RAD-seq data from: Speciation with gene flow between two Neotropical sympatric species (Pitcairnia spp: Bromeliaceae)
Data files
Mar 12, 2026 version files 378.74 MB
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Outfiles_Ipyrad_relaxed.zip
4.81 MB
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Outfiles_Ipyrad_stringent.zip
4.81 MB
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README.md
6.45 KB
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Trinity_albiflos.fasta
185.41 MB
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Trinity_staminea.fasta
183.71 MB
Abstract
The study of mechanisms that generate new species is considered fundamental for broad areas of ecology and evolution. Speciation is a continuous process in which reproductive isolation is established, and it is of fundamental importance to understand the origins of the adaptations that contribute to this process. Hybrid zones are considered natural laboratories for the study of speciation and represent ideal systems for such studies. Here, we investigated genomic differentiation between hybridizing Neotropical species Pitcairnia staminea (G.Lodd.) and P. albiflos (Herb.). Using thousands of SNP genotyped through RAD-seq, we estimate effective population sizes, interspecific gene flow as well as the time of divergence between these two sister species and identify candidate genomic regions for positive selection that may be related to the reproductive isolation. By contrasting different scenarios of speciation using Approximate Bayesian Computation (ABC), we found evidence of divergence with a gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Pitcairnia species. The parameters estimations obtained through ABC suggested that P. albiflos population has a three-time larger effective population size than P. staminea and the divergence was estimated during the Pliocene (4.7 Mya; CI = 1.3-8.5 Mya), allowing such species to accumulate genome-wide differences. We also detected a total of 17 out of 4,165 loci under positive selection with high genetic differentiation (FST>0.85), 12 of these loci were annotated in de novo assembled transcriptomes of both species, and four candidate genes were identified to be putatively involved in reproductive isolation. These four candidate genes were previously associated with the function of pollen development, pollen tube germination and orientation, abiotic stress, and flower scent in plants, suggesting an interplay between extrinsic and intrinsic barriers in the evolution of reproductive isolation between such species.
https://doi.org/10.5061/dryad.qjq2bvqhw
Funding
Fundação de Amparo à Pesquisa do Estado de São Paulo
Conselho Nacional de Desenvolvimento Científico e Tecnológico – Brasil and Fundo de Apoio ao Ensino
Pesquisa e Extensão (FAEPEX) da pró-reitoria de pesquisa da Universidade Estadual de Campinas
Authors
Tavares, Marília, Universidade Estadual de Campinas
Ferro, Milene, Universidade Estadual Paulista
Leal, Bárbara, Universidade Estadual de Campinas
Palma-Silva, Clarisse, Universidade Estadual de Campinas
Citation
Tavares, Marilia; Ferro, Milene; Leal, Bárbara; Palma-Silva, Clarisse (Forthcoming 2026). RAD-seq data from: Speciation with gene flow between two Neotropical sympatric species (Pitcairnia spp: Bromeliaceae) [Dataset]. Dryad. https://doi.org/10.5061/dryad.qjq2bvqhw
Abstract
The study of mechanisms that generate new species is considered fundamental for broad areas of ecology and evolution. Speciation is a continuous process in which reproductive isolation is established, and it is of fundamental importance to understand the origins of the adaptations that contribute to this process. Hybrid zones are considered natural laboratories for the study of speciation and represent ideal systems for such studies. Here, we investigated genomic differentiation between hybridizing Neotropical species Pitcairnia staminea (G.Lodd.) and P. albiflos (Herb.). Using thousands of SNP genotyped through RAD-seq, we estimate effective population sizes, interspecific gene flow as well as time of divergence between these two sister species and identify candidate genomic regions for positive selection that may be related to the reproductive isolation. By contrasting different scenarios of speciation using Approximate Bayesian Computation (ABC), we found evidence of divergence with gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Pitcairnia species. The parameters estimations obtained through ABC suggested that P. albiflos population has a three-time larger effective population size than P. staminea and the divergence was estimated during the Pliocene (4.7 Mya; CI = 1.3-8.5 Mya), allowing such species to accumulate genome-wide differences. We also detected a total of 17 out of 4,165 loci under positive selection with high genetic differentiation (FST>0.85), 12 of these loci were annotated in de novo assembled transcriptomes of both species, and four candidate genes were identified to be putatively involved in reproductive isolation. These four candidate genes were previously associated with the function of pollen development, pollen tube germination and orientation, abiotic stress, and flower scent in plants, suggesting an interplay between extrinsic and intrinsic barriers in the evolution of reproductive isolation between such species.
