trichomycteridae-ufes-2023

Thais de Assis Volpi1, Luisa Maria Sarmento-Soares1, Valeria Fagundes1

1 Universidade Federal do Espirito Santo, Avenida Fernando Ferrari, 514, 29075-910, Vitória, Brazil

Corresponding author(s): Thais de Assis Volpi (thaisvolpi@gmail.com)Luisa Maria Sarmento-Soares (sarmento.soares@gmail.com), Valeria Fagundes (valeria.fagundes@ufes.br)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Abstract

Biological samples collected, fixed, preserved in scientific collections and sequenced.

Keywords: Occurrence, Specimen

General description

Purpose: Doctoral research.
Additional information: Not applicable.

Project details

Project title: Pleistocene aquatic refuges support the east-west breakage of the Neotropical catfish Trichomycterinae (Siluriformes: Trichomycteridae) and high diversity in the Magdalena, Guiana, and Paraná-Paraguay basins
Personnel: Thais de Assis Volpi
Funding: This research was funded by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for the doctoral bursary granted to T.A.V. (1170780/2012-6); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the research bursary granted to L.M.S.S. (PCI-E1 grant 465023/2014-2); and CNPq and Fundação de Amparo à Pesquisa e Inovação do Espírito Santo (FAPES) under Pronem Program to V.F. (CNPq/FAPES 80600417/17).
Study area descriptions/descriptor: Neotropical Region.
Design description: We therefore aimed to explore an unprecedented collection of specimens to investigate the divergence in the lineages of Trichomycterus representatives in a wide geographic area. We expect our study to deepen efforts to understand the structural patterns of species distribution within Trichomycterinae in South America. 

Data published through GBIF: https://ipt.pensoft.net/resource?r=trichomycteridae-ufes-2023

Taxonomic coverage

General taxonomic coverage description: The fish are known as catfish and are delimited at the level of genus and species, contemplating a large representation of the subfamily Trichomycterinae, mainly of the genus Trichomycterus.
Taxonomic ranks
Superfamily: Trichomycterinae
Common names: Catfish

Spatial coverage

General spatial coverage: Subfamily Trichomycteridae is endemic to the Neotropics. The biological samples collected and preserved by my team come exclusively from Brazil.
Coordinates: 90°0'0''S and 90°0'0''N Latitude; 180°0'0''W and 180°0'0''E Longitude 

Natural collections description

Parent collection identifier: MBML-Peixes
Collection name: Museu de Biologia Professor Mello Leitão
Collection identifier: MBML
Specimen preservation method: Alcohol
Curatorial unit: Between 1 and 309 (indivíduo)

Methods

Method step description: DNA samples were extracted following Bruford et al. (1992) and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific™). For the in vitro amplification of the mitochondrial gene cytochrome b (cytb), we used the primers CytbSiluF and CytbSiluR (Villa-Verde et al., 2012). The amplicons were purified by adding 1 μL Exosap to each 10 μL of PCR product. Sequencing reactions were performed using the Big Dye Terminator Cycle Sequencing Kit, following the manufacturer’s protocol. The 332 samples were sequenced in an ABI310 automatic sequencer (Applied Biosystems) at the Núcleo de Genética Aplicada à Conservação da Biodiversidade (NGACB), Universidade Federal do Espírito Santo (UFES). 
Study extent description: We collected 309 samples in eastern Brazil. We revisited the type-localities of the eastern Brazilian species between the Jequitinhonha River basin in the north and the Itabapoana River basin in the south. 
Sampling description: Our analysis involved geo-referenced 566 sequences of 33 species of Trichomycterinae (Table S1), 364 of which belong to Trichomycterus sensu stricto (including sequences of the type species of the genus T. nigricans Valenciennes 1832). The samples from the Brazilian Atlantic coast comprised 13 sequences of Cambeva spp., four of Scleronema spp., and 14 of Ituglanis spp. The Andean samples consisted of 125 sequences of Trichomycterus areolatus Valenciennes 1846, 10 of Hatcheria macraei Girard 1855, and 12 of Bullockia maldonadoi Eigenmann 1928. The sequences from the northern Amazon basin consisted of 14 sequences of the T. guianense group Eigenmann 1909 from the Guiana Shield, eight from the Magdalena basin, and one Trichomycterus sp. from the Tapajós basin. We also used four sequences as an external group, two from Listrura spp. (Glanapteryginae) and two from Trichogenes longipinnis Britski & Ortega 1983 (Trichogeninae). Of the 324 Brazilian  sequenced catfish (323 from Trichomycterus and one from Cambeva), 182 were collected by our team, and 142 were obtained from fish collections. We sequenced these 324 samples and obtained another 246 sequences from GenBank® (ncbi.nlm.nih.gov). 
Fieldwork was carried out between June 2013 and October 2014 on expeditions that revisited the type-localities of the eastern Brazilian species between the Jequitinhonha River basin in the north and the Itabapoana River basin in the south. Specimen sampling procedures followed the standard protocol, mainly using trawl nets. Captured specimens were anesthetized by submersion in eugenol solution and the guidelines for fish euthanasia. Tissue samples of the right flank muscle were obtained from specimens fixed in 90% ethanol and preserved in absolute ethanol for molecular analyses. For morphological comparisons, specimens were fixed in formalin for 15 days and then transferred to 70% ethanol. All specimens were registered in the fish collection at the Instituto Nacional da Mata Atlântica (INMA), formerly the Museu de Biologia Professor Mello Leitão, in Santa Teresa, Espírito Santo, Brazil. We also used sequences from Genbank® of cis- and trans-Andean species of Trichomycterinae, the locations of which ranged from the Isthmus of Panama in the north to Patagonia at the extreme southern limit of the subfamily’s range. 

Quality control description: Each sample was recorded on the field form with the number accompanying each sample. From this, during the sorting we identified the individual material through the tumble number. This information was made available at <http://splink.cria.org.br>.

Datasets

Dataset description
Object name: Darwin Core Archive trichomycteridae-ufes-2023
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: https://ipt.pensoft.net/archive.do?r=trichomycteridae-ufes-2023
Publication date of data: 2023-08-07
Language: English
Licences of use: Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License

External datasets

Dataset description

Metadata language: English
Date of metadata creation: 2023-08-07
Hierarchy level: Dataset