This PIMELODUSreadme.txt file was generated on 2021-09-19 by JOSÉ GREGORIO MARTÍNEZ GENERAL INFORMATION 1. Title of Dataset: Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin 2. Author Information A. Principal Investigator Contact Information Name: Martínez, José Gregorio Institution: Institución Universitaria Colegio Mayor de Antioquia Address: Carrera 78 # 65 - 46 Bloque Patrimonial - Piso 1. Medellín, Antioquia, Colombia Email: jose.martinez@colmayor.edu.co B. Associate or Co-investigator Contact Information Name: Rangel-Medrano, José David Institution: Universidad Nacional de Colombia Address: Cra. 65 # 59A - 110, Campus el Volador, Medellín, Antioquia, Colombia Email: jdrangelm@unal.edu.co Name: Restrepo-Escobar, Natalia Institution: Universidad Nacional de Colombia Address: Cra. 65 # 59A - 110, Campus el Volador, Medellín, Antioquia, Colombia Email: nrestree@unal.edu.co Name: Yepes-Acevedo, Anny Johanna Institution: Universidad Nacional de Colombia Address: Cra. 65 # 59A - 110, Campus el Volador, Medellín, Antioquia, Colombia Email: ajyepesa@unal.edu.co Name: Márquez, Edna Judith Institution: Universidad Nacional de Colombia Address: Cra. 65 # 59A - 110, Campus el Volador, Medellín, Antioquia, Colombia Email: ejmarque@unal.edu.co C. Alternate Contact Information Name: Institution: Address: Email: 3. Date of data collection: from 2011-01-15 to 2018-09-15 4. Geographic location of data collection: Magdalena-Cauca River Basin, Colombia. Orinoco and Amazon basins from Colombia and Brazil. 5. Information about funding sources that supported the collection of the data: This research was supported by the scientific cooperation agreement between Universidad Nacional de Colombia, Sede Medellín and Empresas Públicas de Medellín, Grant CT-2019-000661 ‘‘Variabilidad genética de un banco de peces de los sectores medio y bajo del río Cauca’’. This work was further supported by the cooperation of the Institución Universitaria Colegio Mayor de Antioquia (Grant FCS-2017 and FCSA20) and Universidad Nacional de Colombia (Hermes 40096), Grant “Delimitación de Unidades Evolutivas Significativas para la conservación de especies de peces del género Pimelodus en los Andes colombianos: una aproximación genómico-poblacional y filogenómica para la cuenca Magdalena-Cauca” and “Genética de la conservación de especies de peces Trasandinas colombianas del género Pimelodus: una aproximación genómico-poblacional para la cuenca Magdalena-Cauca”. SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: 2. Links to publications that cite or use the data: 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? yes/no A. If yes, list source(s): 6. Recommended citation for this dataset: José Gregorio Martínez, José David Rangel Medrano, Anny Johanna Yepes Acevedo, Natalia Restrepo Escobar, Edna Judith Márquez. Species limits and introgression in Trans-Andeans Pimelodus from the Magdalena-Cauca River basin. Molecular phylogenetics and Evolution. DATA & FILE OVERVIEW 1. File List: Population module parameteres.txt Contains the population module run parameters used on Stacks software v.2.52 and some basic statistics derived. The analysis included genomic RADseqs data Illumina Hi-Seq-derived from 19 individuals of several Pimelodus species. Demultiplexing statistics.txt Contains the demultiplexing statistics (number of reads and its lenght) across 19 samples of Pimelodus species libraries obtained by Illumina Hi-Seq. De novo loci assembling statistics.txt Contains the de novo loci assembling statistics (number of loci, number of polymorphic loci and number of SNPs) obtained after the RADproc software analysis across 19 samples of Pimelodus species libraries, using the optimized parameters, by – psweep mode. RADseqs Raw data Pimelodus.zip Contains the demultiplexed fastq files from 19 samples of Pimelodus species libraries obtained by Illumina Hi-Seq. Pimelodus.sumstats.summary.txt Contains the summary statistics of variant and fixed positions across loci for each of 19 samples of Pimelodus, after Stacks v.2.52 software analysis (Population module, --fstats). Pimelodus.var.phylip.txt Contains 999 variable sites for each of 19 samples of Pimelodus in the phylip output encoded using IUPAC notation, using Stacks v.2.52 software (Population module, --phylip-var), suitable for SNAPP and SVDquartets species delimitation analyses. No sites with missing data were included. Pimelodus.vcf.txt Contains the output SNPs and haplotypes in Variant Call Format (VCF) for 19 samples of Pimelodus, after Stacks v.2.52 software analysis (Population module, --vcf). rag2 alleles.txt Contains the 40 inferred phased alleles from rag2 sequences from 20 individuals of Pimelodus yuma and P. grosskopfii, by using the application ‘PHASE’ of DnaSP v5.10.1. Confidence intervals.R Contains the modified script from SPIDER software to estimate the confidence interval for GMYC, bGMYC and localMinima single-locus species discovery methods, developed by Machado et al. (2018). 