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International audience; Large carnivores play a pivotal regulating role in maintaining healthy and balanced ecosystems; however, most of them are rare and elusive, and knowledge about their resource consumption is scarce. Traditional methods based on morphological identification of undigested remains are labor intensive and often not sufficiently accurate, leading to errors and biased ecological inferences. Here, we developed a multi-marker DNA metabarcoding approach to analyze the dietary diversity of giant otters (Pteronura brasiliensis) from fecal DNA while controlling predator species identity. We combined two mitochondrial markers, 12S rRNA and cytochrome c oxidase 1 (COI) gene, that target the full range of potential vertebrate and invertebrate prey. We compiled a local reference database of DNA barcodes for most potentially ingested fish, which were used to evaluate the specificity of the metabarcoding primers in silico. Most prey are identified at the species level (>90%) and the dietary profiles provided independently by the two markers are highly similar, whether in terms of list of prey or frequency of occurrences, hence validating the approach. We detected a higher number of rare fish prey with the 12S primers that amplified solely Teleost species while the degenerate COI primers revealed non-fish prey (e.g., amphibians, snakes, birds, and earthworms) and confirmed predator species identity. This study demonstrated that scat DNA metabarcoding is particularly useful to provide in-depth information on elusive carnivorous dietary profile. Our methodology opens up new opportunities to understand how top carnivores diet cope with the effects of anthropogenic alteration of ecosystems and identify conflicts with humans and livestock.

This repository contains the raw data (R1 and R2 fastq files), abundance/final prey occurence tables and scripts used to perform the faecal eDNA metabarcoding analysis in the study "Unravelling the dietary diversity of neotropical top predators using scat DNA metabarcoding: a case study on the elusive Giant Otter". Quéméré E et al.

The Amazon is probably the most diverse realm on Earth, and is considered to be the primary source of diversity and a center of dispersal for Neotropical terrestrial organisms. Yet, the assumption that the Amazon basin is a primordial place of fish species origination and dispersal into other drainages still need to be tested. We addressed this issue by inferring a time-stratified biogeographic history and reconstructing the ancestral habitat preference of Hypostomus, a continentally widespread and species-rich Neotropical genus. We found that Hypostomus emerged in the Western Amazon ([~]14.7 Ma), when the Western Amazon River was flowing northwards and disconnected from the Eastern Amazon. We show that dispersal events in the first half of Hypostomus evolution occurred from the Western Amazon into adjacent basins, initiating its Neotropical radiation. The ancestral preferred habitat consisted in small rivers with running waters, a predominant habitat in river headwaters. Because of strong niche conservatism in the early evolution of Hypostomus, we suggest that most of the out-of-Western-Amazon dispersal occurred via headwater captures. The radiation of Hypostomus was further promoted by major reconfigurations of river basins, which opened dispersal opportunities into new drainages. Diversification in habitat preference coincided with colonization of basins already occupied by congenerics, indicative of niche shifts triggered by inter-specific competition and species coexistence. By analyzing the evolutionary history of Hypostomus, we show that Western Amazon was the main center of fish dispersal in the Neotropical Region from Middle Miocene to the present, supporting the cradle hypothesis of fish origination and dispersal., Laboratorio de Sistemática y Biología Evolutiva

Etablie conformément aux critères de l’Union internationale pour la conservation de la nature (UICN), la Liste rouge des espèces menacées en France vise à dresser un bilan objectif du degré de menace pesant sur les espèces de la faune et de la flore à l’échelle du territoire national. Cet inventaire de référence, fondé sur une solide base scientifique et réalisé à partir des meilleures connaissances disponibles, contribue à mesurer l’ampleur des enjeux, les progrès accomplis et les défis à relever pour la France, en métropole et en outre-mer. La Liste rouge des espèces menacées en France s’organise en chapitres taxonomiques (mammifères, plantes vasculaires, etc.) et géographiques (métropole, La Réunion, Guadeloupe, etc.), avec l’ambition de traiter l’ensemble des espèces présentes sur le territoire national.

