Biodiversity Data Journal :
Data Paper (Biosciences)
|
Corresponding author: Florencia Grattarola (grattarola@fzp.czu.cz)
Academic editor: Ross Mounce
Received: 15 May 2019 | Accepted: 14 Jun 2019 | Published: 20 Jun 2019
© 2019 Florencia Grattarola, Germán Botto, Inés da Rosa, Noelia Gobel, Enrique González, Javier González, Daniel Hernández, Gabriel Laufer, Raúl Maneyro, Juan Martínez-Lanfranco, Daniel Naya, Ana Rodales, Lucía Ziegler, Daniel Pincheira-Donoso
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Grattarola F, Botto G, da Rosa I, Gobel N, González E, González J, Hernández D, Laufer G, Maneyro R, Martínez-Lanfranco J, Naya D, Rodales A, Ziegler L, Pincheira-Donoso D (2019) Biodiversidata: An Open-Access Biodiversity Database for Uruguay. Biodiversity Data Journal 7: e36226. https://doi.org/10.3897/BDJ.7.e36226
|
|
The continental and marine territories of Uruguay are characterised by a rich convergence of multiple biogeographic ecoregions of the Neotropics, making this country a peculiar biodiversity spot. However, despite the biological significance of Uruguay for the South American subcontinent, the distribution of biodiversity patterns in this country remain poorly understood, given the severe gaps in available records of geographic species distributions. Currently, national biodiversity datasets are not openly available and, thus, a dominant proportion of the primary biodiversity data produced by researchers and institutions across Uruguay remains highly dispersed and difficult to access for the wider scientific and environmental community. In this paper, we aim to fill this gap by developing the first comprehensive, open-access database of biodiversity records for Uruguay (Biodiversidata), which is the result of a large-scale collaboration involving experts working across the entire range of taxonomic diversity found in the country.
As part of the first phase of Biodiversidata, we here present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates. The database provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country. The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https://doi.org/10.5281/zenodo.2650169. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date and it represents the first open repository for the country.
Uruguay, Biodiversity, Species Occurrence Records, Tetrapods, Amphibia, Reptilia, Aves, Mammalia
Uruguay encompasses a peculiar area of South America located within the Pampa Province of the Neotropical Region (
Currently, national biodiversity databases are unavailable and, thus, the dominant proportion of the primary biodiversity data produced in the country is highly dispersed and difficult to access for the wider scientific community and for policy-makers. Likewise, the Global Biodiversity Information Facility (GBIF) reveals that Uruguay ranks amongst the countries of America with the lowest levels of available data on their biodiversity (Fig.
Distribution of the number of occurrence records available in the Global Biodiversity Information Facility (GBIF) (as of 7 June 2019) for each country of Latin America, relative to the number of records that have been submitted by eBird users. The respective proportion is shown in the green scale.
Here, we introduce Biodiversidata, the first database derived from the Uruguayan Consortium of Biodiversity Data (biodiversidata.org), a collaborative initiative aimed at hosting and distributing via an open-access platform a comprehensive database on the biodiversity of Uruguay. The total number of records collated is 69,380, from across 673 species (Table
Records collected per tetrapod class showing: number of occurrence records (non-duplicated records/location/year), total number of species, records without information of the date of collection and records collected in the last 30 years, with percentage in parentheses.
