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. 2020 Mar 19;7:96. doi: 10.1038/s41597-020-0436-4

A database of freshwater fish species of the Amazon Basin

Céline Jézéquel 1,✉, Pablo A Tedesco 1, Rémy Bigorne 1, Javier A Maldonado-Ocampo 2, Hernan Ortega 3, Max Hidalgo 3, Koen Martens 4,5, Gislene Torrente-Vilara 6, Jansen Zuanon 7, Astrid Acosta 8, Edwin Agudelo 8, Soraya Barrera Maure 9, Douglas A Bastos 7, Juan Bogotá Gregory 8, Fernando G Cabeceira 10, André L C Canto 11, Fernando M Carvajal-Vallejos 12, Lucélia N Carvalho 13, Ariana Cella-Ribeiro 14, Raphaël Covain 15, Carlos Donascimiento 16, Carolina R C Dória 17, Cleber Duarte 7, Efrem J G Ferreira 7, André V Galuch 7, Tommaso Giarrizzo 18, Rafael P Leitão 19, John G Lundberg 20, Mabel Maldonado 12, José I Mojica 21, Luciano F A Montag 22, Willian M Ohara 23, Tiago H S Pires 7, Marc Pouilly 24, Saúl Prada-Pedreros 2, Luiz J de Queiroz 25, Lucia Rapp Py-Daniel 7, Frank R V Ribeiro 11, Raúl Ríos Herrera 26, Jaime Sarmiento 9, Leandro M Sousa 27, Lis F Stegmann 7, Jonathan Valdiviezo-Rivera 28, Francisco Villa 29, Takayuki Yunoki 30, Thierry Oberdorff 1
PMCID: PMC7081286  PMID: 32193422

Abstract

The Amazon Basin is an unquestionable biodiversity hotspot, containing the highest freshwater biodiversity on earth and facing off a recent increase in anthropogenic threats. The current knowledge on the spatial distribution of the freshwater fish species is greatly deficient in this basin, preventing a comprehensive understanding of this hyper-diverse ecosystem as a whole. Filling this gap was the priority of a transnational collaborative project, i.e. the AmazonFish project - https://www.amazon-fish.com/. Relying on the outputs of this project, we provide the most complete fish species distribution records covering the whole Amazon drainage. The database, including 2,406 validated freshwater native fish species, 232,936 georeferenced records, results from an extensive survey of species distribution including 590 different sources (e.g. published articles, grey literature, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions conducted during the project. This database, delivered at both georeferenced localities (21,500 localities) and sub-drainages grains (144 units), represents a highly valuable source of information for further studies on freshwater fish biodiversity, biogeography and conservation.

Subject terms: Freshwater ecology, Tropical ecology, Biodiversity

Measurement(s) Diversity • Fish • spatial pattern
Technology Type(s) digital curation
Factor Type(s) geographic location
Sample Characteristic - Organism fish
Sample Characteristic - Environment drainage basin
Sample Characteristic - Location Amazon Basin
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Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11920800

Background & Summary

The Amazon Basin covers more than 6,000,000 km2, produces about 20% of the world’s freshwater discharge1–3 and contains the highest freshwater richness on Earth4. This is especially true for Amazonian fishes that represent ~15% of all freshwater fish species described worldwide5,6. The processes having generated this highly diverse fish fauna are incompletely understood. However, low rates of species extinction over several millions of years due to the diversity in aquatic habitats and the stability in favourable climatic conditions are most probably involved7,8. Compared to other large riverine ecosystems on Earth, the Amazon Basin and its fish fauna are still in a relatively good state of conservation9,10. Nevertheless, recent expansion of infrastructures and economic activities are likely to endanger this fish fauna in the near future due to the substantial increase in threats such as habitat fragmentation and river flow modification by dams, deforestation, roads, mining, urban and/or agricultural pollutions, species introduction and overfishing11. Climate change will probably exacerbate these threats further amplifying changes in the structure and function of fish communities11,12.

Our knowledge on fish species occurrence and spatial distribution within the Amazon Basin is far from complete. Numerous new species are described each year13,14 and some large areas are still unknown in several portions of the basin15,16. This was among the key motivations of the transnational collaborative project AmazonFish (https://www.amazon-fish.com/) that aimed to compile the most complete and up-to-date information currently available on freshwater fish species distribution for the entire Amazon drainage basin and to initiate scientific collecting expeditions in under-sampled areas to fill the gaps. This database is thus the result of mobilizing information available from various sources (published articles, grey literature, field expedition reports, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions organized during the project. This compilation, covering a time span of almost two hundred years (1834–2019), currently comprises 2,406 valid native freshwater fish species recorded from 590 different sources representing more than 235,064 occurrence records (232,936 georeferenced and 2,128 non-georeferenced) and 21,500 sampled localities (hereafter called sampling sites). Two parallel compilation efforts on the distribution of freshwater fish species in the Amazon Basin have been recently released17,18. The field guide book from van der Sleen and Albert17 delivers a general view of the current knowledge of fish ecology and distribution maps at the genus level only. The compilation from Dagosta & De Pinna18 provides species lists for 30 Amazonian sub-drainages but suffers from a lack of information19. Here, we complement and refine these previous initiatives by providing species-level distributions on a database format combining available information at both sampling site and sub-drainage grains (144 units).

