DOI: 10.5281/zenodo.15529828
title: Metabolomics-Guided Genomic Comparisons Reveal Convergent Evolution of Hibernation Genes in Mammals

description: Genes Underlying Adaptive Physiological Shifts Among Hibernating Mammals========================================================================

This dataset accompanies the manuscript "Genes Underlying Adaptive Physiological Shifts Among Hibernating Mammals" and includes genomic, phylogenetic, and functional enrichment data to investigate the evolution of hibernation-associated traits—particularly carnitine metabolism—across mammals.

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1. Phylogenetic Resources-------------------------

- RERConverge_120MasterTree.tre  Format: Newick (.tre)  Description: Species tree of 120 mammals used in RERconverge to detect gene-specific evolutionary rate shifts.

- 206Species_MasterTree.tre  Format: Newick (.tre)  Description: Full species tree including 206 species across 404 carnitine-related genes. Used for pruning gene trees prior to selection analyses.

- 19610_mammalGeneTrees.txt  Format: Plain text (multi-line Newick)  Description: 19,610 protein-based gene trees across 120 mammalian genomes.

- 19610_mammalGeneTrees.trees  Format: Serialized (.trees, RERconverge-compatible)  Description: Serialized version of the same 19,610 gene trees for use in RERconverge pipelines.

- TimeTree_SpeciesList_Metadata.txt  Format: Plain text  Description: Species list and reconciliation notes for divergence time estimation using TimeTree. Notes include species replacements and manual placements.

2. Functional Enrichment Data-----------------------------

- RawEnrichmentData.xlsx  Excel file containing GO, KEGG, and UniProt-based functional enrichment analyses.

  SHEET DETAILS:  • Summary_Unique_Enrichment:    - GO terms uniquely enriched in genes under positive or relaxed selection.    - Terms not enriched in the full 371-gene carnitine dataset.    - Red text = uniquely enriched only in selection group.

  • ALL_371_GenesVS_ALL_Human:    - GO and pathway enrichment of all 371 carnitine-related genes vs. full human genome.

  • PosSelGenesVS_ALL_Human:    - Enrichment results for genes under positive selection.

  • RelaxedSelGenesVS_ALL_Human:    - Enrichment results for genes under relaxed constraint.

  • 33_RERGenes_VS_19610_background:    - Enrichment of RERconverge-significant genes (n=33) vs. full background of 19,610 genes.

-------------------------------------------------------------------------------DATA SOURCES AND REFERENCES-------------------------------------------------------------------------------

• Orthologs sourced from NCBI Ortholog Database.• Species tree: http://www.timetree.org

-------------------------------------------------------------------------------CITATION-------------------------------------------------------------------------------

If you use this dataset, please cite:

Drabeck, D.H., Perry, B.W., Iles, T.L. et al. "Genes Underlying Adaptive Physiological Shifts Among Hibernating Mammals." Dryad Dataset. https://doi.org/10.5061/dryad.sn02v6xgw