Number of Occurrence Records |
Number of Species |
Records without Date (%) |
Records from the last 30 years (%) |
|
Amphibia |
2,530 |
51 |
1,780 (70.4) |
683 (27.0) |
Reptilia |
2,308 |
68 |
1,999 (86.6) |
224 (9.7) |
Aves |
60,627 |
437 |
131 (0.2) |
60,308 (99.5) |
Mammalia |
3,915 |
117 |
1,687 (43.1) |
1,122 (28.7) |
Total |
69,380 |
673 |
The database was developed, based on the collection of data from a range of different sources. A significant proportion of the data was collected by expert members of Biodiversidata. These records can be found with the value ‘Unpublished data’ under the term ‘associatedReference’. A proportion of them has been deposited in national specimen collections such as the Mammalogy collection of the Museo Nacional de Historia Natural of Uruguay and the Vertebrate collection of the Facultad de Ciencias, Universidad de la República (Uruguay). In addition to the large volume of original data, we have also incorporated all readily available records from multiple sources, including online databases (i.e. GBIF) as well as data currently published but not available in the format of other sources of compiled information. These include data from primarily field guides and books and primary literature such as monographs, systematic accounts, species descriptions, reviews and reports of range extensions, in journals such as “Check List” and the local “Boletín de la Sociedad Zoológica del Uruguay”, amongst others. A complete list of sources for the occurrence records is shown in Table
List of sources used to build the dataset, including the source type and the number of records extracted from each of the sources.
Source | Source type | Number of records | Groups |
|
Journal Article | 8 | Aves |
|
Journal Article | 13 | Mammalia |
|
Journal Article | 54 | Aves |
|
Journal Article | 20 | Amphibia |
|
Journal Article | 70 | Reptilia |
|
Journal Article | 1 | Reptilia |
|
Journal Article | 4 | Reptilia |
|
Journal Article | 13 | Reptilia |
|
Thesis | 86 | Mammalia |
|
Journal Article | 2 | Reptilia |
|
Journal Article | 1 | Reptilia |
|
Book | 1880 | Reptilia |
|
Journal Article | 2 | Reptilia |
|
Journal Article | 1 | Reptilia |
da Rosa | This study | 13 | Amphibia + Reptilia |
|
Thesis | 67 | Aves |
|
Journal Article | 1 | Amphibia |
GBIF.org | Online Database | 58355 | Amphibia + Reptilia + Aves + Mammalia |
Gobel & Laufer | This study | 285 | Amphibia + Reptilia |
|
Journal Article | 3 | Reptilia |
González & González | This study | 1848 | Mammalia |
Grattarola | This study | 53 | Mammalia |
|
Thesis | 36 | Mammalia |
Hernández | This study | 944 | Aves |
|
Journal Article | 2 | Amphibia |
|
Journal Article | 2 | Amphibia |
|
Journal Article | 1 | Amphibia |
|
Journal Article | 11 | Mammalia |
|
Journal Article | 2 | Amphibia |
|
Journal Article | 2 | Amphibia |
Maneyro | This study | 165 | Amphibia + Reptilia |
|
Journal Article | 6 | Mammalia |
Martínez-Lanfranco | This study | 1712 | Aves + Mammalia |
|
Conference Paper | 48 | Amphibia + Reptilia + Aves |
|
Journal Article | 85 | Reptilia |
|
Journal Article | 5 | Mammalia |
Naya | This study | 220 | Aves |
|
Book | 1764 | Amphibia |
|
Journal Article | 43 | Amphibia + Reptilia |
|
Journal Article | 18 | Reptilia |
|
Journal Article | 3 | Mammalia |
|
Journal Article | 1041 | Mammalia |
Rodales, Botto & González | This study | 91 | Mammalia |
|
Journal Article | 4 | Aves |
|
Report | 151 | Amphibia + Reptilia + Mammalia |
|
Journal Article | 1 | Amphibia |
|
Report | 189 | Amphibia + Reptilia + Aves + Mammalia |
|
Journal Article | 1 | Aves |
|
Journal Article | 4 | Reptilia |
|
Journal Article | 3 | Reptilia |
|
Journal Article | 1 | Reptilia |
|
Journal Article | 15 | Reptilia |
Ziegler | This study | 31 | Amphibia |
The GBIF dataset was obtained by searching for Uruguay in the ‘country or area’ field (as for 15 January 2018), retrieving 185,519 occurrences from 573 datasets, including 8,925 species of Animalia, Plantae, Fungi, Bacteria, Chromista, Protozoa and Archaea. These data on species occurrences are available on the GBIF portal at https://doi.org/10.15468/dl.dmul8x. Most of these records were submitted by the eBird project (56.1% of the total amount) and the rest derive from diverse specimen collections around the world, such as the National Museum of Natural History Smithsonian Institution (4.2%), the Instituto de Botánica Darwinion in Argentina (3.9%), the Missouri Botanical Garden’s Herbarium (3%), the Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (2.1%), the Swedish Museum of Natural History (1.6%), the Museum of Comparative Zoology at Harvard University (0.72%), the American Museum of Natural History of New York (0.68%) and the Natural History Museum of London (0.57%). None of the records was submitted by Uruguayan institutions, most likely because of the major public sources of specimen biodiversity information (government and academia) are not open nor publicly available.