Methods
We collected 24 specimens of Pitcairnia albiflos and P. staminea from the most well studied hybrid zone between these species, located in an inselberg named “Pão de Açúcar”, in the Serra do Mar Mountain located in Rio de Janeiro city, southeast Brazil. The genomic DNA was extracted from silica gel dried leaves of each sampled individual using the Qiagen DNA plant mini kit (Qiagen, Finland). Library preparation and sequencing of RAD markers from genomic DNA of the twelve samples from each species was performed by Floragenex Inc. (Eugene, Oregon) using the restriction enzyme SbfI and sample-specific barcodes. The amplification and single-ended sequencing (150 pb) were performed on a single lane of Illumina HiSeq 2000 platform.
The quality of raw reads was checked using FastQC v.0.11.3 (Andrews, 2014) and alignments were exported as bam files, sorted, and indexed using SAMtools version 0.1.16 (Li et al. 2009). The GC content was checked using BBMap v.35.85 (Bushnell, 2010) (Table S1; Supporting Information). We then used iPyrad v.0.7.30 (Eaton, 2014) to filter low quality base calls (Q<20), trim adaptors and perform de novo assembly using the vsearch tool (Rognes et al., 2016).
The de novo transcriptome assembly was performed using Trinity (version 2.0.6, Grabherr et al., 2011) with default parameters, assembling together reads from leaves and flowers tis- sues per each species (P. albiflos and P. staminea)
Description of files
DE NOVO ASSEMBLED RAD-SEQ DATA
The compressed folder Outfiles_Ipyrad_stringent.zip contains the stringent parameter file and the results from de novo assembly using two different filters for missing data: allowing a maximum of 25% missing data per locus (stringent_2.vcf) and no missing data (stringent_1.vcf) and a dataset filtered for outliers (stringent_3.vcf).
- params_stringent.txt - params used for stringent dataset
- stringent.phy - stringent assembly phy file
- stringent.vcf - stringent assembly vcf file
- stringent.loci - stringent assembly loci file
- stringent.hdf5 - stringent assembly hdf5 file
- stringent.snps - stringent assembly snps file
- stringent.snps.map - stringent assembly snps.map file
- stringent_stats.txt - stringent assembly stats file
The compressed folder Outfiles_Ipyrad_relaxed.zip contains the relaxed parameter file and the result from de novo assembly.
- params_relaxed.txt - params used for relaxed dataset
- pitcairnia.phy - relaxed assembly phy file
- pitcairnia.vcf - relaxed assembly vcf file
- pitcairnia.loci - relaxed assembly loci file
- pitcairnia.hdf5 - relaxed assembly hdf5 file
- pitcairnia.snps - relaxed assembly snps file
- pitcairnia.snps.map - relaxed assembly snps.map file
- pitcairnia_stats.txt - relaxed assembly stats file
For all files, the samples of Pitcairnia albiflos strats with "alb" and Pitcairnia staminea starts with "sta".
LOCI UNDER SELECTION ANALYSIS
The file Trinity_staminea.fasta and Trinity_albiflos.fasta contains the RNA assembly.
Files on Zenodo, Supplemental Information
Table transcripts_KaKs>1.xlsx contains transcripts shown to be under positive selection by kaks analysis.
Table FST_values_Stringent_II.xlsx contains FST values for each locus of dataset Stringent II.
ABC ANALYSIS
The file locfile_alb_sta.txt is the file used as input for msABC simulations.
We collected 24 specimens of Pitcairnia albiflos and P. staminea from the most well studied hybrid zone between these species, located in an inselberg named “Pão de Açúcar”, in the Serra do Mar Mountain located in Rio de Janeiro city, southeast Brazil. The genomic DNA was extracted from silica gel dried leaves of each sampled individual using the Qiagen DNA plant mini kit (Qiagen, Finland). Library preparation and sequencing of RAD markers from genomic DNA of the twelve samples from each species was performed by Floragenex Inc. (Eugene, Oregon) using the restriction enzyme SbfI and sample-specific barcodes. The amplification and single-ended sequencing (150 pb) were performed on a single lane of Illumina HiSeq 2000 platform.
The quality of raw reads was checked using FastQC v.0.11.3 (Andrews, 2014) and alignments were exported as bam files, sorted, and indexed using SAMtools version 0.1.16 (Li et al. 2009). The GC content was checked using BBMap v.35.85 (Bushnell, 2010) (Table S1; Supporting Information). We then used iPyrad v.0.7.30 (Eaton, 2014) to filter low quality base calls (Q<20), trim adaptors and perform de novo assembly using the vsearch tool (Rognes et al., 2016).