Electrophorus varii, sp. nov. de Santana, Wosiacki, Crampton, Sabaj, Dillman, Mendes-Júnior and Castro e Castro Holotype: MPEG 25422, 1000 mm TL; Goiapi River, Marajó Island, Pará, Brazil. Paratypes: INPA 46378, INPA 46379 (3); MHNG 2748.083; MPEG 30480 (3). Etymology: In honor of Richard Peter Vari (1949–2016) for his contributions to ichthyology. Diagnosis: Eleven nucleotides in COI: A(64), A(80), G(146), G (164), T (190), A(251), A(467), C(512), T (517), A(536), and C (569). Pectoral-fin rays 20–28 and lateral-line pores 124–186 (versus 32–38, and 88–101, respectively, in E. electricus). Distinguished by head narrow, Fig. 2a (versus wide, Fig. 2b, in E. voltai; distance between medial margins of contralateral dentaries at transverse through last two ventral pores 2–3 times shorter in E. varii than E. voltai, Fig. 2a, b), skull deep, cleithrum lies between vertebrae 1 and 2, Fig. 2b (versus skull depressed, cleithrum lies between vertebrae 5 and 6, in both E. electricus and E. voltai Fig. 2a, c). Description: As for E. electricus, except as noted in Diagnosis and except clear band along body always absent. Species illustrated in Figs. 2, 3, and 6. Maximum size examined specimens 1485 mm TL. Morphometric and meristic data in Supplementary Data 2. Low-voltage EOD duration 1.24–1.78 ms (Fig. 4d), highvoltage EOD 151 V (200 mm TL) to 572 V (609 mm TL) (Fig. 4d), n = 4. For distribution see Fig. 1a; Supplementary Data 1.

Electrophorus Gill, 1864 Electrophorus ref. 33: 152. Type species: Gymnotus electricus Linnaeus, 1766. Type by monotypy. Gender: masculine., Published as part of de Santana, C. David, Crampton, William G. R., Dillman, Casey B., Frederico, Renata G., Sabaj, Mark H., Covain, Raphaël, Ready, Jonathan, Zuanon, Jansen, de Oliveira, Renildo R., Mendes-Júnior, Raimundo N., Bastos, Douglas A., Teixeira, Tulio F., Mol, Jan, Ohara, Willian, Castro, Natália Castro e, Peixoto, Luiz A., Nagamachi, Cleusa, Sousa, Leandro, Montag, Luciano F. A., Ribeiro, Frank, Waddell, Joseph C., Piorsky, Nivaldo M., Vari, Richard P. & Wosiacki, Wolmar B., 2019, Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator, pp. 1-10 in Nature Communications 10 (4000) on page 6, DOI: 10.1038/s41467-019-11690-z, http://zenodo.org/record/3405402, {"references":["33. Gill, T. N. Several points in ichthyology and conchology. Proc. Acad. Natl Sci. Phila. 16, 151 - 152 (1864).","1. Linnaeus, C. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Laurentii Salvii, Holmiae. 12 th ed. v. 1 (pt 1): 1 - 532 (1766)."]}