By compiling the knowledge on the spatial distribution of freshwater fishes and addressing the taxonomic and sampling gaps, the Amazon Fish database should become a valuable and long-lasting source of information for ecological and conservation studies. The database is currently being used to analyse fish diversity patterns at the Amazon Basin scale19, to evaluate the potential effect of climate change20 and fragmentation21 on this biodiversity and to define diversity hotspots for the whole basin conservation priorities22. Besides improving our fundamental knowledge of the patterns and processes involved in the generation of Neotropical freshwater fish diversity, the information provided can also help developing regional conservation programs and contributing to largescale transnational ecosystem management initiatives.

Species occurrences are delivered here at two spatial grains, sampling sites (with precise geographic coordinates) and sub-drainage (144 units) grains. The database is organised in two sub-datasets and one shapefile. The first dataset contains the species list by sub-drainage with the taxonomic FishBase reference name (Family, Genus, Referent species valid name and Author), the species status (‘native’ or ‘exotic’) and the occurrence species status (‘valid’, ‘to be verified’, ‘marine’; see Technical validation for more details). The second dataset contains the geographic coordinates for the georeferenced records, the information source of each record, and the original name of the species cited in the source (‘synonym’, ‘typing error’). Finally, the shapefile delineates all the sub-drainages, along with the corresponding geographic information (e.g. main river name, main country, geographic coordinates and surface area of the sub-drainage). The database is obviously not complete, regular updates are planned in the future to include new occurrence records from literature, collections and new field expeditions planned to cover sampling gaps, together with the distribution of newly described species and nomenclatural changes.

Methods

Information sources

The database results from the transnational collaborative project AmazonFish (ERANetLAC/DCC-0210) whose purpose was to identify and compile all known information sources available on freshwater fish species occurrences for the entire Amazon drainage basin. The original project included researchers from (1) the French Institute for Development (IRD) in France, (2) the Pontificia Universidad Javeriana (PUJ-UNESIS) in Colombia, (3) the Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos (MUSM) in Peru and (4) the Royal Belgian Institute of Natural Sciences in Belgium. The project also benefited from official collaborations with researchers from Brazil (Instituto Nacional de Pesquisas da Amazônia INPA; Universidade Federal de São Paulo UNIFESP; Universidade Federal de Rondônia UNIR; Universidade Federal do Pará UFPA; Universidade Federal do Oeste do Pará UFOPA; Universidade Federal de Mato Grosso UFMT), Colombia (Instituto Alexander von Humboldt IAvH, Universidad Nacional de Colombia UN ICN-MHN, Universidad del Tolima UT-CZUT, Instituto Amazónico de Investigaciones Científicas SINCHI-CIACOL, Instituto para la Investigación y la Preservación del Patrimonio Cultural y Natural del Valle del Cauca INCIVA, Universidad Católica de Oriente UCO), Ecuador (Museo Ecuatoriano de Ciencias Naturales MECN-DP, Instituto Nacional De Biodiversidad INABIO), Bolivia (Universidad Mayor de San Simon UMSS-ULRA, Colección Boliviana de Fauna MNHN–IE UMSA, Universidad Autónoma del Beni CIRA) and Switzerland (Museum d’Histoire Naturelle de Genève, MHNG). All these partners brought into the project, besides their Neotropical fish taxonomic expertise needed to produce a high-quality database, existing fish databases from their own collections and expeditions, and a large networking capacity that was essential for identifying and involving other data providers.

In order to build the AmazonFish database, an inventory of the possible data sources was conducted at the beginning of the project in early 2016 and data from a wide range of sources were compiled and standardized in a single dataset.

The information used includes five source types:

  • A.

    Information extracted from the literature (published articles, books, grey literature)

  • B.

    Data from online biodiversity databases (i.e. GBIF and others)

  • C.

    Data from museums and universities collections

  • D.

    Data held or compiled by the project partners (e.g. country level)

  • E.

    New data from sampling campaigns organized within the framework of the project

An inventory of all the literature sources (published articles, books, technical reports) existent for the Amazon Basin led to more than 800 different documents that were subsequently analysed, from which 459 provided valuable data on fish species distribution, not redundant with any official collection. An important amount of data was extracted from the most used and frequently updated online biodiversity databases (see details in Table 1). These repositories release biological data under a Creative Commons licence in which the user agrees to acknowledge the data sources. Data from museums and universities collections not available through these online facilities were obtained by contacting the curators or researchers in charge and integrating them as official project collaborators (curators and researchers mainly from Brazil, Ecuador and Bolivia). The project partners (Colombia and Peru) compiled data at the country level. For Colombia23,24, the data were previously published through the GBIF network. For Peru, the AmazonFish project has supported the numeric digitalization of the national freshwater fish collections25,26, which is still an ongoing work (51% of the records have been digitalized so far). Finally, supplementary occurrence data were obtained during five sampling campaigns in Brazil, Colombia and Peru and targeting under-sampled areas identified during the project.

