Data from: Paleogenomics reveals arctic range and local dietary specialization in the American "cheetah", Miracinonyx trumani
Data files
Apr 07, 2026 version files 252.18 KB
-
README.md
10.26 KB
-
Table_S10.csv
6.75 KB
-
Table_S11.csv
463 B
-
Table_S4.csv
29.54 KB
-
Table_S5.csv
2.69 KB
-
Table_S6.csv
122.77 KB
-
Table_S7.csv
27.84 KB
-
Table_S8.csv
3.73 KB
-
Table_S9.csv
48.14 KB
Abstract
The extinct “American cheetah” (Miracinonyx trumani) has long been considered a North American ecological analog of the African cheetah (Acinonyx jubatus) based on convergent cursorial morphology, yet this paradigm rests on limited data and untested assumptions about its evolutionary relationships and ecology. Here, we generate nuclear paleogenomes from M. trumani specimens from Wyoming (~23 ka; thousand years ago) and Yukon (~31 ka), definitively placing this enigmatic felid within the evolutionary tree of cats. Phylogenomic analyses confirm M. trumani as sister to pumas (Puma concolor), not cheetahs, with divergence ~2.6 million years ago during rapid Plio-Pleistocene climate oscillations. The Yukon specimens extend the species' known range by over 20˚ latitude into the Arctic and stable isotope analyses reveal striking ecological differentiation, with the Yukon population occupying an elevated trophic position consistent with exploitation of anadromous fish while the Wyoming population functioned as a generalist terrestrial predator. Genomic scans identified positive selection in sensory perception genes associated with auditory processing and cognitive functioning and loss-of-function mutations in circadian regulators, providing mechanistic insights into behavioral flexibility. Rather than specialized pursuit predators, M. trumani exhibited remarkable ecological versatility, underscoring how morphological convergence can obscure the true diversity and complexity of extinct megafaunal ecosystems.
Dataset DOI: 10.5061/dryad.2ngf1vj3p
Description of the data and file structure
Data were collected to resolve the phylogenetic placement, biogeographic range, and paleoecology of Miracinonyx trumani ("American cheetah"). Data cover two specimen localities: Wyoming and Yukon . Stable isotope data include bulk stable isotope results for Miracinonyx specimens alongside published comparative data, as well as compound-specific stable isotope results, to facilitate dietary reconstruction and trophic position inference across populations. Genomic data include candidate genes identified through HyPhy BUSTED and aBSREL analyses testing for gene-wide and branch-specific positive selection, overlapping candidates between methods, SnpEff-predicted loss-of-function variants and associated missense mutation counts, and an exploratory aBSREL analysis with all branches tested. A summary of specimens and reference genomes used across analyses is also provided. All NA values indicate not applicable or data missing for that particular value. Empty cells indicate NA and do not represent missing or lost data.
Files and variables
File: Table_S4.csv
Description: Bulk stable isotope results for Miracinonyx specimens and published comparative data
Variables
- Taxon: Species or taxonomic identification of the specimen
- Region: Broad geographic region of specimen origin
- Site: Locality or site name where specimen was collected or recovered
- Latitude: Decimal latitude of specimen locality (degrees N)
- Longitude: Decimal longitude of specimen locality (degrees E/W)
- Museum: Institution housing the specimen
- Catalog_Number: Museum catalog or accession number uniquely identifying the specimen
- Radiocarbon_Lab: Laboratory that performed radiocarbon dating
- Radiocarbon_Age_14C_BP: Conventional radiocarbon age of specimen (years before present, BP; present = 1950 CE)
- Radiocarbon_Error: One-sigma analytical error on radiocarbon age (years)
- Cal_BP_From: Younger bound of calibrated radiocarbon age range (calibrated years BP)
- Cal_BP_To: Older bound of calibrated radiocarbon age range (calibrated years BP)
- Cal_BP_Median: Median calibrated radiocarbon age (calibrated years BP)
- delta13C_permil: Stable carbon isotope ratio expressed as δ¹³C (‰, per mil)
- delta13C_sd: Standard deviation of replicate δ¹³C measurements (‰)
- delta15N_permil: Stable nitrogen isotope ratio expressed as δ¹⁵N (‰, per mil)
- delta15N_sd: Standard deviation of replicate δ¹⁵N measurements (‰)
- C_to_N: Atomic carbon-to-nitrogen ratio of collagen extract
- Material: Skeletal element or tissue type sampled for isotope analysis
- Collagen_Extraction: Protocol or method used for collagen extraction prior to isotope analysis
- Radiocarbon_Method: Radiocarbon dating method used
- Reference: Citation for published data
- Notes: Miscellaneous notes on specimen quality, provenance, or data interpretation
File: Table_S5.csv
Description: Compound-specific stable isotope results for Miracinonyx specimens
Variables
- Date: Date of isotope analysis run
- Sample: Specimen or sample identifier
- Element: Skeletal element
- ASIF_ID: Internal lab identifier assigned by the Stable Isotope Facility (ASIF)
- Injections: Number of analytical injections used for the measurement
- AminoAcid: Amino acid analyzed
- d15N_Avg: Mean δ¹⁵N value for the amino acid across injections (‰, per mil)
- d15N_Stdev: Standard deviation of δ¹⁵N measurements across injections (‰)
File: Table_S6.csv
Description: Candidate genes identified by HyPhy BUSTED analysis testing for gene-wide positive selection
Variables
- ortho: Ortholog group identifier
- rna acccession: NCBI RNA accession number for the reference transcript
- gene_symbol: Gene symbol
- num_codons_ER>10: Number of codons with an evolutionary rate (ER) greater than 10, indicating sites under strong positive selection
- num_codons_tested: Total number of codons tested in the alignment