Electrophorus electricus (Linnaeus, 1766) Gymnotus electricus 1; Gymnoti tremuli ref. 34: 27, pl. 3; Gymnotus tremulus ref. 35: 111; Gymnotus electricus ref. 1: 427; Gymnotus regius ref. 36: 273. Diagnosis: Ten nucleotides in COI (BOL-COIfishF1/ R 1; 569- bp fragment): G(8), A(50), T (76), T (77), T (107), C(119), C(182), G(272), G(494), A(560). Ventral outline of head U-shaped, widest at terminus of branchial opening (Fig. 2a) and lateral-line pores 88–101 (versus ovoid, widest anterior to branchial opening, Fig. 2b; 112–146 in E. voltai). Distinguished by skull depressed, cleithrum lies between vertebrae 5 and 6 (Fig. 2a), pectoral-fin rays 32–38, and lateral-line pores 88–101 (versus skull deep, cleithrum lies between vertebrae 1 and 2, Fig. 2c, 20–28, and 124–186 in E. varii, respectively). Description: Species illustrated in Figs. 2, 3, and 5. Maximum size examined specimens 1000 mm TL (total length). Morphometric and meristic data in Supplementary Data 2. Body elongate; sub-cylindrical at pectoral girdle, progressively compressed posteriorly. Mouth superior. Scales absent. Anal and caudal fins seamlessly conjoined. Anus and urogenital papilla separated, located anterior to ventral margin of branchial opening. Head and body color brown to blackish. Clear band along body, below lateral line, variably present. Low-voltage (Sachs’ organ) EOD and high-voltage (main/ Hunter’ s organ) with head-positive monophasic waveform. Lowvoltage EOD 2.03–2.19 ms duration, n = 2 (Fig. 4d). High-voltage EOD 480 V at 760 mm TL, n = 1 (Fig. 4d). For distribution see Fig. 1a and Supplementary Data 1., Published as part of de Santana, C. David, Crampton, William G. R., Dillman, Casey B., Frederico, Renata G., Sabaj, Mark H., Covain, Raphaël, Ready, Jonathan, Zuanon, Jansen, de Oliveira, Renildo R., Mendes-Júnior, Raimundo N., Bastos, Douglas A., Teixeira, Tulio F., Mol, Jan, Ohara, Willian, Castro, Natália Castro e, Peixoto, Luiz A., Nagamachi, Cleusa, Sousa, Leandro, Montag, Luciano F. A., Ribeiro, Frank, Waddell, Joseph C., Piorsky, Nivaldo M., Vari, Richard P. & Wosiacki, Wolmar B., 2019, Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator, pp. 1-10 in Nature Communications 10 (4000) on page 6, DOI: 10.1038/s41467-019-11690-z, http://zenodo.org/record/3405402, {"references":["1. Linnaeus, C. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Laurentii Salvii, Holmiae. 12 th ed. v. 1 (pt 1): 1 - 532 (1766)."]}

International audience

The recent description of a distinctive new pimelodid catfish, Pimelabditus moli Parisi {&} Lundberg, 2009, from the Maroni River basin of Suriname and French Guiana, added an unresolved taxon to the family. Here we include P. moli in ongoing molecular and morphological phylogenetic studies of the Pimelodidae. We sequenced > 7.5 KB of aligned bases from the nuclear rag1 and rag2 genes and the mitochondrial mt-rnr1, mt-rnr2 and mt-cyb genes. Results provide strong support for the placement of P. moli as the sister taxon to Pimelodus ornatus Kner, 1858. We also describe a structurally complex pterotic-epioccipital fossa shared by P. moli and P. ornatus that provides an unambiguous synapomorphy indicating their close relationship. Furthermore, the molecular and morphological data recover the P. moli -P. ornatus Clade as the sister group to the Calophysus-Pimelodus Clade. Pimelabditus moli is a rare species, known from just five specimens. Notes on the provenance, capture and habitat of P. moli are provided.

Data derived from the literature supplemented by examination of specimens in collections show that 481 species of fish live in the fresh and brackish inland waters of Suriname, with 394 of these restricted to fresh waters. These 481 species represent 16 orders and 64 families. Orders with the largest numbers of freshwater species in the Surinamese inland fish fauna are the Siluriformes (157 species), Characiformes (147 species), Perciformes (40 species), Gymnotiformes (21 species) and Cyprinodontiformes (21 species). At the family level, the Characidae has the greatest number of freshwater species (83 species), followed by the Loricariidae (60 species), the Cichlidae (30 species), the Callichthyidae (23 species), the Heptapteridae (19 species) and the Anostomidae (17 species). Present data indicate that 25 of the species are known solely from locations within Suriname and 89 species solely in Surinamese river systems including the Marowijne/Mana and Corantijn watersheds which in part extend into French Guiana and Guyana, respectively. Of 481 total species, 187 (38.9%) were based on type series that originated within Suriname. Continued descriptions of new species from the inland waters of Suriname demonstrate that the present total most likely distinctly underestimates the species level diversity of the fish fauna. In terms of species per square kilometer, the presently documented richness of the Surinamese freshwater fish fauna is comparable to, or even greater than, the richness of fish faunas of several other tropical South American countries.

