Abstract
Data supporting "Exceptional Mitochondrial Diversity Under Strong Purifying Selection in Admixed Populations, and How Reference Choice Can Mask It" (Fundulus heteroclitus mitochondrial genomics). Analysis code is at https://github.com/DLCrawford/MT_Genomics.
141_MT_variants.vcf.gz (+ .tbi) is the analysis-ready variant call set: 927 variable protein-coding sites across 141 individuals, with per-cell GT/DP/AD and SnpEff annotation. It reproduces the core F. heteroclitus results (variant counts, dN/dS, haplotypes, per-clade analyses).
pileup_cds_141.vcf.gz (+ .tbi) is a per-base read-count table across the coding region — one row for each of the 11,395 CDS positions (all 13 protein-coding genes) for all 141 individuals, recording DP (read depth) and AD (allelic depths) at every position, whether variable or not. It is required for the heteroplasmy analysis (including private-ALT sites).
The five .tsv tables are per-site nucleotide diversity (π) and Watterson's θ for the cross-species comparison (manuscript Table 5), one set per comparison dataset. They allow the comparison table to be regenerated without re-downloading the third-party source data (gnomAD, Lankheet et al. 2026, CaeNDR, DGRP).
MT_Genomics_metafile.txt maps each individual (matching the VCF sample IDs) to population (DC/PA/TR), sex, mitochondrial clade (N/S), mass, and plate well.
Files
> 141_MT_variants.vcf.gz (+ .tbi) — 141-sample, 927-variant coding call set (all Fhet analyses)> pileup_cds_141.vcf.gz (+ .tbi) — per-position DP/AD pileup, 11,395 CDS sites × 141 individuals (heteroplasmy)> dros_pi_results.tsv — Drosophila (DGRP) π/θ — Table 5> celegans_pi_per_site.tsv — C. elegans (N=540) π/θ — Table 5> human_mt_pi_per_site.tsv — human, sub-Saharan African, whole-mt (Lankheet et al. 2026, N=1,176) — Table 5> human_mt_cds_pi_per_site.tsv — human, sub-Saharan African, CDS — Table 5> amr_pi_per_site.tsv — human, AMR admixed (gnomAD v3.1, N=5,718) — Table 5> MT_Genomics_metafile.txt — per-individual metadata (population, sex, clade, mass, plate well)