DNA BARCODING: FOUNDATIONS AND APPLICATIONS FOR SOUTHEAST ASIAN FRESHWATER FISHES

Identifying and delineating species are the primary tasks of taxonomy. Owing to the decreasing interest of the nations for taxonomy and the inventory of living beings, funds have been drastically decreasing during the last two decades for taxonomic studies. As a consequence, the worldwide pool of taxonomists has dramatically decreased. DNA barcoding, as an automated tool for species delineation and identification, proved to rejuvenate the field of taxonomy and open new perspectives in ecology and conservation. In the present review, we will discuss how DNA barcoding established as a new paradigm in taxonomy and how DNA barcoding has been recently integrated in taxonomic studies. We will further detail the potential applications for species identifications and discuss how DNA barcoding may positively impact the inventory and conservation of living beings, particularly in biodiversity hotspots. We emphasise the benefit of DNA barcoding for the conservation of Southeast Asian freshwater fishes

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed

Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebratecommunities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.Fieldwork and laboratory activities were supported by the Lengguru 2014 Project (www.lengguru.org), conducted by the French National Research Institute for Sustainable Development (IRD), the Indonesian Institute of Sciences (LIPI) with the Research Centre for Biology (RCB), and the Politeknik KP Sorong, with the help of the Institut Français in Indonesia (IFI) and the French embassy in Jakarta, with corporate sponsorship from COLAS SA Company (Environment Department), Total Foundation, ABS, Wasco, Veolia Eau, SDV-Bolloré,Peer reviewe

Characterization of Sundaland ichthyofauna through DNA barcodes : a case study in Java island

