Data from: Dispersal across headwaters determines fish population structure between interdigitating river systems in the Guiana Shield highlands
Data files
Jun 13, 2026 version files 48.24 GB
-
Data-for-dryad-Morgan-et-al-2026-Pakaraimas.zip
48.24 GB
-
README.md
3.71 KB
-
Table-S1-Morgan-et-al-2026-sample-details.csv
6.88 KB
-
TableS2-Pakaraimas-loci-stats-2026.csv
3.02 KB
Abstract
Riverine aquatic species primarily occupy the dendritic networks that define river basins, and population-structure models for riverine taxa, including freshwater fishes, generally assume strictly longitudinal dispersal within these networks. River configurations, however, are dynamic: hydrologic connections change seasonally and over geologic time, potentially enabling out-of-network dispersal, a process that remains poorly studied. Because such dispersal violates key assumptions of existing models, its prevalence may require the development of new frameworks for understanding riverine population structure. To test for out-of-network connectivity between interdigitating river systems, we analyzed genetic population structure in Krobia potaroensis, a cichlid fish endemic to the rivers draining the Pakaraima Mountains in western Guyana, South America. We detected genetic associations among populations that do not correspond to contemporary river configurations, indicating historical or ongoing dispersal between adjacent river systems. These results demonstrate that within-network longitudinal dispersal cannot always be assumed and that alternative dispersal routes can shape population structure, genetic diversity, and genetic differentiation in riverine taxa.
Dataset DOI: 10.5061/dryad.jwstqjqpc
Genomic (RADseq) data for Krobia species (subfamily Cichlinae). Each sample has two associated fastq files, derived matrices are also included, as well as metadata for each individual.
Description of the data and file structure
Double digest RADseq data (RAW fastq and derived sequence matrices) for 79 Krobia individuals (Subfamily: Cichlinae) from across the Guianas of South America. Files are separated by individual with file names corresponding to metadata in the associated text files. Dataset corresponds to a phylogenetic dataset with broader representation of fishes within the genus (n=79), and more focused dataset that corresponds to fishes from within the rivers of the Pakaraima Mountains of western Guyana (n=63 and n=59). The data was used for phylogenetic analyses and population genetic analyses across a set of putatively disconnected river systems. The analyses and interpretations are further detailed in Morgan et al. (2026), Ecology and Evolution 16 (5), e73603.
Each individual (fish) has two FASTQ files (R1 & R2) corresponding to PE150 Illumina sequencing. From these raw files, as well as various output matrices generated by ipyrad. Files were generated with default parameters in ipyrad, but with a 0.85 clustering threshold, a minimum depth of 6 per locus. Each sequence/SNP-matrix was then generated using different thresholds for line 21 in the ipyrad params file "[min_samples_locus]". The minimum number of samples per included locus in the matrix is indicated in the file name for each matrix: e.g. "45of59" indicates a file that has data for 59 individuals with all loci that were present in at least 45 of those individuals (>75% in this example). Ipyrad then outputs the same dataset in multiple common formats (e.g. ".str" for STRUCTURE; Pritchard et al. 2000)
Files+folders
Files zipped within Data-for-dryad-Morgan-et-al-2026-Pakaraimas.zip
- "Demultiplexed-sequences": Folder containing raw fastq files, as described above and in Table S1.
- "ipyrad-output": Folder containing ipyrad outputs. Various SNP and sequence matrices. Three runs of ipyrad were used to generate these outputs. Default parameters were used in ipyrad, but with 0.85 clustering threshold and a minimum depth of 6. The differing matrices were generated by altering the number of samples included and the minimum number of individuals that needed to have the locus for it to be included (Line 21 in the parameters file).
Table-S1-Morgan-et-al-2026-sample-details.csv - Sample naming conventions, GPS coordinates, Species identities. ** indicate two samples originally listed as 'Kuri' (Kuribrong) are from within the Potaro River.
TableS2-Pakaraimas-loci-stats-2026.csv - genotype data stats for each individual after fastqs have been processed through ipyrad.
Code/software
The FASTQ files can be processed as in the manuscript using ipyrad (Eaton and Overcast 2020), but can be processed by any of the typical RADseq or alignment pipelines.
Csv files containing sample information can be viewed in any text editor or spreadsheet software.
References
Eaton, D. A. R., & Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq datasets. Bioinformatics, 36(8), 2592–2594. https://doi.org/10.1093/bioinformatics/btz966
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of Population Structure Using Multilocus Genotype Data. Genetics, 155(2), 945–959.