., Kielgast J.O.S., Iversen L.L., Wiuf C., Rasmussen M., Gilbert M.T.P., et al., Monitoring endangered freshwater biodiversity using environmental DNA, Mol. Ecol., 2012, 21, 2565-2573CrossrefGoogle Scholar

  • [204] Darling J.A., Mahon A.R., From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments, Environ. Res., 2011, 111, 978-988CrossrefGoogle Scholar

  • [205] Smith A.M., Fisher B.L., Hebert P.D.N., DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: The ants of Madagascar, Phil. Trans. R. Soc. B, 2005, 360, 1825-1834 Google Scholar

  • [206] Witt J.D.S., Threloff D.L., Hebert P.D.N., DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: Implications for desert spring conservation, Mol. Ecol., 2006, 15, 3073-3082CrossrefGoogle Scholar

  • [207] Kerr K.C., Stoeckle M.Y., Dove C.J., Weigt L.A., Francis C.M., Hebert P.D.N., Comprehensive DNA barcode coverage of north american birds, Mol. Ecol. Notes, 2007, 7, 535-543CrossrefGoogle Scholar

  • [208] Rasmussen R.S., Morrissey M.T., Hebert P.D.N., DNA barcoding of commercially important salmon and trout species (Onchorhynchus and Salmo) from North America, J. Agri. Food Chem., 2009, 57, 8379-8385CrossrefGoogle Scholar

  • [209] Wilson J.J., Rougerie R., Schonfeld J., Janzen D.H., Hallwachs W., Hajibabaei M., et al., When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths, BMC Ecol., 2011, 11, 18Google Scholar

  • [210] Ratnasingham S., Hebert P.D.N., Bold: The Barcode of Life Data system (http://www.barcodinglife.org), Mol. Ecol. Notes, 2007, 7, 355-364 CrossrefGoogle Scholar

  • Google Scholar

About the article

Received: 2014-12-12

Accepted: 2015-09-29

Published Online: 2015-11-26

Published in Print: 2015-01-01


Citation Information: DNA Barcodes, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0018.

Export Citation

© 2015. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

Supplementary Article Materials

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[2]
Hadi Dahruddin, Aditya Hutama, Frédéric Busson, Sopian Sauri, Robert Hanner, Philippe Keith, Renny Hadiaty, and Nicolas Hubert
Molecular Ecology Resources, 2017, Volume 17, Number 2, Page 288
[3]
John-James Wilson, Kong-Wah Sing, Ping-Shin Lee, and Alison K. S. Wee
Conservation Biology, 2016, Volume 30, Number 5, Page 982

Comments (0)

Please log in or register to comment.
Log in