Dataset Information

Checklist of the freshwater fishes of Colombia: a Darwin Core alternative to the updating problem.

ABSTRACT: The present work is part of a process to create a Catalogue of the Freshwater Fishes of Colombia and consisted in the depuration and updating of the taxonomic and geographic components of the checklist of the freshwater fishes of Colombia. An exhaustive revision of the 1435 species recorded in 2008 was necessary to: 1. Add new species described since 2009 and species originally described from Colombia but inadvertently omitted in 2008; 2. Add new records of already described species; 3. Delete species whose presence in Colombia was not supported by voucher specimens in ichthyological collections; and 4. Revise the geographic distribution of the species listed in 2008. This process resulted in the following numbers: 1. Total number of freshwater fish species in Colombia: 1494; 2. Number of species recorded by hydrographic region - Amazon: 706, Orinoco: 663, Caribbean: 223, Magdalena-Cauca: 220, Pacific: 130; and 3. Number of endemic species: 374 (76% from the trans-Andean region). Updating the current checklist is a fundamental requirement to ensure its incorporation in the decision-making process with regard to the conservation of Colombian aquatic species and ecosystems, which are facing transformation processes as a result of activities such as mining, construction of hydroelectric plants, expansion of the agricultural frontier and subsequent deforestation, industrial and domestic pollution, development of waterways, introduction of exotic species, and climate change.

SUBMITTER: DoNascimiento C

PROVIDER: S-EPMC5674168 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Checklist of the freshwater fishes of Colombia: a Darwin Core alternative to the updating problem.

DoNascimiento Carlos C Herrera-Collazos Edgar Esteban EE Herrera-R Guido A GA Ortega-Lara Armando A Villa-Navarro Francisco A FA Oviedo José Saulo Usma JSU Maldonado-Ocampo Javier A JA

ZooKeys 20171013 708

The present work is part of a process to create a Catalogue of the Freshwater Fishes of Colombia and consisted in the depuration and updating of the taxonomic and geographic components of the checklist of the freshwater fishes of Colombia. An exhaustive revision of the 1435 species recorded in 2008 was necessary to: 1. Add new species described since 2009 and species originally described from Colombia but inadvertently omitted in 2008; 2. Add new records of already described species; 3. Delete s ...[more]

PMID: 29118633

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Project description:BackgroundDNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.Methodology/principal findingsWe bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.Conclusions/significanceThe present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

Project description:BackgroundMolecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs - Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015-2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only.New informationWe enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoología of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.

Dataset Information

Checklist of the freshwater fishes of Colombia: a Darwin Core alternative to the updating problem.

Publications

Checklist of the freshwater fishes of Colombia: a Darwin Core alternative to the updating problem.

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