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Nuclear genomic data and mitochondrial DNA sequence alignment of ancient and modern Felis specimens

Version 1.0

Popović, Danijela, 2026, "Nuclear genomic data and mitochondrial DNA sequence alignment of ancient and modern Felis specimens", https://doi.org/10.18150/ZV9KIY, RepOD, V1

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Description

This dataset contains nuclear genomic data and a mitochondrial genome alignment.

Nuclear genomic data

Genomic data are provided in EIGENSTRAT format (dataset.geno, dataset.ind, and dataset.snp). The pseudohaploid dataset was generated using samtools mpileup and pileupCaller (sequenceTools) with the --randomHaploid option to randomly sample a single read per site.

The final dataset includes 154 genomes:

·      23 specimens generated in this study

·      56 modern specimens representing five Felis species (De Martino et al., 2025, DOI: 10.1126/science.adt2642)

·      3 museum specimens of European wildcats from Bulgaria (20th century)(De Martino et al., 2025, DOI: 10.1126/science.adt2642)

·      2 ancient specimens from the UK (Jamieson et al., 2023, DOI: 10.1016/j.cub.2023.08.031)

·      70 ancient genomes described in De Martino et al., 2025, DOI: 10.1126/science.adt2642

Prior to downstream analyses, the dataset was filtered for genotyping rate, minor allele frequency (MAF), and linkage disequilibrium (LD) using the following parameters: --geno 0.4 --maf 0.02 --indep-pairwise 10 2 0.4.

The final panel consists of 507,373 SNPs (transversions only), with an overall genotyping rate of 0.624962.

Mitochondrial genome alignment

The dataset also includes a multiple sequence alignment of mitochondrial genomes from ancient and modern Felis specimens.

(2026-11-02)
Subject
Earth and Environmental Sciences
Keyword

ancient DNA, palaeogenomics, Felis, introgression

Related Publication

doi:

CC BY - Creative Commons Attribution 4.0 CC BY - Creative Commons Attribution 4.0

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dataset.geno
Unknown - 23.2 MB - Nov 3, 2026 - 0 Downloads
MD5: 1aad3c0bde00c0e4e45da8a5e9486113
License: CC BY - Creative Commons Attribution 4.0
Genotype matrix containing allele counts (0, 1, 2) and missing data (9).
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dataset.ind
Plain Text - 5.7 KB - Nov 3, 2026 - 0 Downloads
MD5: 74ab340c66e31eec8152a82c53c28ddf
License: CC BY - Creative Commons Attribution 4.0
Individual identifiers, sex, and population assignments.
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dataset.snp
Plain Text - 30.5 MB - Nov 3, 2026 - 0 Downloads
MD5: b32771e1c8407504f323b6d99ae96d19
License: CC BY - Creative Commons Attribution 4.0
SNP identifiers, chromosome numbers, genetic and physical positions, and allele information.
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mtDNAalignement.fa
Plain Text - 1.3 MB - Nov 3, 2026 - 0 Downloads
MD5: 813b4049230815ced5cad68ee3fe0633
License: CC BY - Creative Commons Attribution 4.0
Mitochondrial genome alignment
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