Different methods were applied to treat the data derived from each of the above-mentioned sources. For the GBIF data, only records of amphibians, reptiles, birds and mammals were included in this first version. Exotic species and records without complete date of collection/observation or geographic location information were excluded. The data from literature were manually extracted and added to the data collected by members of Biodiversidata. These records were controlled by collection and catalogue number to check their complete independence from the GBIF data. To avoid pseudo-replication in posterior analyses, records were filtered by considering only one record per locality/year. If more than one organism of the same species was collected in a locality in the same year (i.e. same geographic coordinates), we kept the first and most complete record (i.e. the most informative record for the year).
In line with FAIR data Principles (
A significant number of the data lacked crucial information in terms of taxon, time and place of collection/observation, a common issue with observational and specimen data (
The database includes all native and extant species of tetrapods reported in any area within the borders of Uruguay. The occurrence records are not evenly distributed through space as a result of oversampling in some areas and of limited (or no) sampling in other areas (Fig.
Higher numbers of records are seen in the coast area, whilst the centre of the country holds low sampling densities. The most sampled area of Uruguay is in Montevideo (the capital of the country), followed by the surroundings of Maldonado and Rocha cities, all Atlantic coast areas. We observed this pattern particularly in Aves which, despite being the most sampled group, with 87.4% of the database records, they are strongly spatially biased. Reptiles, on the other hand, with the least number of records in the database, cover the Uruguayan territory better than any other tetrapod group.
After our data collation, we can observe some areas of the country that remain systematically ignored. This disparity in sampling is mostly due to the lack of systematisation in the efforts of zoological exploration of the national territory and responds to the realisation of research projects, faunistic inventories or intensive occasional sampling in a few locations, generally near the main population centres or close to easily accessible areas (
-34.973188 and -30.10818 Latitude; -58.43882 and -53.266525 Longitude.
The database incudes 69,380, representing 129 families, 446 genera and 673 species: 51 amphibians, 68 reptiles, 437 birds and 117 mammals. The taxonomic coverage is uneven (Fig.
Rank | Scientific Name | Common Name |
---|---|---|
kingdom | Animalia | Animals |
subkingdom | Eumetazoa | |
phylum | Chordata | |
subphylum | Vertebrata | |
superclass | Tetrapoda | |
class | Amphibia | Amphibians |
class | Reptilia | Reptiles |
class | Aves | Birds |
class | Mammalia | Mammals |
The records included in Biodiversidata cover samples reported in Uruguay during the period of 1806–2018 (Fig.
In particular, bird occurrence records are disproportionally superior in the database (i.e. 87.4% of total number of records), presenting an intense period of sampling effort between 2000 and 2016, mostly derived from citizen science efforts from eBird users (collected from GBIF). Regardless of the spatial bias of these records, it is valuable to note the significant contribution of local ornithologists and birdwatchers (i.e. Aves Uruguay) to the international initiative, which probably stands as the richest and oldest practice of data-sharing known in Uruguay.