2. Relationship between files, if important: 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? yes/no A. If yes, name of file(s) that was updated: i. Why was the file updated? ii. When was the file updated? METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: 2. Methods for processing the data: A RAD-seq library was prepared for 19 individuals representing five putative morphospecies of Pimelodus, previously identified by DNA barcoding: three corresponded to P. grosskopfii, P. yuma and P. crypticus from Magdalena-Cauca River basin and two corresponded to the cis-Andean P. blochii stricto sensu and P. pictus. Samples were processed through a single-end sequencing step conducted by Floragenex inc. (http://floragenex.com) on one lane of an Illumina HiSeq 2000 machine. The raw data were de-multiplexed by barcode, quality-filtered, and made a de novo loci construction using RADproc v3 (Nadukkalam Ravindran, Bentzen, Bradbury, & Beiko, 2019) setting up -a psweep mode for the optimization of locus assembling parameters to produce a catalog of RAD-seq tag loci, alleles and SNPs from the raw NGS reads through the different parameter values for m, M and n. Parameters to run RADproc included a Phred Score base quality threshold > 20, a minimum coverage depht of 3 (-m), a maximum distance (in nucleotides) allowed between stacks of 4 (-M), a maximum distance (in nucleotides) allowed between putative loci during catalog construction of 1 (-n), a maximum number stacks per locus of 2 (-x) and minimum sample percentage of 0.9 (-S). Then, we used STACKS v2.53 (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013) to generate ouputfiles for population and phylogenomics analyses from the optimal constructed Catalogs obtained by the RADproc analysis. First, we ran in pipeline mode the modules SSTACKS, TSV2BAM, GSTACKS using defaults parameters. Finally we ran the POPULATIONS module following the parameter settings provided in "Population module parameteres.txt". Each individual was considered a population into the STACKS map file. In POPULATIONS module, the minimum number of populations that a locus must be present in to process it, was set to 100% (-p = 19). Likewise, the minimum percentage of individuals in a population required to process a locus for that population was set to 100% (-r = 1) and a minnor allele frequency (MAF) of 0.01. All other parameters for analysis were kept as default. Finally, we obtained VAR.PHYLIP (Pimelodus.var.phylip.txt) and VCF (Pimelodus.vcf.txt) output files containing, respectively, useful dataset for SNPs-based species delimitation and admixture tests. These archives, the summary statistic (Pimelodus.sumstats.summary.tsv.txt) 3. Instrument- or software-specific information needed to interpret the data: RADproc v3 (Nadukkalam Ravindran, Bentzen, Bradbury, & Beiko, 2019) and STACKS v2.53 (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013). 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: J.G.M. conceived and designed the study, performed field and laboratory work, analyzed and interpreted the data, prepared figures and/or tables, edited and wrote the manuscript. J.D.R.M. performed field and laboratory work, analyzed and interpreted the data, prepared figures and/or tables, edited and wrote the manuscript. A.J.Y.A. and N.R.E. performed field and laboratory work, analyzed and interpreted the data, edited and wrote the manuscript. E.J.M. conceived and designed the study, analyzed and interpreted the data, edited and wrote the manuscript. All authors approved the final manuscript. DATA-SPECIFIC INFORMATION FOR: [FILENAME] 1. Number of variables: 2. Number of cases/rows: 3. Variable List: 4. Missing data codes: n 5. Specialized formats or other abbreviations used: