DNA Barcoding Indonesian freshwater fishes: challenges and prospects

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 Review Open Access © 2015 Nicolas Hubert et al. licensee De Gruyter Open. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License. Nicolas Hubert*, Kadarusman, Arif Wibowo, Frédéric Busson, Domenico Caruso, Sri Sulandari, Nuna Nafiqoh, Laurent Pouyaud, Lukas Rüber, Jean-Christophe Avarre, Fabian Herder, Robert Hanner, Philippe Keith, Renny K. Hadiaty DNA Barcoding Indonesian freshwater fishes: challenges and prospects *Corresponding author: Nicolas Hubert, Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France, E-mail: nicolas.hubert@ ird.fr Domenico Caruso, Laurent Pouyaud, Jean-Christophe Avarre, Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 CC065, Place Eugène Bataillon, 34095 Montpellier cedex 5, France Nicolas Hubert, Sri Sulandari, 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. Kadarusman, Akademi Perikanan Sorong (APSOR), Kementerian Kelautan dan Perikanan, Jl. Kapitan Pattimura, Tanjung Kasuari, Sorong 98401, Papua Barat, Indonesia. 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. Frédéric Busson, 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. Domenico Caruso, Nuna Nafiqoh, Jean-Christophe Avarre, Research and Development Institute for Fish Health Control, Indonesian Agency for Marine & Fisheries Research and Development, Jalan perikanan 12A, Depok, Java Barat, Indonesia Lukas Rüber, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern 3005, Switzerland. Fabian Herder, Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany. Robert Hanner, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada Unauthenticated Download Date | 12/4/15 10:41 PM DNA Barcoding Indonesian freshwater fishes: challenges and prospects 145 nearly 1200 species of freshwater fishes have been either described or reported from Indonesian inland waters and the rate of species discovery is still high as several tenth of species have been described from Indonesia during the last years [10-12]. The inventory of Indonesian freshwater fishes has been challenged since its earliest developments by several limitations: (1) the Indonesian archipelago hosts nearly 17,000 islands and most of them are remote islands with limited access, (2) due to a complex political history, tracing the type specimens has been sometimes challenging, particularly for the species described before the 1950’s [11], (3) the Indonesian ichthyofauna hosts several large radiation of morphologically similar species that have been subject to either multiple descriptions, recurrent systematic revisions or overlooked diversity [11]. Recently, the use of standardized molecular approaches in some remote rivers in Indonesia emphasized that the sole use of morphology in taxonomy was limiting the estimation of species richness in some cases, as observed in Papuan rainbowfishes, for instance [13]. DNA barcoding is a system designed to provide accurate, fast and automatable species identification by using short and standardized gene regions as internal species tags [14]. Initially proposed to circumvent the lack of taxonomists and available tools for species identification [15-17], DNA barcoding has also been foreseen by several authors as a solution to speed up the pace of species discovery and open new perspectives in conservation [1820]. Given their high diversity and dramatic phenotypic threatened and Sundaland in particular, is the one that experienced the fastest increase of threat levels during the last decade [3]. Including Peninsular Malaysia and the islands of Sumatra, Java and Borneo (Fig. 1), this hotspot exhibits one of the highest species richness and endemism for vertebrates in SEA [2] and freshwater fishes are no exception. For instance, among the 1200 species described in Indonesia, nearly 900 species are observed in the Sundaland hotspot – c.a. 400 endemics – and constitute an important source of incomes from the international trade of ornamental fishes. The impoverishment of the ichthyodiversity in the Indonesian hotspots is of great concern, however, the taxonomic knowledge is still incomplete and scattered in the scientific literature, what arguably bridles the establishment of sounds conservation plans. Filling this gap is currently jeopardized by the fast degradation of the Indonesian natural habitats due to a large array of perturbations including mining, logging activities, land burning for crop cultivation, deforestation for land conversion (e.g. palm plantations) and water contamination [4, 5]. Freshwater fishes are particularly at risk in Indonesia as their persistence is currently jeopardized by the interactions between ecological and biotic (e.g. inland fisheries, introduction of alien species) perturbations resulting in the modification of habitats, destruction of spawning grounds and the decline of populations [6-9]. The inventory of the Indonesian ichthyodiversity is ongoing since the second half of the 18th century. So far, Figure 1. Map of Indonesia including the 23 islands considered in the present review (Appendix) with biogeographic provinces and their boundaries. 