Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin
Creators
- 1. Institución Universitaria Colegio Mayor de Antioquia
- 2. Universidad Nacional de Colombia
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.
Notes
Data from: Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin
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
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).
Funding provided by: Empresas Públicas de Medellín*
Crossref Funder Registry ID:
Award Number: CT-2019-000661
Funding provided by: Universidad Nacional de Colombia, Sede Medellín*
Crossref Funder Registry ID:
Award Number: Hermes 40096
Funding provided by: Institución Universitaria Colegio Mayor de Antioquia*
Crossref Funder Registry ID:
Award Number: FCSA-2017
Funding provided by: Institución Universitaria Colegio Mayor de Antioquia*
Crossref Funder Registry ID:
Award Number: FCSA20
Files
De_novo_loci_assembling_statistics.txt
Additional details
Related works
- Is derived from
- 10.5061/dryad.rr4xgxd93 (DOI)