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: Extended_Table_1.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: Extended_Table_2.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: Extended_Table_3.csv

Description: Overlapping candidate genes identified by BUSTED and aBSREL analyses after substitution-evidence filtering.

Variables

• ortholog: OrthoFinder ortholog group identifier
• rna id: NCBI RNA accession number for the reference transcript (Prionailurus bengalensis annotation)
• gene name: Gene symbol
• busted_p: BUSTED uncorrected p-value
• busted_q: BUSTED Benjamini-Hochberg FDR-corrected q-value (computed across all valid BUSTED tests)
• busted_LRT: BUSTED likelihood ratio test statistic
• busted_num_codons_tested: Total codons tested in the BUSTED analysis
• busted_num_codons_ER_gt10: Number of codons with evidence ratio (ER) > 10 in the BUSTED constrained model (sites contributing most strongly to the positive-selection signal)
• busted_n_NS: Non-synonymous substitutions counted on the foreground branch
• busted_n_NS_unambig: Non-synonymous substitutions on the foreground branch at alignment columns where parent and root codons were unambiguously called
• busted_n_S: Synonymous substitutions counted on the foreground branch
• absrel_p: aBSREL uncorrected p-value for the Bluefish Caves foreground branch
• absrel_q: aBSREL Benjamini-Hochberg FDR-corrected q-value (computed across all valid aBSREL tests)
• absrel_LRT: aBSREL likelihood ratio test statistic
• absrel_rate_classes: Number of ω rate classes fit by aBSREL on the foreground branch
• absrel_baseline_BL: Baseline MG94xREV branch length on the foreground branch
• absrel_full_adaptive_BL: Branch length on the foreground branch under the full adaptive model
• absrel_nonsyn_subs_per_site: Non-synonymous substitutions per site on the foreground branch (full adaptive model)
• absrel_syn_subs_per_site: Synonymous substitutions per site on the foreground branch (full adaptive model)
• absrel_n_NS: Non-synonymous substitutions counted on the foreground branch
• absrel_n_NS_unambig: Non-synonymous substitutions on the foreground branch at alignment columns where parent and root codons were unambiguously called
• absrel_n_S: Synonymous substitutions counted on the foreground branch

File: Extended_Table_4.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: Extended_Table_5.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

File: Extended_Table_6.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: Extended_Figure_1.png

Description: Quantile-quantile (Q-Q) plots of uncorrected p-values from BUSTED and aBSREL selection tests on the M. trumani foreground branch, plotted against the uniform null expectation.

File: Extended_Figure_2.png

Description: Boxplot comparing transcript lengths (kb, log10 scale) of candidate genes vs. background single-copy orthologs, generated to assess long-gene bias in the candidate set. Long genes can artificially inflate likelihood ratio test statistics in selection scans due to greater statistical power on longer alignments; this figure tests whether our candidate set is enriched for unusually long transcripts. Wilcoxon rank-sum test comparing transcript lengths in the "Both" candidate set vs. the background ortholog set; p = 0.137, indicating no significant long-gene bias.

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.