Table 1.

Online Biodiversity Repository Sources with the complete name, the number of occurrences and institutions, the last consulted date and the internet link.

Biodiversity Repository Online Biodiversity Repository complete name Number of occurrences Number of institutions Last consulted date Internet link
GBIF Global Biodiversity Information Facility 84,507 60 1/5/2020 https://www.gbif.org/
SpeciesLink SpeciesLink Portal, Brazil 38,656 21 1/5/2020 http://splink.cria.org.br
Fishnet2 Fishnet2 Portal, USA 32,133 26 9/27/2016 http://fishnet2.net/
iDigBio Integrated Digitized Biocollections 21,021 24 4/10/2019 https://www.idigbio.org/
ICMBio Instituto Chico Mendes de Conservaçao da Biodiversidade, Brazil 9,054 1 10/31/2019 https://portaldabiodiversidade.icmbio.gov.br/portal/
AMNH American Museum of Natural History, New York, USA 223 1 9/27/2016 https://www.amnh.org/research/vertebrate-zoology/ichthyology
SiBBr Sistema de Informaçao sobre a Biodiversidade Brasileira, Brazil 130 6 9/27/2016 https://www.sibbr.gov.br/
IABIN Inter-American Biodiversity Information Network 39 1 9/27/2016 https://www.oas.org/en/sedi/dsd/iabin/default.asp
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Species, taxonomy and status

All occurrences not identified to species level were discarded (i.e. occurrences giving only genus names commonly abbreviated to sp., species affinis commonly abbreviated to: sp. aff., aff., or affin. or species confer abbreviated to cf.). All species scientific names are reported in the database as appearing in each information source and were carefully checked for typing errors and misspellings. Because taxonomy is a ‘moving target’, species names were standardized and linked to an internationally accepted standardized name and associated taxonomic information in order to find synonymies and provide accepted names. All species names were first searched in FishBase through the ‘rfishbase’ package27 from the R environment28 allowing to easily obtain the valid species names. For species names absent from FishBase, a manual search was applied in the Eschmeyer’s Catalog of Fishes (http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp). This last step allowed finding valid names and recently described species not yet included in FishBase. The final standardized species list contains 3,366 valid species names avoiding biases due to synonyms and uncertain identifications (see ‘Technical Validation’). We also integrated all remaining species names, i.e. not listed in any of the two scientific catalogues, as ‘unknown name at present’ (294 species names).

A species status (‘native’ or ‘exotic’) and an occurrence species status (‘valid’, ‘to be verified’ or ‘marine’) were assigned to each species. The species status distinguishes ‘native’ from ‘exotic’ species (i.e. non-native species introduced in the Amazon Basin)5 and the occurrence species status is divided in three criteria: (1) ‘valid’ (species known to belong to the Amazon Basin); (2) ‘to be verified’ (species whose presence in the Amazon Basin is not certain because of possible mis-identification or localisation errors); and (3) ‘marine’ (species whose primary habitat is not freshwater, based on information available in FishBase or Eschmeyer’s Catalog of Fishes).

At this time, the database contains 2,406 ‘native’ and ‘valid’ freshwater fish species, 837 ‘to be verified’ species, 105 ‘marine’, 18 ‘exotic’ and 294 ‘unknown’ species. The species considered as ‘native’ and ‘valid’, i.e. freshwater species belonging to the Amazon Basin, were the only species considered in all species numbers reported below.

Sub-drainages delineation

The Amazon Basin was defined here as the area of land where precipitation collects and drains off into a common outlet. This excludes de facto the Tocantins basin and Guiana coastal streams (see Fig. 1), but constitutes for freshwater fishes an ideal grain for conducting biogeographical and/or macroecological studies29.

Fig. 1.

Fig. 1

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(a) Distribution of sampling sites recorded in the AmazonFish database and (b) delimitation and codes of the 144 sub-drainages units (see corresponding names in Online-only Table 1), based on a modified version of HydroBASINS (see methods). The major tributaries of the Amazon Basin are represented in different colours and their names are added in bold.

The hydrological sub-drainage units within the Amazon Basin were delineated using the HydroBASINS framework, a subset of the HydroSHEDS database30. The levels 5 and 6 were combined with a constraint area of >20,000 km2, at the exception of sub-drainages located in the river mainstem where delineation was based on the distance between two main tributaries entering the mainstem. This led to obtain a total of 144 sub-drainages covering the entire Amazon system (Fig. 1).

Data Records

The database31 provides a comprehensive overview of the current knowledge of the fish species diversity and distribution in the Amazon Basin, with 21,500 sites (Fig. 1), 232,936 georeferenced occurrence records and 2,128 non-georeferenced records from 590 different sources combining literature, scientific collections, sampling campaigns and partner’s datasets. Some of the online biodiversity repositories (Table 1) showed some redundancies because often referring to the same collections. In this specific case, only one occurrence record was retained.