The Indonesian archipelago hosts 1218 freshwater fish species disseminated across 14,000 islands. Encompassing three majors geographic assemblages (Sundaland, Wallacea, Sahul) separated by two majors faunistic transitions (Wallace and Lyddeker lines), Indonesian islands display heterogeneous levels of species richness resulting from diverse geological and paleoecological histories. Sundaland itself hosts 68% of the total number of freshwater fish species and constitutes one of the world’s most endangered fauna worldwide. By contrast with Wallacea that results from an early settlement through subduction around 40 Mya, Sundaland (Borneo, Sumatra and Java) has acquired its modern configuration during the last 5 Mya through a combination of continental fragmentation and subduction. The alarming state of Sundaland ichthyodiversity, combined with major taxonomy and distribution knowedge gaps, urges for a modern reapparaisal through standardized DNA-based methods. The ichtyodiversity of Java in particular, is the most threatened and the less known of Sundaland. This dissertation aims at addressing two main questions: (1) Is DNA barcoding a suitable approach to characterize the ichthyodiversity of Java? (2) Is the geological and paeloecological history of Java a good predictor of diversity patterns and population genetic structure? The main results evidence: (1) large discrepancies between the checklist of the Java freshwater fishes based on historical records and a modern re-appraisal through DNA barcodes. Reasons invoqued are the taxonomic bias related to the interrupted inventory of Java ichthyofauna during the last 3 centuries and the rarefaction of several species targeted by artisanal fisheries. (2) A DNA-based reappraisal of species boundaries and distribution for the genera Nemacheilus and Rasbora indicated two new taxa, several cases of cryptic diversity and several cases of wrong assignement of populations to the species levels. Species range distributions appear to be much more restricted than previously thoughts and question the persistence of these species in changing landscapes. (3) A DNA-based assessment through DNA barcodes of the population genetic structure of three widespread species in Java evidences high levels of cryptic diversity and deep genetic divergences among geographically restricted and non-overlapping mitochondrial lineages. Consistent with a fragmentation related to the rise of volcanic arches in Java that prompted a long-term declines of historical effective population size, this pattern argue for the sensitive conservation status of these mitochondrial lineages. The results presented here highlights the benefits of using a standardized DNA-based approach for the fast characterization of a poorly known fauna and open new perspectives in the conservation of the ichtyofauna of Java and Bali.L'archipel indonésien abrite 1218 espèces de poissons d'eau douce disséminées sur 14 000 îles. Englobant trois ensembles géographiques majeurs (Sundaland, Wallacea, Sahul) séparés par deux transitions faunistiques majeures (lignes de Wallace et de Lyddeker), les îles indonésiennes présentent des niveaux hétérogènes de richesse spécifique résultant de divers antécédents géologiques et paléoécologiques. Sundaland abrite 68% du nombre total d’espèces de poissons d’eau douce et constitue l’une des faunes les plus menacées au monde. Contrairement à Wallacea qui résulte d'une mise en place précoce par subduction autour de 40 Mya, Sundaland (Bornéo, Sumatra et Java) a acquis sa configuration moderne au cours des 5 derniers Mya grâce à une combinaison de fragmentation continentale et de subduction. L’état alarmant de l’ichtyodiversité de Sundaland, associé à des lacunes importantes en matière de taxonomie et de connaissances de la distribution des espèces, plaide en faveur d’une réinterprétation moderne au moyen de méthodes standardisées et basées sur l’ADN. L'ichtyodiversité de Java, en particulier, est la plus menacée et la moins connue de Sundaland. Cette thèse vise à répondre à deux questions principales: (1) Les code-barres ADN constituent-ils une approche appropriée pour caractériser l'ichtyodiversité de Java? (2) L’histoire géologique et paléoécologique de Java est-elle un bon prédicteur des profils de diversité et de la structure génétique de la population? Les principaux résultats obtenus sont les suivants: 1) d’importants écarts entre la liste de référence des poissons d’eau douce de Java fondée sur des données historiques et une réévaluation moderne au moyen de code-barres à ADN. Les raisons invoquées sont le biais taxonomique lié à l'inventaire interrompu de l'ichthyofaune de Java au cours des 3 derniers siècles et la raréfaction de plusieurs espèces ciblées par la pêche artisanale. (2) Une réévaluation basée sur l’ADN des limites et de la distribution des espèces pour les genres Nemacheilus et Rasbora a indiqué deux nouveaux taxons, plusieurs cas de diversité cryptique et plusieurs cas d’attribution erronée de populations aux niveaux de l’espèce. Les aires de distribution des espèces semblent être beaucoup plus limitées que considéré précédemment et questionne les modalités de persistance des espèces dans des paysages en mutation. (3) Une évaluation basée sur l'ADN, grace aux code-barres ADN, de la structure génétique des populations de trois espèces largement répandues à Java met en évidence des niveaux élevés de diversité cryptique et des divergences génétiques profondes entre lignées mitochondriales géographiquement restreintes et ne se chevauchant pas. Conformément à une fragmentation liée à la montée des arcs volcaniques à Java qui a entraîné un déclin à long terme de la taille effective de la population, cette tendance plaide en faveur du statut de conservation sensible de ces lignées mitochondriales. Les résultats présentés ici soulignent les avantages d'utiliser une approche standardisée et basée sur l'ADN pour la caractérisation rapide d'une faune mal connue et ouvrir de nouvelles perspectives pour la conservation de l'ichtyofaune de Java et de Bali

Caractérisation de l'ichtyofaune du plateau de la sonde par l'approche de code-barre ADN : une étude de cas sur l'île de Java