1, Bali; 2, Bangka; 3, Batam and Bintan; 4, Belitong; 5, Buru; 6, Java; 7, Kalimantan; 8, Madura; 9 Natuna and Riau; 10, Sumatera; 11, Bacan; 12, Celebes; 13, Ceram; 14, Flores; 15, Halmahera; 16, Indonesian Timor; 17, Lombok; 18, Sumba; 19, Sumbawa; 20, Ternate; 21, Talaud; 22, Aru; 23, Indonesia New Guinea. Unauthenticated Download Date | 12/4/15 10:41 PM 146 N. Hubert, et al. To date, 1218 species belonging to 84 families have been reported from Indonesian freshwaters including 1172 native species from 79 families among which 630 species are endemic of the country (Table 1, Appendix). Amongst the 1218 species, 28 are exotic species corresponding to: (1) introduced species (i.e. 21 species from 7 families), among which several belong to exotic families for Indonesian waters (e.g. Cichlidae, Loricariidae, Peociliidae, Serrasalmidae), (2) imported species that have not established yet (i.e. 7 species from 5 families), among which several species belong to 3 exotic families (Poecilidae, Cichlidae, Salmonidae). Finally, 18 species are cited from Indonesian waters but their presence is questionable and is likely to result from misidentifications. With a density of 0.6 species per 1000 km2 (Table 1), Indonesia hosts one of the world’s highest density of fish species ahead of Brazil (0.37 species per 1000km2) and the Democratic Republic of Congo (0.48 species per 1000km2), two countries known to host some the world largest and speciose tropical rivers [12]. The main reasons for this exceptional diversity are the important fragmentation of the rivers across the numerous islands of the archipelago, together with the occurrence of several major biogeographical boundaries in the country including the Wallace and Lydekker lines (Fig. 1) and complex palaeoecological and geological histories [33-37]. The existence of biogeographic provinces in the Indonesian vertebrate fauna is known since the seminal study of Wallace [38] and later by Lydekker in 1895, Weber [39] and Mayr [40]. Two major biogeographical boundaries are still recognized today in Indonesia (Fig. 1) including the Wallace’s line separating Sundaland from Wallacea and the Lydekker’s line separating Wallacea from Sahul [33]. Yet, two biodiversity hotspots have been described by Myers and colleagues [1] that match those biogeographical boundaries (Sundaland and Wallacea). The distribution of species richness varies among those three regions and Sundaland is the most speciose, both in terms of absolute species richness and number of endemic species with 899 and 431 species, respectively (Table 1). Sundaland also hosts the highest density of species with 0.8 species and 0.38 endemic species per 1000km2. The endemism, however, is higher in Sahul with nearly 50% of endemism while hosting only 20 percent of all the Indonesian endemic species. The family Cyprinidae is the most speciose family of the archipelago with 241 species followed by the families Gobiidae with 122 species, Osphronemidae with 81 species and Bagridae with 60 species (Fig. 2A). The dominant families, however, varies among biogeographical provinces as Sundaland is dominated by the Cyprinidae (231 species; changes during ontogeny, fish identification is not an easy task. After almost a decade, it has become evident that DNA barcoding presents several advantages compared to morphological characters for species identification including: (1) intraspecific phenotypic variation often overlaps that of sister taxa in nature, which can lead to incorrect identifications or species delineations [21,22], (2) DNA barcodes are effective whatever the life stages under scrutiny [23,24] or available biological materials for identification [25, 26], (3) spectacular levels of cryptic diversity have been frequently reported using DNA barcoding [21, 27-31]. An Indonesian initiative to DNA barcode all freshwater fishes is currently handled by the co-authors with the aim to assemble comprehensive DNA barcode libraries for the Indonesian ichthyofauna. In this context, the present review aims at exploring the potential contribution of DNA barcoding for the conservation of the Indonesian ichthyodiversity. First, we provide updated statistics on the Indonesian ichtyodiversity that we compiled from several sources [10-12]. Second, we produce an overview of the ichthyological exploration of Indonesian freshwaters and highlight the major challenges ichthyology is facing in the country. To conclude, we discuss the prospects and challenges associated to the assembly of comprehensive DNA barcode libraries for the Indonesian freshwater fishes. 2 Indonesian freshwater fishes: general considerations The statistics presented here have been compiled from Fishbase [12] and the Eschmeyer’s catalog of fishes [32] as available on September 2014. An updated checklist of the SEA freshwater fishes has been recently published by Kottelat [11] but this updated list was not incorporated in fishbase and Eschemeyer at the time we compiled the present statistics and connections with known species range distribution was not available at that time. As our objective is to provide an updated assessment of the distribution of the Indonesian ichthyodiversity, we opted for the conservative list of species name in Fishbase. In this context, the species list provided here (Appendix) is readily available for the DNA barcoding campaign of Indonesian fishes. Species range distributions were compiled from Fishbase species page whenever they were detailed at the island level (Fishbase1 in the Appendix) or based on Fishbase Aquamap using valid records only (Fishbase2 in the Appendix). Occurrences were refined or invalidated using Eschmeyer [32] and Kottelat’s checklists [10,11] whenever additional or contradictory occurrences where found. Unauthenticated Download Date | 12/4/15 10:41 PM DNA Barcoding Indonesian freshwater fishes: challenges and prospects 147 Ta bl e 1. S um m ar y st at is tic s of th e In do ne si an ic ht hy of au na in cl ud in g su rfa ce o f i sl an ds , s pe ci es ri ch ne ss , e nd em is m a nd s pe ci es d en si ty fo r t he 2 3 m aj or is la nd s co ns id er ed in th e pr es en t re vi ew . Al l s pe ci es En de m ic s Co de M ap Bi og eo gr ap hi c do m ai n Is la nd Su rfa ce (k m 2) N. o f f am ily N. o f s pe ci es Pe rc en t ( to ta l al l s pe ci es ) De ns ity (S p/ 10 00 km 2 ) N. o f s pe ci es Pe rc en t ( to ta l en de m ic s) Pe rc en t ( to ta l al l s pe ci es ) De ns ity