The main sources of the database are online biodiversity databases (56% of the occurrences), followed by locally hosted data from the scientific partners (Peru and Colombia), museums and universities from Brazil, Bolivia and Ecuador (38%), literature data (5% of the records) and data obtained during sampling campaigns by partners from Colombia, Peru and Brazil (1%). This represents 93 different collections from Scientific Institutions, 31 Partners references, 459 literature references and five AmazonFish expeditions.

The database includes information for 56 families, 514 genera and 2,406 native valid freshwater species, virtually half of the circa 4,760 total number of species known for the whole Neotropical biogeographic region5,6. Among these 2,406 species, 1,402 are found exclusively in the Amazon Basin (i.e. species appearing nowhere else on Earth; Amazonian endemic species) based on the global species distribution provided by Tedesco et al.5.

The lowland Amazon and its two main tributaries, the Negro and Madeira Rivers regroup the highest number of sites, occurrences and the highest diversity (Table 2), whereas less information is available for some small tributaries. At the sub-drainage grain, the density of sites presents an important spatial variability (Online-only Table 1 and Fig. 2). For instance, the Curuçá sub-drainage belonging to the Javari River, currently lacks information about its ichthyofauna. The ‘updates and limitations’ section below presents a more detailed overview of the spatial data gaps.

Table 2.

Summary table with the total number of sites, occurrences and total number of families, genera, species and endemic species (i.e. Amazon endemic species present only in the sub-drainage) for each Amazon major tributary (with their surface area in km2).

Major Tributary Area Number of sites Number of occurrences Number of Families Number of Genera Number of species Number of endemic species
Amazonas 100,687 1,463 16,365 51 342 971 11
Jari 58,207 80 471 41 160 227 9
Xingu 511,169 1,701 13,215 50 314 821 73
Paru 39,289 10 28 13 20 22 1
Curuá-una 31,116 123 1,025 38 119 195 2
Curuá 25,291 42 189 25 58 80 —
Tapajós 492,570 1,804 17,765 52 334 982 66
Trombetas 126,619 243 2,883 47 237 494 5
Nhamundá 28,609 108 630 36 129 235 1
Uatumã 67,920 174 1,692 47 191 416 —
Madeira 1,496,852 5,514 73,048 52 404 1,406 135
Negro 711,562 2,566 27,983 53 393 1,233 83
Solimões 186,654 1,856 23,732 51 362 1,113 35
Purus 377,158 631 9,310 48 319 836 5
Coari 35,588 59 795 46 189 323 —
Japurá 268,954 793 6,399 51 314 838 12
Tefé 24,269 230 2,226 48 245 545 2
Juruá 188,895 293 3,337 47 256 557 1
Jutaí 78,109 96 1,354 43 175 322 —
Putumayo 120,579 282 3,282 48 287 705 2
Javari 108,966 150 3,140 48 254 552 1
Napo 102,190 639 6,832 48 298 744 9
Marañon 363,296 1,088 8,356 49 286 747 39
Ucayali 352,304 1,555 11,007 49 289 727 28
Amazon Basin 5,896,853 21,500 235,064 56 514 2,406 1,402
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Online-only Table 1.

List of the 144 sub-drainage units with total number of sites, occurrences, families, genera, species and endemics (i.e. Amazon endemics present only in the sub-drainage) for each sub-drainage.

