Data from: Low genetic diversity and complex population structure in black piranha (Serrasalmus rhombeus), a key Amazonian predator
Data files
Jan 07, 2025 version files 218.43 MB
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A00_results.zip
211.04 MB
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Metadata_BlackPiranha_Thomas.xls
49.66 KB
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README.md
1.24 KB
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SNPs_Black_Piranha.fasta
7.34 MB
Abstract
This dataset contains 29,587 SNPs from 248 black piranha (Serrasalmus rhombeus) samples collected across 14 study sites from various tributaries in the central Amazonia, covering diverse water types (black, white, and clear water). The SNPs were obtained using a Genotyping-by-Sequencing approach. Additionally, we have included a file with spatio-temporal information about the samples collected and the A00 analyses outputs from the Bayesian Phylogenetics and Phylogeography (BPP) software.
README: Data from: Low genetic diversity and complex population structure in black piranha (Serrasalmus rhombeus), a key Amazonian predator
https://doi.org/10.5061/dryad.p8cz8wb00
Description of the data and file structure
Data preparation, genotyping and filtration were processed using STACKS v2.62 (https://catchenlab.life.illinois.edu/stacks/) and stacks_workflow v2.62 (https://github.com/enormandeau/stacks_workflow).
Files and variables
File: Metadata_BlackPiranha_Thomas.xls
Description: This file contains spatio-temporal information about the Serrasalmus rhombeus samples collected.
Variables
- Country (Country where the samples were collected)
- Locality (Site where the samples were collected
- SampleID (The ID of every individuals)
- YearCollected (The year in which the samples were collected)
File: SNPs_Black_Piranha.fasta
This file contains the SNPs for each individual.
File: A00_results
This zip file contains the theta and tau values generated from the A00 analyses conducted at each tree level, with triplicates for each tree.
Methods
A total of 248 individuals of S. rhombeus were collected in the Amazon Basin (Amazonas and Pará states, Brazil) in 2018 and 2019 during the dry season at 14 sites in different Amazon River tributaries, including seven white water, four black water and three clear water sites. Fin clip samples were collected and immediately preserved in nucleic acid preservation (NAP) buffer to preserve maximum DNA integrity. The samples were then stored at -20°C. We then applied a Genotyping-By-Sequencing (GBS) approach to identify and analyze single nucleotide polymorphisms (SNPs).