The Neotropical Copepoda DatabaseAbstract
The Neotropical Copepoda Database project (NEOCOP) aims at documenting and cataloguing the species of copepods in the Neotropics in a readily accessible form. The database is based on a generic conceptual scheme for taxonomic databases using a standard set of biological data classes. This scheme assures the integrity of stored data and efficiency in its storage and retrieval of basic checklist data, including accepted scientific name, synonyms, name status, original acceptance and synonymic literature citations, position within a genus and higher taxa, structured notes, user-defined morphological descriptors, genomic/proteomic, and geographical distribution records, with every fact in the database linked to bibliographic references. Data entry and editing is made possible by means of a Web-based specialized client interface. It is also possible to export user-selected sets of data to the DELTA format, to permit data exchange with other software for constructing dichotomous keys, interactive identification, and production of data matrices for phylogenetic analyses. The current version of the NEOCOP database is available at http://neocop.biotupe.org.
Keywords:
ACACIA; Arthropoda; Copepoda; DELTA; Neotropics; taxonomic databases
Keywords:
ACACIA; Arthropoda; Copepoda; DELTA; Neotropics; taxonomic databases
Keywords:
ACACIA; Arthropoda; Copepoda; DELTA; Neotropics; taxonomic databases
Copepods are a large and ancient group of microcrustaceans, comprising about 12,000 species, dating from at least the Carboniferous period (Selden et al., 2010) and occurring in freshwater and marine environments all over the planet, of which they are a key component of the food webs.
The taxonomy and distribution of Neotropical copepods are still largely unknown. With nearly 600 copepod species and two endemic genera (Notodiaptomus Kiefer, 1936 and Argyrodiaptomus Brehm, 1933, both in family Diaptomidae Baird, 1850), the Neotropical region is one of the most diverse, second only to the Paleartic region in copepod species richness. The copepod fauna of this region is still poorly known and various new species remain to be described, and many of those already known lack adequate distributional records (Boxshall and Defaye, 2008).
Biodiversity databases have increasingly gained importance in basic and applied research by allowing global integration of data on biological diversity at different levels, e. g., taxonomic, ecological, and genomic/proteomic (Heberling et al., 2021). In this context, an integrated database, including data from diverse, publicly available, sources can constitute an effective tool for the mobilization and aggregation of biodiversity data on the copepods of the Neotropical region, and so contribute to improving the organization and dissemination of knowledge on this group.
To build the database, an initial master species list (sensu Bisby, 1994), comprising the Neotropical species in the families Diaptomidae, Pseudodiaptomidae, and Centropagidae was compiled from querying the World Register of Marine Species and the Catalogue of Life online databases. Each species in this list was then checked in the literature for synonyms and other nomenclatural issues. The final list was used for building the NEOCOP database.
The NEOCOP database was implemented using the MySQL database management system (https://www.mysql.com) and built on top of ACACIA, a generic conceptual scheme for taxonomic databases using a standard set of biological data classes (Cavalcanti, 2023). This scheme assures the integrity of stored data and efficiency in its storage and retrieval. For each species, basic checklist data was stored in the database, including accepted scientific name, synonyms, name status, position within higher taxa, structured notes, conservation status, user-defined morphological descriptors, genomic/proteomic sequences, and geographical distribution records, with every fact in the database linked to bibliographic references. Distribution maps are automatically generated using the OpenLayers JavaScript library (https://www.openlayers.org), based on the georeferenced occurrence records available in the database.
Of special importance is the ability to export user-selected sets of data to the DELTA (Description Language for Taxonomy) format (Dallwitz, 1980), to permit data exchange with the available suites of software for constructing dichotomous keys, interactive identification, and production of data matrices for phylogenetic analyses.