Major Tributary Sub-drainage code Sub-drainage name Area Number of sites Number of occurrences Number of Families Number of Genera Number of species Number of endemic species
Amazonas 1 Amazon1 15,948 96 849 37 110 176 2
Amazonas 2 Amazon2 2,655 64 410 17 48 65 —
Amazonas 3 Amazon3 21,135 130 1,051 44 185 312 —
Amazonas 4 Amazon4 21,969 246 3,401 49 245 540 3
Amazonas 5 Amazon5 5,915 129 1,409 47 200 381 —
Amazonas 6 Amazon6 5,729 163 1,967 48 259 533 2
Amazonas 7 Amazon7 3,992 19 450 40 128 209 —
Amazonas 8 Amazon8 17,154 260 3,344 48 263 597 2
Amazonas 9 Amazon9 6,190 356 3,484 47 248 555 —
Solimões 10 Amazon10 22,036 420 6,428 48 272 616 —
Solimões 11 Amazon11 32,871 120 1,339 43 179 309 1
Solimões 12 Amazon12 17,459 152 1,154 47 196 353 —
Solimões 13 Amazon13 11,906 160 1,028 41 170 278 —
Solimões 14 Amazon14 4,105 70 650 37 150 224 —
Solimões 15 Amazon15 8,626 143 1,020 39 154 227 —
Solimões 16 Amazon16 29,147 98 876 41 193 332 —
Solimões 17 Amazon17 32,795 350 6,002 49 283 723 11
Solimões 18 Amazon18 27,709 343 5,235 47 287 682 17
Jari 19 Jari 58,207 80 471 41 160 227 9
Xingu 20 Xingu1 31,315 558 3,861 48 263 550 1
Xingu 21 Xingu2 10,125 323 3,772 44 224 491 8
Xingu 22 Xingu3 48,113 182 1,050 39 142 237 —
Xingu 23 Xingu4 78,902 101 633 34 103 160 2
Xingu 24 Xingu5 4,770 3 4 3 3 3 —
Xingu 25 Xingu6 44,731 89 460 39 109 182 6
Xingu 26 Bacajá 25,642 43 573 38 119 189 1
Xingu 27 Iriri 141,746 206 1,703 42 184 365 15
Xingu 28 Fresco 43,785 68 409 28 64 103 1
Xingu 29 Manissauá - Miçu 28,015 53 385 22 45 83 —
Xingu 30 Suiá-Missu 23,705 39 152 20 43 67 —
Xingu 31 Ronuro 30,320 36 213 29 63 106 —
Paru 32 Paru 39,289 10 28 13 20 22 1
Curuá-una 33 Curuá-una 31,116 123 1,025 38 119 195 2
Curuá 34 Curuá 25,291 42 189 25 58 80 —
Tapajós 35 Tapajós1 42,528 585 6,380 51 291 703 11
Tapajós 36 Tapajós2 59,069 192 2,549 45 192 373 —
Tapajós 37 Juruena1 38,454 71 713 29 78 134 1
Tapajós 38 Juruena2 93,687 238 1,791 35 94 198 8
Tapajós 39 Jamanxim 58,520 89 841 42 163 320 2
Tapajós 40 Teles Pires 141,420 486 4,652 45 197 470 10
Tapajós 41 Arinos 58,892 143 839 32 75 157 1
Trombetas 42 Trombetas1 7,054 186 2,305 46 212 426 3
Trombetas 43 Trombetas2 51,860 33 359 32 116 172 1
Trombetas 44 Paru do Oeste 41,917 18 157 30 84 119 —
Trombetas 45 Mapuera 25,788 7 62 22 47 57 —
Nhamundá 46 Nhamundá 28,609 108 630 36 129 235 1
Uatumã 47 Uatumã1 3,480 16 305 43 130 215 —
Uatumã 48 Uatumã2 29,947 114 984 40 143 291 —
Uatumã 49 Jatapu 34,493 44 403 39 94 169 —
Madeira 50 Madeira1 9,293 278 3,128 47 246 479 —
Madeira 51 Madeira2 31,133 78 907 45 206 358 —
Madeira 52 Madeira3 19,105 103 1,501 45 241 465 —
Madeira 53 Madeira4 3,644 49 1,404 42 205 370 —
Madeira 54 Madeira5 24,509 505 6,087 48 295 640 —
Madeira 55 Madeira6 5,262 83 943 42 190 353 —
Madeira 56 Andira1 21,770 35 442 42 122 210 —
Madeira 57 Andira2 10,725 53 593 41 120 186 —
Madeira 58 Maués 26,329 75 665 42 116 192 1
Madeira 59 Luna 45,792 143 2,111 47 240 519 —
Madeira 60 Abacaxis 22,114 21 347 31 74 115 —
Madeira 61 Canuma 52,208 51 514 38 133 222 —
Madeira 62 Aripuanã 87,229 311 3,696 50 271 587 12
Madeira 63 Roosevelt 59,330 50 362 35 98 154 1
Madeira 64 Marmelos 27,456 57 590 40 128 212 —
Madeira 65 Jiparaná 74,738 421 10,062 48 251 596 4
Madeira 66 Candeias 29,265 89 1,411 45 243 485 1
Madeira 67 Abunã 31,970 58 527 38 147 255 —
Madeira 68 Orthon 33,576 198 4,425 42 193 385 1
Madeira 69 Madre de Dios 128,843 735 6,666 46 256 610 17
