Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin
Creators: name: Martínez, José Gregorio
name: Rangel-Medrano, José David
name: Restrepo-Escobar, Natalia
name: Yepes-Acevedo, Anny Johanna
name: Márquez, Edna Judith
Publisher: name: Zenodo
Year: 2022

description: Low morphological differentiation among taxa hampers its appropriate identification, basic biological studies, and promotion of any conservation effort. Aiming to clarify the evolution and speciation among members of <i>Pimelodus </i>from the Magdalena-Cauca River basin, this study tested the hypothesis that <i>P. yuma, P. grosskopfii </i>and<i> P. crypticus</i> represent<i> </i>three independently evolving species and explored signals of interspecific hybridization. Likewise, we test the ancient hypothesis that the <i>trans</i>-Andean <i>Pimelodus yuma</i> and <i>P. crypticus</i> belong to the <i>cis</i>-Andean <i>P. blochii </i>species complex. The outcomes based on mitochondrial (<i>cox1</i>) and nuclear [RADseq (Illumina Hi-Seq), microsatellites and <i>rag2</i>] markers combined with coalescence-based and allele-frequency methods, confirm that each studied <i>trans</i>-Andean species represent<i> </i>an independently evolving unit. We used Stacks v.2.52 for <i>de novo</i> SNP genotyping. Contrary to expectations, <i>P. yuma </i>was<i> </i>found as a sister clade of <i>P. blochii</i>, while <i>P. crypticus </i>(confused for a long time with <i>P. blochii</i>) was phylogenetic closer to <i>P. grosskopfii</i>. Additionally, we found strong evidence of historical introgression between the non-sibling species <i>Pimelodus yuma </i>and<i> P. grosskopfii, </i>breaking the absence of interbreeding and the independent evolutionary trajectory among Trans-Andean <i>Pimelodus </i>during their diversification history, a pre-requisite to define species limits. However, non-significant values of current gene flow were evidenced between them, supporting the hypothesis of full isolation.
description: <strong>Data from: Species limits and introgression in <em>Pimelodus</em> from the Magdalena-Cauca River basin</strong> José Gregorio Martínez, José David Rangel Medrano, Anny Johanna Yepes Acevedo, Natalia Restrepo Escobar, Edna Judith Márquez* *Corresponding author: Edna J. Márquez, Grupo de Investigación Biotecnología Animal, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 65 Nro. 59A – 110, Medellín, Antioquia, Colombia. Email: ejmarque@unal.edu.co <strong>Population module parameteres.txt </strong>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 <em>Pimelodus</em> species. <strong>Demultiplexing statistics.txt </strong>Contains the demultiplexing statistics (number of reads and its lenght) across 19 samples of <em>Pimelodus</em> species libraries obtained by Illumina Hi-Seq. <strong><em>De novo</em></strong><strong> loci assembling statistics.txt</strong> Contains the <em>de novo</em> loci assembling statistics (number of <em>loci</em>, number of polymorphic <em>loci</em> and number of SNPs) obtained after the RADproc software analysis across 19 samples of <em>Pimelodus</em> species libraries, using the optimized parameters, by – psweep mode. <strong>RADseqs Raw data Pimelodus.zip </strong>Contains the demultiplexed fastq files from 19 samples of <em>Pimelodus</em> species libraries obtained by Illumina Hi-Seq. <strong>Pimelodus.sumstats.summary.txt</strong> Contains the summary statistics of variant and fixed positions across <em>loci</em> for each of 19 samples of <em>Pimelodus, </em>after Stacks v.2.52 software analysis (Population module, --fstats). <strong>Pimelodus.var.phylip.txt</strong> Contains 999 variable sites for each of 19 samples of <em>Pimelodus</em> 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. <strong>Pimelodus.vcf.txt</strong> Contains the output SNPs and haplotypes in Variant Call Format (VCF) for 19 samples of <em>Pimelodus, </em>after Stacks v.2.52 software analysis (Population module, --vcf). <strong>rag2 alleles.txt</strong> Contains the 40 inferred phased alleles from <em>rag2</em> sequences from 20 individuals of <em>Pimelodus yuma</em> and <em>P. grosskopfii</em>, by using the application 'PHASE' of DnaSP v5.10.1. <strong>Confidence intervals.R</strong> 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).Funding provided by: Empresas Públicas de Medellín*<br>Crossref Funder Registry ID: <br>Award Number: CT-2019-000661Funding provided by: Universidad Nacional de Colombia, Sede Medellín*<br>Crossref Funder Registry ID: <br>Award Number: Hermes 40096Funding provided by: Institución Universitaria Colegio Mayor de Antioquia*<br>Crossref Funder Registry ID: <br>Award Number: FCSA-2017Funding provided by: Institución Universitaria Colegio Mayor de Antioquia*<br>Crossref Funder Registry ID: <br>Award Number: FCSA20
description: A RAD-seq library was prepared for 19 individuals representing five putative morphospecies of <em>Pimelodus</em>, previously identified by DNA barcoding: three corresponded to <em>P. grosskopfii, P. yuma and P. crypticus</em> from Magdalena-Cauca River basin and two corresponded to the cis-Andean <em>P. blochii</em> stricto sensu and <em>P. pictus</em>. Samples were provided by: 1) Integral S.A., through two scientific cooperation agreements (19th September 2013; Grant CT-2013-002443), 2) <em>Coleção de Tecidos de Genética Animal (CTGA) </em>of the <em>Laboratório de Evolução e Genética Animal (LEGAL)</em>, Federal University of Amazonas, Brazil, and by 3) Armando Ortega Lara from the <em>Museo de Ciencias Naturales del Instituto para la Investigación y la Preservación del Patrimonio Cultural y Natural del Valle del Cauca – INCIVA. </em>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, &amp; 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 &gt; 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, &amp; 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.