DOI: 10.5061/dryad.rr4xgxd93
title: Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin

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 Pimelodus from the Magdalena-Cauca River basin, this study
 tested the hypothesis that P. yuma, P. grosskopfii and P. crypticus
 represent three independently evolving species and explored signals of
 interspecific hybridization. Likewise, we test the ancient hypothesis that
 the trans-Andean Pimelodus yuma and P. crypticus belong to the cis-Andean
 P. blochii species complex. The outcomes based on mitochondrial (cox1) and
 nuclear [RADseq (Illumina Hi-Seq), microsatellites and rag2] markers
 combined with coalescence-based and allele-frequency methods, confirm that
 each studied trans-Andean species represent an independently evolving
 unit. We used Stacks v.2.52 for de novo SNP genotyping. Contrary to
 expectations, P. yuma was found as a sister clade of P. blochii, while P.
 crypticus (confused for a long time with P. blochii) was phylogenetic
 closer to P. grosskopfii. Additionally, we found strong evidence of
 historical introgression between the non-sibling species Pimelodus yuma
 and P. grosskopfii, breaking the absence of interbreeding and the
 independent evolutionary trajectory among Trans-Andean Pimelodus 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: 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, & 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,
 & 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.
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).