Madeira 70 Beni 118,948 312 2,759 46 215 443 4
Madeira 71 Mamoré1 45,675 226 3,207 46 243 523 4
Madeira 72 Mamoré2 19,246 46 878 38 154 258 —
Madeira 73 Mamoré3 43,774 170 3,009 40 184 342 2
Madeira 74 Mamoré4 3,260 11 38 11 26 29 —
Madeira 75 Guaporé - Iténez 151,316 520 7,649 45 269 688 13
Madeira 76 Blanco Baures 76,639 138 3,158 40 182 374 1
Madeira 77 Itonamas 125,073 158 2,127 42 182 364 7
Madeira 78 Yacuma 21,386 37 806 36 142 232 —
Madeira 79 Isiboro 21,046 169 1,318 38 144 209 1
Madeira 80 Chapare 20,139 135 1,084 38 143 243 1
Madeira 81 Grande 106,059 199 634 32 90 147 2
Negro 82 Negro1 52,502 676 8,431 49 304 798 2
Negro 83 Negro2 36,700 294 2,078 45 210 420 2
Negro 84 Negro3 91,495 305 3,027 45 241 591 10
Negro 85 Negro4 18,934 134 1,162 44 168 328 2
Negro 86 Negro5 3,061 12 75 26 51 64 —
Negro 87 Negro6 88,274 362 4,440 44 222 487 5
Negro 88 Unini 27,310 67 802 45 145 268 —
Negro 89 Jauaperí 38,882 26 163 29 68 105 3
Negro 90 Branco 189,945 401 5,645 50 309 754 14
Negro 91 Demini 39,592 64 479 41 130 230 1
Negro 92 Marié 25,266 6 15 5 7 11 —
Negro 93 Vaupés 64,085 214 1,613 38 153 326 8
Negro 94 Içana 35,516 5 53 18 37 52 —
Purus 95 Purus1 61,569 300 5,614 48 283 632 1
Purus 96 Purus2 26,028 67 854 42 161 261 —
Purus 97 Purus3 29,525 6 45 18 33 39 —
Purus 98 Purus4 22,944 5 24 15 20 23 —
Purus 99 Purus5 5,691 10 72 10 23 34 —
Purus 100 Purus6 36,639 50 494 32 108 156 —
Purus 101 Tapaua 62,893 25 187 29 77 108 —
Purus 102 Ituxi 43,748 18 161 27 50 73 —
Purus 103 Pauini 25,128 9 49 17 29 35 —
Purus 104 Acre 36,526 126 1,423 43 171 322 3
Purus 105 Iaco 26,467 15 387 34 105 149 —
Coari 106 Coari 35,588 59 795 46 189 323 —
Japurá 107 Japurá 62,545 423 3,499 48 273 579 6
Japurá 108 Caquetá1 44,315 57 683 41 141 271 —
Japurá 109 Caquetá2 14,182 34 331 37 113 183 —
Japurá 110 Caquetá3 33,591 197 1,229 40 147 297 6
Japurá 111 Apaporis 56,490 44 430 38 108 189 —
Japurá 112 Yarí 36,650 23 133 20 51 70 —
Japurá 113 Caguán 21,181 15 94 18 31 35 —
Tefé 114 Tefé 24,269 230 2,226 48 245 545 2
Juruá 115 Juruá1 53,073 156 1,768 44 211 377 —
Juruá 116 Juruá2 81,109 124 1,412 41 188 327 1
Juruá 117 Envira 54,713 13 157 29 71 86 —
Jutaí 118 Jutaí 78,109 96 1,354 43 175 322 —
Putumayo 119 Putumayo 120,579 282 3,282 48 287 705 2
Javari 120 Javari1 1,391 39 590 43 157 260 1
Javari 121 Javari2 6,315 53 1,186 46 206 358 —
Javari 122 Javari3 32,845 27 399 34 119 191 —
Javari 123 Ituí 43,215 31 965 45 186 315 —
Javari 124 Curuçá 25,200 0 0 — — — —
Napo 125 Curaray 26,586 66 1,327 48 284 599 3
Napo 126 Napo1 22,578 48 649 41 153 267 —
Napo 127 Napo2 53,026 525 4,856 46 243 509 4
Marañon 128 Marañon1 2,213 20 166 29 79 108 —
Marañon 129 Marañon2 40,458 50 677 39 151 232 2
Marañon 130 Marañon3 31,657 80 811 41 166 293 1
Marañon 131 Marañon4 81,150 180 1,191 34 115 236 7
Marañon 132 Tigre 42,905 219 1,752 39 150 280 2
Marañon 133 Pastaza 42,271 207 1,633 42 182 339 2
Marañon 134 Santiago 32,951 139 1,116 35 121 210 3
Marañon 135 Huallaga 89,691 193 1,010 39 141 252 12
Ucayali 136 Ucayali1 110,606 552 4,949 47 269 607 10
Ucayali 137 Ucayali2 21,956 19 91 17 50 66 —
Ucayali 138 Pachitea 28,908 235 1,530 35 131 229 1
Ucayali 139 Urubamba 59,359 536 3,764 34 125 248 2
Ucayali 140 Tambo 32,277 126 529 27 79 124 4
Ucayali 141 Mantaro 34,535 51 75 6 6 11 1
Ucayali 142 Apurimac1 6,875 4 11 2 6 6 —
Ucayali 143 Apurimac2 34,568 18 35 5 12 14 —
Ucayali 144 Pampas 23,220 14 23 4 10 12 —
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Fig. 2.

Fig. 2

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(a) Number of records, (b) density of sites (number of sites divided by the sub-drainage area and areas without information using the HydroBASINS Level7 spatial grain unit30), (c) total number of species and (d) number of endemic species (species present only in the Amazon Basin and only in the sub-drainage) for the 144 sub-drainage units.

The whole dataset is organised in three sub-sets31: a table of the species list by sub-drainage (‘GeneralDistribution’), a table of occurrence records with sources (‘CompleteDatabase’), and a shapefile of the 144 sub-drainages (‘SubDrainageShapefile’).

The first sub-set (‘GeneralDistribution’) contains the species list by sub-drainage with the taxonomic reference name (Family, Genus, Referent species valid scientific name and Author), the species status (‘native’ or ‘exotic’) and the occurrence species status (‘valid’, ‘to be verified’, ‘marine’). The corresponding table has nine columns (see Table 3).

Table 3.

Detailed legend of the information given in each column of the 2 datasets (9 columns for the GeneralDistribution file and 22 columns for the CompleteDatabase file).

Column Name Description
General Distribution Complete Database Family.Referent.Species Family name of the referent species
Genus.Referent.Species Genus name of the referent species
Referent.Species.Name Referent species: valid scientific species name (FishBase or Eschmeyer’s Catalog of Fishes) at the time of releasing the database
Author.Referent.Species Author’s name of the referent species
Species.Status Species status: ‘native’, ‘exotic’ or ‘unknown name at present’
Occurrence.Status Occurrence species status for native species: ‘valid’, ‘to be verified’ or ‘marine’
Major.Tributary.Name Major Amazon Tributary name
SubDrainage.Name Unique name of the sub-drainage
SubDrainage.Code Unique code of the sub-drainage
Original.Species.Name.Source Original species name in the source
Species.State State of the original species name: ‘synonym’ or ‘typing error’
Longitude.X Longitude coordinates (3 decimal rounded)
Latitude.Y Latitude coordinates (3 decimal rounded)
Data.Source Data source: ‘AmazonFish Expedition’, ‘Literature’, ‘Online Biodiversity Database’ or ‘Partners Datasets’
Biodiversity.Repository Biodiversity Repository source for the ‘Online Biodiversity Database’ source. The combination of two or more repositories mean that the museum or university collection is available from different sources: GBIF, SpeciesLink, FishNet2, iDigBio, AMNH, SiBBr, IABIN, see Table 1
Institution.Code Scientific Institution Code
Institution.Name Scientific Institution complete name
GBIF.Citation GBIF Citation of the Scientific Institution
GBIF.DOI GBIF DOI of the Scientific Institution
Literature.Reference Complete literature reference (Author, Date, Title and Scientific Journal)
Partners.Citation Citation reference of the Partner dataset
Non.Georeferenced Occurrences non-georeferenced: Sub-drainage Information (species occurrence information at the sub-drainage grain), Approximated Coordinates (species occurrence information at river or reach scales), Geographic Error (given coordinates of the site do not correspond to the sub-drainage information of the source)
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The second sub-set (‘CompleteDatabase’) provides the geographic coordinates for the georeferenced sampling sites and the information source of each record. It is complemented with the original name of the species cited in the source (‘synonym’ or ‘typing error’) and those species with status ‘unknown name at present’. The detailed sources contain the source type of the data (‘Literature’, ‘Online Biodiversity Database’, ‘Partners Datasets’ and ‘AmazonFish Expedition’), the Biodiversity Repository source for the Online Biodiversity Database, the Scientific Institution Code and complete name, the GBIF Citation and DOI, the complete literature reference and the citation reference of the Partner dataset. Finally, the non-georeferenced occurrences are separated in three categories, ‘sub-drainage information’ (species occurrence information at the sub-drainage grain), ‘approximated coordinates’ (species occurrence information at river or reach scales) and ‘geographic error’ (the geographical coordinates of a site do not correspond to the geographical location given in the source). The corresponding table has 22 columns (see Table 3).

The third sub-set (‘SubDrainageShapefile’), corresponds to shapefile delineating all the sub-drainages and their corresponding geographic information and is organized in eight columns: (1) the major Amazon tributary name (MTRIB_NM), (2) the unique major Amazon tributary code (MTRIB_CD), (3) the unique sub-drainage name (SBD_NM), (4) the unique sub-drainage code (SBD_CD), (5) the surface area of the sub-drainage (AREA, in km2), (6) the main country where it belongs (COUNTRY), (7,8) the centroid longitude and latitude coordinates of the sub-drainage (CENT_X and CENT_Y).

The two table sub-sets (‘GeneralDistribution’ and ‘CompleteDatabase’) are in CSV format (columns separated by commas) and the shapefile sub-set (‘SubDrainageShapefile’) in ArcGis SHP format31. Both formats can be linked to the species occurrence table using the unique sub-drainage code or name to visualize and analyse species distribution using any adapted software (e.g. R or QGIS, http://qgis.osgeo.org). The sampling coordinates and shapefile are in the World Geodetic System 1984 (WGS84) datum and geographic coordinate system. The files of the database are in ‘CSV’ format (UTF-8 encoding, comma separator) and can be uploaded by most statistical software, spreadsheets or any other database management systems. The current version of the database can be retrieved from Figshare31, the AmazonFish website (https://www.amazon-fish.com/) and the Freshwater Biodiversity data portal (https://data.freshwaterbiodiversity.eu/).