L'archipel indonésien abrite 1218 espèces de poissons d'eau douce disséminées sur 14 000 îles. Englobant trois ensembles géographiques majeurs (Sundaland, Wallacea, Sahul) séparés par deux transitions faunistiques majeures (lignes de Wallace et de Lyddeker), les îles indonésiennes présentent des niveaux hétérogènes de richesse spécifique résultant de divers antécédents géologiques et paléoécologiques. Sundaland abrite 68% du nombre total d’espèces de poissons d’eau douce et constitue l’une des faunes les plus menacées au monde. Contrairement à Wallacea qui résulte d'une mise en place précoce par subduction autour de 40 Mya, Sundaland (Bornéo, Sumatra et Java) a acquis sa configuration moderne au cours des 5 derniers Mya grâce à une combinaison de fragmentation continentale et de subduction. L’état alarmant de l’ichtyodiversité de Sundaland, associé à des lacunes importantes en matière de taxonomie et de connaissances de la distribution des espèces, plaide en faveur d’une réinterprétation moderne au moyen de méthodes standardisées et basées sur l’ADN. L'ichtyodiversité de Java, en particulier, est la plus menacée et la moins connue de Sundaland. Cette thèse vise à répondre à deux questions principales: (1) Les code-barres ADN constituent-ils une approche appropriée pour caractériser l'ichtyodiversité de Java? (2) L’histoire géologique et paléoécologique de Java est-elle un bon prédicteur des profils de diversité et de la structure génétique de la population? Les principaux résultats obtenus sont les suivants: 1) d’importants écarts entre la liste de référence des poissons d’eau douce de Java fondée sur des données historiques et une réévaluation moderne au moyen de code-barres à ADN. Les raisons invoquées sont le biais taxonomique lié à l'inventaire interrompu de l'ichthyofaune de Java au cours des 3 derniers siècles et la raréfaction de plusieurs espèces ciblées par la pêche artisanale. (2) Une réévaluation basée sur l’ADN des limites et de la distribution des espèces pour les genres Nemacheilus et Rasbora a indiqué deux nouveaux taxons, plusieurs cas de diversité cryptique et plusieurs cas d’attribution erronée de populations aux niveaux de l’espèce. Les aires de distribution des espèces semblent être beaucoup plus limitées que considéré précédemment et questionne les modalités de persistance des espèces dans des paysages en mutation. (3) Une évaluation basée sur l'ADN, grace aux code-barres ADN, de la structure génétique des populations de trois espèces largement répandues à Java met en évidence des niveaux élevés de diversité cryptique et des divergences génétiques profondes entre lignées mitochondriales géographiquement restreintes et ne se chevauchant pas. Conformément à une fragmentation liée à la montée des arcs volcaniques à Java qui a entraîné un déclin à long terme de la taille effective de la population, cette tendance plaide en faveur du statut de conservation sensible de ces lignées mitochondriales. Les résultats présentés ici soulignent les avantages d'utiliser une approche standardisée et basée sur l'ADN pour la caractérisation rapide d'une faune mal connue et ouvrir de nouvelles perspectives pour la conservation de l'ichtyofaune de Java et de Bali.The Indonesian archipelago hosts 1218 freshwater fish species disseminated across 14,000 islands. Encompassing three majors geographic assemblages (Sundaland, Wallacea, Sahul) separated by two majors faunistic transitions (Wallace and Lyddeker lines), Indonesian islands display heterogeneous levels of species richness resulting from diverse geological and paleoecological histories. Sundaland itself hosts 68% of the total number of freshwater fish species and constitutes one of the world’s most endangered fauna worldwide. By contrast with Wallacea that results from an early settlement through subduction around 40 Mya, Sundaland (Borneo, Sumatra and Java) has acquired its modern configuration during the last 5 Mya through a combination of continental fragmentation and subduction. The alarming state of Sundaland ichthyodiversity, combined with major taxonomy and distribution knowedge gaps, urges for a modern reapparaisal through standardized DNA-based methods. The ichtyodiversity of Java in particular, is the most threatened and the less known of Sundaland. This dissertation aims at addressing two main questions: (1) Is DNA barcoding a suitable approach to characterize the ichthyodiversity of Java? (2) Is the geological and paeloecological history of Java a good predictor of diversity patterns and population genetic structure? The main results evidence: (1) large discrepancies between the checklist of the Java freshwater fishes based on historical records and a modern re-appraisal through DNA barcodes. Reasons invoqued are the taxonomic bias related to the interrupted inventory of Java ichthyofauna during the last 3 centuries and the rarefaction of several species targeted by artisanal fisheries. (2) A DNA-based reappraisal of species boundaries and distribution for the genera Nemacheilus and Rasbora indicated two new taxa, several cases of cryptic diversity and several cases of wrong assignement of populations to the species levels. Species range distributions appear to be much more restricted than previously thoughts and question the persistence of these species in changing landscapes. (3) A DNA-based assessment through DNA barcodes of the population genetic structure of three widespread species in Java evidences high levels of cryptic diversity and deep genetic divergences among geographically restricted and non-overlapping mitochondrial lineages. Consistent with a fragmentation related to the rise of volcanic arches in Java that prompted a long-term declines of historical effective population size, this pattern argue for the sensitive conservation status of these mitochondrial lineages. The results presented here highlights the benefits of using a standardized DNA-based approach for the fast characterization of a poorly known fauna and open new perspectives in the conservation of the ichtyofauna of Java and Bali