- LRT: Likelihood ratio test statistic comparing the positive selection model to the null model
- pval: P-value for the LRT
- functional_summary: Succinct functional summary from NCBI and UniProt data
- mouse_phenotype_summary: Summary of associated phenotypes from the Mouse Genome Informatics (MGI) database
- protein_name: Full protein name corresponding to the gene symbol
- ensembl_id: Ensembl gene identifier
- mgi_gene_id: Mouse Genome Informatics (MGI) gene identifier
- mgi_phenotypes: Phenotype terms associated with the gene from the MGI database
- go_terms: Gene Ontology (GO) terms associated with the gene
- codon_position_ER>10: Alignment positions of codons with ER > 10
- unconstratined_ER_per_codon_>10: Unconstrained (estimated) evolutionary rate at each codon position with ER > 10
File: Table_S7.csv
Description: Overlapping candidate genes identified by BUSTED and aBSREL analyses
Variables
- ortholog: Ortholog group identifier
- rna acccession: NCBI RNA accession number for the reference transcript
- gene_symbol: Official gene symbol
- BUSTED_num_codons_ER>10: Number of codons with evolutionary rate (ER) > 10 in the BUSTED analysis
- BUSTED_num_codons_tested: Total codons tested in the BUSTED analysis
- BUSTED_LRT: BUSTED likelihood ratio test statistic
- BUSTED_pval: BUSTED p-value
- aBSREL_LRT: aBSREL likelihood ratio test statistic for the Miracinonyx foreground branch
- aBSREL_pval: aBSREL p-value
- aBSREL_nonsyn_subs_per_site: Nonsynonymous substitutions per site estimated by aBSREL on the Miracinonyx foreground branch
- functional_summary: Succinct functional summary from NCBI and UniProt data
- mouse_phenotype_summary: Summary of associated phenotypes from the Mouse Genome Informatics (MGI) database
- protein_name: Full protein name corresponding to the gene symbol
- ensembl_id: Ensembl gene identifier
- mgi_gene_id: Mouse Genome Informatics (MGI) gene identifier
File: Table_S8.csv
Description: Candidate genes from aBSREL foreground (branch-specific) tests of positive selection
Variables
- ortholog: Ortholog group identifier
- PriBen_rna_accession: NCBI RNA accession number from the Prionailurus bengalensis (Asian leopard cat) reference
- Gene: Official gene symbol
- LRT: Likelihood ratio test statistic for the foreground branch test
- pval: P-value for the LRT; values ≤ 0.05 indicate significant branch-specific positive selection
- nonsyn_subs_per_site: Nonsynonymous substitutions per site on the Miracinonyx foreground branch
- rate_classes: Number of rate classes inferred by aBSREL for the foreground branch
- notes: Miscellaneous notes on gene function or result interpretation
File: Table_S9.csv
Description: SnpEff-predicted loss-of-function variants and associated missense mutation counts per gene
Variables
- shared_all: Gene name; genes listed share predicted LOF variants across both Miracinonyx specimens and both reference annotations
- moderate_high_mutation_count_puma: Count of moderate- and high-impact mutations (missense + LOF) against the puma (Puma concolor) reference alignment
- gene_length_puma: Length of the gene in the puma reference (base pairs)
- puma_norm_count_divided_length: Mutation count normalized by gene length for puma (moderate_high_mutation_count_puma / gene_length_puma)
- moderate_high_mutation_count_priben: Count of moderate- and high-impact mutations in the Prionailurus bengalensis (Asian leopard cat; "priben") reference alignment
- gene_length_priben: Length of the gene in the Prionailurus bengalensis reference (base pairs)
- priben_norm_count_divided_length: Mutation count normalized by gene length for P. bengalensis (moderate_high_mutation_count_priben / gene_length_priben)
- functional_summary: Succinct functional summary from NCBI and UniProt data
- mouse_phenotype_summary: Summary of associated phenotypes from the Mouse Genome Informatics (MGI) database
- description: Full gene name or description
- ensembl_id: Ensembl gene identifier
File: Table_S10.csv
Description: Candidate genes from aBSREL exploratory analysis with all branches tested
Variables
- ortho: Ortholog group identifier linking sequences across taxa
- rna_accession: NCBI RNA accession number for the reference transcript
- gene_symbol: gene symbol
- sig_branches: Number of branches in the phylogeny showing significant evidence of positive selection for this gene
- branches_tested: Total number of branches tested for this gene
- sig_branch: Identity of the branch(es) showing significant positive selection
- pval: P-value for the branch-specific test
- notes: Miscellaneous notes on gene function or result interpretation
File: Table_S11.csv
Description: Summary of samples and reference genomes used in each analysis
Variables
- Analysis: Name or description of the analysis performed
- Bluefish: Inclusion indicator for this specimen
- NTC: Inclusion indicator for this specimen
- YG 407.114: Inclusion indicator for this specimen
- YG 489.754: Inclusion indicator for this specimen
- UW 57220: Inclusion indicator for this specimen
- UW 57690: Inclusion indicator for this specimen
- Puma Reference Genome: Inclusion indicator for the Puma concolor reference genome; X means this was the reference genome for the analysis indicated
- Asian Leopard Cat Reference Genome: Inclusion indicator for the Prionailurus bengalensis reference genome; X means this was the reference genome for the analysis indicated
Code/software
All data files are provided in comma-separated values (.csv) format. No specialized software is required to view the data.
Access information
Other publicly accessible locations of the data:
- Raw sequencing data have been deposited in NCBI under BioProject ID PRJNA1413399. Mitochondrial genome assemblies are deposited in NCBI GenBank under accession numbers PZ050836, PZ055810, PZ055811, and PZ055812.