The dataset provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country area between 1806-2018. The total number of records collated is 69,380, including 673 species. Suppl. material
Column label | Column description |
---|---|
occurrenceID | An identifier for the Occurrence (as opposed to a particular digital record of the occurrence), constructed from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. |
scientificName | The full scientific name, with authorship and date information |
scientificNameAuthorship | The authorship information for the scientificName |
vernacularName | Common or vernacular name in Uruguay (in Spanish) |
kingdom | The full scientific name of the kingdom in which the taxon is classified |
phylum | The full scientific name of the phylum or division in which the taxon is classified |
class | The full scientific name of the class in which the taxon is classified |
order | The full scientific name of the order in which the taxon is classified |
family | The full scientific name of the family in which the taxon is classified |
genus | The full scientific name of the genus in which the taxon is classified |
specificEpithet | The name of the first or species epithet of the scientificName |
infraspecificEpithet | The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation |
countryCode | The standard code for the country in which the Location occurs |
stateProvince | The name of the next smaller administrative region than country (department) in which the Location occurs |
verbatimLocality | The original textual description of the place |
decimalLatitude | The geographic latitude (in decimal degrees) |
decimalLongitude | The geographic longitude (in decimal degrees) |
georeferenceSources | A list of maps, gazetteers or other resources used to georeference the Location |
georeferencedBy | A person, group or organisation who determined the georeference (spatial representation) for the Location. |
eventDate | The date when the event was recorded. Format: dd-mm-yyyy |
year | The four-digit year in which the Event occurred. Format: yyyy |
month | The ordinal month in which the Event occurred. Format: mm |
day | The integer day of the month on which the Event occurred. Format: dd |
basisOfRecord | The specific nature of the data record |
institutionCode | The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record |
collectionCode | The name or acronym identifying the collection or dataset from which the record was derived |
catalogNumber | An identifier (preferably unique) for the record within the dataset or collection |
recordedBy | A list (concatenated and separated) of names of people, groups or organisations responsible for recording the original Occurrence |
recordNumber | An identifier given to the Occurrence at the time it was recorded. Often serves as a link between field notes and an Occurrence record, such as a specimen collector's number. |
identifiedBy | A list (concatenated and separated) of names of people, groups or organisations who assigned the Taxon to the subject |
dynamicProperties | Structured content about the record key:value encoding IUCN red list category of the taxon at the Global level |
associatedReferences | A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence |
The Uruguayan Consortium of Biodiversity Data, is a collaborative association of experts whose aim is to improve Uruguay’s biodiversity knowledge. It was created in 2018 by Florencia Grattarola as part of her PhD project. Its open-access platform (biodiversidata.org) aims to make available the biodiversity data of Uruguay by integrating a broad range of resources including databases, publications, maps, reports and infographics, derived from the work of the team members. The database presented in this study and the original research that is currently emerging from it are the first products of the initiative and will be available in the platform. The database may continue to be updated with new records periodically; check the Zenodo repository for the latest version: https://doi.org/10.5281/zenodo.2650169.
The research leading to these results has received funding from Agencia Nacional de Investigación e Innovación (ANII POS_EXT_2016_1_136663). Laufer G., Maneyro R., Naya D. E. and Ziegler L. wish to thank the National System of Researchers (Sistema Nacional de Investigadores, SNI-ANII, Uruguay).
F.G. was responsible for data compilation, standardisation, quality control and management. F.G. and D.P.D. have drafted the first manuscript. G.B., I.D.R., N.G., E.M.G., J.G., F.G., D.H., G.L., R.M., J.A.M.L., D.E.N., A.L.R. and L.Z. contributed with acquisition of data. All authors collaboratively contributed to analysis and interpretation of the data and finalised the manuscript.
We declare that the joint co-authorship of this article, or the affiliation to the Biodiversidata initiative, does not imply responsibility of any individual, directly or indirectly, for the principles and values of other members or co-authors.
Tab-delimited csv data file and xml metadata file corresponding to the 69,380 species occurrence records held in the database