Perilaku Harian Simpai (Presbytis melalophos) dalam Kandang Penangkaran

Mitred Leaf Monkey (Presbytis melalophos) is one of species from genus Presbytis, existing on theisland of Sumatra, which lives in primary forests in the interior ranging from lowland altitude till 2500 mabove of the sea level. The main food of the animal is fruits, and young leaves. Besides, they also eatflowers, seeds, shoots, and some species of insects. This species has social groups that can consist of oneor several males and several females. Mitred Leaf Monkeys spend more than half day resting and feedingfruits and young leaves. The purpose of this study was to determine the behavior and activities of theMitred leaf Monkey in captivity in order to stimulate the animal breeding out of their natural habitat. Theresearch was using One-Zero Sampling methods that noted every activity (behaviours) during a specificperiod of the time. The behaviour observation was eating, grooming, locomotion, defecation, urination anddrinking. The results showed that, the main activities were locomotion with average 27.93%, 25.57% forgrooming, and 24.425% for feeding. The positional behavior of the animals was characterized byquadrupedalism as the major locomotion mode, while sitting was the most common posture when theywere resting and feeding

Une nouvelle espèce de Schismatogobius (Teleostei : Gobiidae) d’Halmahera (Indonésie).

International audienceA new species of Schismatogobius, a freshwater goby, is described from Halmahera (Indonesia). It differs from other species belonging to the genus 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, the pectoral fin colour pattern and the jaw length/head length ratio of male and female.Une espèce nouvelle de Schismatogobius, gobie dulçaquicole, est décrite sur la base de spécimens collec- tés à Halmahera (Indonésie). Elle diffère des autres espèces du genre par un fort pourcentage de divergence au niveau du gène COI partiel (652 pb) et par plusieurs caractères incluant, principalement, le nombre de rayons aux nageoires pectorales, la coloration de la surface ventrale de la tête, la coloration des nageoires pectorales et le ratio longueur de la mâchoire/longueur de la tête du mâle et de la femelle

KARAKTERISTIK MORFOMETRIK RUSA SAMBAR (RUSA UNICOLOR) SEBAGAI DASAR KRITERIA SELEKSI SIFAT PERTUMBUHAN

Study on the morphometric characteristic of sambar deer (Rusa unicolor) which will be used as a baseline of growth trait selection had been conducted. The aim of this study is to set up criteria for better selection of sambar deer progeny. Morphometric characteristic observed in this study including : body weight, body length, chest width, chest girth, head length, head width, ear width, and ear length respectively. Result indicated that chest girth correlates significantly with the body weight (y=-108.004+1.875x). In conclusion chest girth can be used as a criteria for selection of growth trait of sambar deer.</div

Schismatogobius (Gobiidae) from Indonesia, with description of four new species

International audienceThe 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.Des collections de spécimens de Schismatogobius provenant d’Indonésie ont été étudiées et comparées aux espèces décrites de la région. huit espèces ont été répertoriées dont quatre nouvelles. Celles-ci sont décrites en utilisant des approches génétique et morphoméristique. elles diffèrent par un fort pourcentage de divergence de la séquence partielle du gène Coi (652 pb) et par plusieurs caractères incluant, principalement, le nombre de rayons aux nageoires pectorales, la coloration de la surface ventrale de la tête du mâle et/ou de la femelle, le ratio longueur de la mâchoire/longueur de la tête ou la longueur de la mâchoire du mâle et/ou de la femell

Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species

International audienceAmong 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