Technical Validation

Taxonomic and status validation

Each species name found in a given information source was confronted to the valid and synonym species names lists from FishBase and Eschmeyer’s Catalog of Fishes to ensure the identifications validity provided by the information source. This taxonomic validation identified 1,332 synonyms, 781 typing errors and 294 unknown species names (names not listed in any of the two scientific catalogues). The original scientific names of the species are reported in the expanded table of the database (‘CompleteDatabase’), where users can extract sub-species, synonyms or unknown species names.

After having validated the taxonomic names, we further verified the presence certainty in the Amazon Basin of all the taxonomically valid species recorded in our database. This careful review was an essential step in the elaboration of the database and resulted in assigning a status to each species. The species status is based on the information provided by the data source, expert opinion from the AmazonFish partners and information about the species general distribution available in FishBase or Eschmeyer’s Catalog of Fishes catalogues. When the presence of a taxon was inconsistent with its actual known distribution, the species was classified as ‘to be verified’. A recently published database on the global distribution of freshwater fish species5 was also consulted to verify the overall distribution of each species, their exotic status and to identify species endemic to the Amazon Basin.

As a result, the database provides not only information on the validity of each species, but also on species occurrences and names that need further attention (‘to be verified’ and ‘unknown name at present’). This gives the opportunity for database users to refer to their own expertise and knowledge to validate or not the accuracy of the original source, species name and distribution (ideally, giving feedback to the AmazonFish project, https://www.amazon-fish.com/).

Species distribution validation

The geographic coordinates of the sites were compared to the location name of the sub-basin given in the source. In case of mismatch, the coordinates were removed from the database and the information was kept only at the sub-basin grain and referenced as ‘geographic error’.

The geographic accuracy of the species distribution (for ‘native’ and ‘valid’ species) inside the Amazon Basin was checked using a basic geographic analysis. A convex hull envelop was delineated for each species based on its occurrence points, resulting in a list of sub-drainages potentially occupied by a given species. This list was then compared to the list of sub-drainages where the species had at least one record. From this comparison, circa 200 species showed some inconsistent distributions (outlying occurrences). All these occurrences were consequently carefully checked and further validated or excluded (see ‘ExcludedOccurrences’ file31).

Updates and limitations

The database is obviously not complete and definitive, and we aim to keep the high-quality level of the database with regular updates, ideally with bi-annual steps, depending on human and financial resources. More than 100 new fish species were described between 2017 and 2019, which makes this update effort crucial in order to improve our knowledge about the distribution of freshwater fish within the Amazon Basin. The technical and taxonomic validation procedures described above will be applied to any new information included in the database. Three main factors will be considered in future updates: (1) new or previously non-available data sources with species lists or records; (2) occurrences of newly described species; and (3) nomenclature changes in the taxonomic classification.

If the main rivers of the Amazon Basin appear well surveyed, some gaps do exist, however in various parts of the basin (Fig. 2). These gaps are mainly located in zones either difficult to access due to the topography and/or located in protected areas (indigenous lands or protected areas). Identifying never-sampled (to our knowledge) or under-sampled sub-drainages is a first step to guide increasing sampling efforts in these areas. The AmazonFish project has already initiated this process, by supporting the numeric digitalization of the national freshwater fish collections from Peru25,26 and by initiating sampling campaigns in detected gaps in Colombia, Peru and Brazil. All these spatial gaps in the database will also be prioritized in future updates through literature and web-based sources checking. Researchers holding fish distribution data from any of the current gaps or under-sampled areas (Fig. 2) and that wish to share these data are welcome to join the project. This information will be included with the complete source, after validation, in the next update of the database.

Acknowledgements

The construction of this database was supported by the AMAZONFISH project (ERANet-LAC: ELAC2014/DCC-0210, www.amazon-fish.com). Colombian partners received support from Colciencas (44842-519-2015) and Peruvian partners from Fondecyt – Concytec (203-2015). Members of the EDB laboratory were also supported by ‘Investissement d’Avenir’ grants (CEBA, ANR-10-LABX-25-01; TULIP, ANR-10-LABX-0041). The Javari River sampling campaign was supported by a grant from FAPESP (#2016/07910-0 to G.T.V.). We also thank the Brazilian Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and the Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM) for long-term financial support to the Igarapés Project. The Brazilian Conselho Nacional de Desenvolvimento Científico e Tecnológico provided a productivity grant to J.Z. (CNPq#313183/2014-7).

Online-only Table

Author contributions

C.J. compiled the data, created the first database version and wrote the first version of the manuscript with inputs from P.A.T. and T.O. R.B., P.A.T. and C.J. entered literature occurrences and checked the information on distribution and status of the species. All authors contributed substantially to providing data, checking the information on distribution and status of the species. T.O. initiated the Database project.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Deceased: Javier A. Maldonado-Ocampo.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. Jézéquel C, 2020. A database of freshwater fish species of the Amazon Basin. figshare. [DOI] [PMC free article] [PubMed]

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