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the mostspeciose catfish family in the world, and are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous works conducted on this group, no phylogeny is presently available. Prior to conduct evolutionary studies, an exhaustive and robust phylogeny was reconstructed using mitochondrial and nuclear data. Then, this phylogeny was used in multivariate and multi-table analyses to reveal the main evolutionary trends of the subfamily. The resulting phylogeny indicated that the Harttiini tribe, as classically defined, formed a paraphyletic assemblage and was restricted to three genera, and within the Loricariini tribe, two sister subtribes were distinguished, Farlowellina and Loricariina, both displaying complex evolutionary patterns. In addition several new taxa were highlighted and described. Subsequently using this phylogeny as exploratory tool, we demonstrated: (1) using co-inertia analysis that the diagnostic features provided to define the different genera were phylogenetically dependent; (2) using multiple co-inertia analysis that the underlying evolutionary forces shaping their diversification included intraphenotypic (morphology and genetics) and extraphenotypic (ecology and distribution) components; (3) using the RLQ analysis that co-dispersion events occurred between co-distributed species responsible for the current fish distribution; and (4) using the multi-scale pattern analysis that the co-evolution in traits related to the mouth characteristics was linked to reproductive functions responsible for a tertiary evolution of this organ.; Les Loricariinae appartiennent à la famille des poissons-chats néotropicaux cuirassés Loricariidae, la famille de poissons-chats la plus riche en espèce au monde, et se caractérisent par un pédoncule caudal long et aplati et par l’absence de nageoire adipeuse. Préalablement aux études évolutives réalisées, une phylogénie exhaustive et robuste a été établie sur la base de données mitochondriales et nucléaires. Cette phylogénie a ensuite été utilisée dans des analyses multivariées et multi-tableaux afin de révéler les principales tendances évolutives de la sous-famille. La phylogénie obtenue indique que la tribu Harttiini forme un groupe paraphylétique et est restreinte à trois genres, et que dans la tribu Loricariini, deux sous-tribus soeurs se distinguent, les Farlowellina et les Loricariina, chacune présentant des patterns évolutifs complexes. Plusieurs nouveaux taxa ont aussi été mis en évidence et décrits. En utilisant la phylogénie comme outil exploratoire, nous avons démontré : (1) avec l’analyse de co-inertie que les caractères diagnostiques fournis pour définir les différents genres étaient sous dépendance phylogénétique ; (2) avec l’analyse de co-inertie multiple que les forces évolutives sous-jacentes dirigeant leur diversification incluaient des composantes intraphénotypiques (morphologie et génétique) et extraphénotypique (écologie et distribution) ; (3) avec l’analyse RLQ que des évènements de co-dispersion entre espèces codistribuées avaient eu lieu et étaient responsables de la distribution actuelle des espèces ; et (4) avec l’analyse de patterns multi-échelles que la co-évolution des traits liés aux caractéristiques de la bouche était liée à des fonctions reproductrices responsables d’une évolution tertiaire de cet organe.

National audience

National audience

Les poissons-chats du genre Harttia se répartissent principalement dans l’est du continent sud-américain : dans les fleuves côtiers du Sud-Est brésilien, dans la région amazonienne et sur le bouclier guyanais. Quatre espèces sont recensées en Guyane française : H. maculata, H. fowleri, H. surinamensis et H. guianensis. Cette dernière présente certaines incertitudes taxinomiques et n’est fondée que sur du matériel provenant de deux bassins (Approuague et Sinnamary). Afin de clarifier le statut taxinomique des différentes populations de l’Ouest du département et de préciser la répartition de chaque espèce, une étude morphologique de toutes les espèces et populations de Harttia présentes en Guyane française et de la série type de H. surinamensis du Surinam a été réalisée grâce à des analyses multivariées effectuées sur de nombreux caractères morphologiques. Il en résulte que H. surinamensis est absente de Guyane française et que sa répartition géographique pourrait être restreinte à la rivière Suriname. Les paratypes de H. surinamensis du haut Tapanahoni (bassin du Maroni, rive surinamienne) sont à rattacher à H. guianensis ainsi que toutes les autres populations du système fluvial du Maroni et de la Mana ; les paratypes de la rivière Coppename pourraient représenter une nouvelle espèce. Harttia fowleri est relativement proche morphologiquement de H. guianensis alors que H. maculata s’en distingue significativement. Quelques différences sont relevées entre les populations de H. guianensis. Les spécimens de la localité type de H. guianensis, l’Approuague, ont un corps plus haut que les spécimens de toutes les autres localités et les individus du Sinnamary présentent des caractéristiques méristiques particulières qui les distinguent de toutes les autres populations. Une clef de détermination pratique de toutes les espèces de Harttia de Guyane française et du Surinam étudiées dans ce travail est proposée.

