Origin and Fate of Supergenes in Atlantic Cod: Phylogenetic Analysis Files

Michael Matschiner from the University of Oslo provides input and output files for phylogenetic analyses of Atlantic cod and related species. The dataset includes alignments, configuration files, and result trees for divergence time and introgression analyses using tools like StarBEAST2, AIM, Dsuite, IQ-TREE, PLINK, SNAPP, and Relate. It supports research into supergene evolution and population history within the Gadinae subfamily.

Use Cases

• Estimating divergence times among Gadinae species based on StarBEAST2 input and output files.
• Analyzing introgression signals among Gadus, Arctogadus, and Boreogadus using Dsuite and IQ-TREE datasets.
• Investigating linkage disequilibrium within specific supergene regions of Gadus morhua using PLINK map and ped files.
• Reconstructing demographic history of Gadus morhua populations with Relate input data.

Strengths

• Dataset is associated with a specific research project and author from the University of Oslo.
• Includes files for multiple established phylogenetic analysis tools (StarBEAST2, Dsuite, PLINK, etc.), suggesting methodological breadth.
• Focuses on specific genomic regions (supergenes) and species groups (Gadus, Arctogadus, Boreogadus) for targeted analysis.

Limitations

• Row count and file sizes are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Michael Matschiner, University of Oslo, via paperswithcode.

Collection Method

Likely generated from genomic sequencing data for phylogenetic analysis.

Geography

Primarily Atlantic cod (Gadus morhua) and related Gadinae species.