Metabolomics-Guided Genomic Comparisons Reveal Convergent Evolution of Hibernation Genes in Mammals

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. -------------------------------------------------------------------------------FILE DESCRIPTIONS------------------------------------------------------------------------------- 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