The fish fauna of French Guiana is among the best known of South America. Various fieldwork campaigns have been conducted since the publication of the “Atlas des poissons d’eau douce” de Guyane, particularly in poorly surveyed areas, leading to the discovery of new taxa, and numerous scientific publications have provided new insights concerning this fauna. An updated checklist of the fishes of French Guiana, including all of this new information, is therefore desirable. The list contains 416 species, 367 of which are strictly freshwater. Fish diversity is strongly correlated with catchment size and is, on average, higher in French Guiana than in Suriname. The largest groups are the Characiformes (41{%}), Siluriformes (33{%}) and Perciformes (13{%}). The relative abundance of taxonomic groups differs between catchments, probably reflecting the ecological character of the rivers. Eighty seven species, around a quarter of the ichthyofauna, are listed as endemic, but this may be an underestimate because a rather strict definition of endemism is used. The rate of endemism is strongly correlated with catchment size, with some families showing higher than average rates. Comparison of the number of species shared by the different catchments suggests a highly complex pattern of dispersal as a function of the catchment size, topography, and species. The Oyapock River seems to belong to a relatively distinct biogeographic zone influenced by the Amazon basin, but it is not possible to show a broader trend. These results provide an additional tool for environmental managers and decision makers.

Ce master présente une étude exploratoire se voulant exhaustive sur l'évolution des patrons de coloration et de la morphologie chez la famille des Loricariidae (1000 espèces). Afin d'y parvenir, les données morphologiques de 604 espèces ont été rassemblées pour 13 variables réparties sur le corps des poissons. Les données phylogénétiques de 760 espèces ont été compilées grâce à une approche en supertree rassemblant 35 arbres informatifs sur les espèces de la famille. Enfin, les données relatives aux patrons de coloration ont été codées manuellement de manière binaire pour 11 couleurs et 7 textures sur 4 zones informatives chez 712 espèces. Des analyses en composantes principales ainsi que des analyses en coordonnées principales ont été utilisées pour décrire les structures observables.

The Neotropical freshwater fish fauna represents 20% of the known fish species diversity. Although several historical and ecological mechanisms involved in the distribution of this diverse ichtyofauna have been explored, few studies have analyzed a complete community. Here, we report a study of the distribution and diffusion of eco-morphological traits across the phylogeny of the fish community of the Maroni Basin, located at the border between French Guiana and Suriname. We also test the eco-morphological hypothesis stating that morphology can be used as a predictor of ecology. Nuclear (five markers) and mitochondrial (one marker) sequences of 236 species were collected to reconstruct their phylogeny, morphometric measurements of 680 individuals were taken and a data table of each species' general ecology was compiled. Multivariate analyses showed a strong structuration of morphometric data on the axes segregating the orders and successive ranks. Axis 1 (27.14%) was a component of shape, and separated compressed, deep-bodied big-eyed fishes (negative values) from depressed, long-snouted fishes with small eyes positioned upward (positive values). The second axis (25.47%) was mainly related to fin-based locomotion and showed a negative correlation between length of anal fin (negative values) and the relative area of pectoral, dorsal and caudal fins. Ecological traits showed a more diffuse pattern since some niches can be occupied by several species belonging to different orders. Co-inertia analyses showed that morphological and ecological traits were significantly linked (RV=0.23; p

The Guiana Shield is located in North-Eastern South America. The river system of the Atlantic slope of the Shield is composed of non-interconnected rivers. Although some connections exist, its freshwater ichtyofauna is in great part different from the Amazon basin one. In this study, we investigated the faunistic assemblage of the Guiana shield's river system. We redefined the map of the freshwater biogeographic areas of the northern Guiana Shield. We first excluded the Essequibo from the Guyana Shield system and assiocated it with the Amazonian fauna. In the Guyanas, we observed 3 regions: one in the west (Corantijn to Suriname), one in the East (Sinnamary to Oyapock) and one in the centre (Commewijne to Mana). In a second stage, we reconstructed the process of dispersion through these biogeographical areas. We studied genera of the Heptapteridae (Rhamdia, Chasmocranus and Pimelodella) using molecular data. We observed that these genera dispersed differently within the system: results indicated that Rhamdia and Pimelodella could overcome natural barriers and spread easier while Chasmocranus seemed more restricted.