A Python script written by MJC was used to populate the database tables, by automatically fetching relevant data from several online sources: the World Register of Marine Species (WoRMS), via the Catalogue of Life (CoL) for taxonomy (Cachuela-Palacio, 2006; Costello et al., 2013), Genbank/NCBI for genome/proteome data (Benson et al., 2008), and the Global Biodiversity Information Facility (GBIF) for occurrence records (Edwards, 2004; Lane, 2003). Subsequent data entry and editing was done by means of a Web-based specialized client interface, implemented in PHP and JavaScript. The current version of the NEOCOP database is freely available at http://neocop.biotupe.org.
For regular users of well-established biodiversity platforms such as The World of Copepods (https://www.marinespecies.org/copepoda/), the Global Biodiversity Information Facility (https://www.gbif.org/), the Catalogue of Life (https://www.catalogueoflife.org/), and related resources, NEOCOP offers a distinctive advantage by compiling and cross-referencing information from these and other sources into a single, integrated environment. This broader scope not only consolidates taxonomic, genomic/proteomic, and distributional data in one place, but also provides additional features such as DELTA-format exports, interactive mapping, and structured morphological descriptors, thereby enhancing research efficiency and data completeness.
Currently, the database includes 133 valid copepod species, distributed in three families: Diaptomidae with 97 species (72.9% of the total), Centropagidae Giesbrecht, 1893, 26 species (19.5%), and Pseudodiaptomidae Sars G.O., 1902, 10 species (7.5%). The most frequent genera are Notodiaptomus with 36 species (27.1%), followed by Boeckella De Guerne and Richard, 1889 with 21 species (15.8%), Diaptomus Westwood, 1836 and Argyrodiaptomous with 12 species each (9.0%), and Pseudodiaptomus Sars G.O., 1902, with 10 species (7.5%).
Regarding the geographical distribution in the Neotropical region, there are 672 records of occurrence in 13 countries, with Mexico, 436 records (64.9% of the total), Brazil, 176 records (26.2%), Guatemala, 19 records (2.8%) and Colombia, 11 records (1.6%), the countries with the largest number of records. This uneven distribution of occurrence records may reflect the already mentioned lack of knowledge on the geographical distribution of Neotropical copepods.
In the genome/proteome table, there are 242 nucleotide sequences (59.46% of the total) and 165 protein sequences (40.54% of the total) for just 25 species (18.8% of the total). The low availability of sequences for this group may present a severe shortcoming for initiatives intending to resolve phylogenetic relationships of copepod taxa using only biomolecular data.
Regarding the conservation status, according to the International Union for the Conservation of Nature (IUCN) criteria, three species, Boeckella calcaris (Harding, 1955), Mastigodiaptomus purpureus (Marsh, 1907), and Notodiaptomus dubius Dussart, 1986 are in the Vulnerable (VU) category, and four species, Argyrodiaptomus neglectus (S. Wright, 1937), Idiodiaptomus gracilipes (Douwe, 1911), Mastigodiaptomus montezumae (Brehm, 1955), and Odontodiaptomus thomseni (Brehm, 1933) are in the Data Deficient (DD) category, with the majority of the species (126, corresponding to 94.74% of the total species) in the Not Evaluated (NE) category. If it is taken into account that many species red-listed by IUCN as Data Deficient may in fact be endangered (Borgelt et al., 2022), as well as the fact that most of the species have not even been evaluated, the number of endangered copepod species is expected to increase upon further evaluation.
Although the current version of the NEOCOP database comprises only representatives of three families, it should be emphasized that this is a work in progress, and its taxonomic coverage will be enhanced in the future, to include the whole taxa of Neotropical Copepoda. Other relevant data categories are also to be included in future versions, especially concerning the biological behavior of copepod species (such as: “free-living,” “symbiont,” “parasitic,” etc.).
The NEOCOP database is, to date, the only initiative of its kind implemented in the world, aiming to consolidate in an integrated and easily accessible database the information available on this Neotropical Copepoda. The free, generic, and flexible information technology developed for the implementation of the database can also be adapted to the development of biodiversity databases for many other taxonomic groups of interest.
ACKNOWLEDGMENTS
We thank the anonymous reviewers for the useful comments and corrections to the manuscript.
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All study data are included in the article.
