My dataset includes the mitogenomes sequence (bam format file) of two Chinese straight-tusked elephants (genus: Palaeoloxodon, sample number: CADG1074 and CADG841).

We perform DNA extraction, library preparation, pre-sequencing, target-enrichment capture and sequencing procedures for fossil samples. After obtaining the Illumina raw reads, fastp v0.22.0 was used to trim adapters, remove reads shorter than 30 bp, and merge overlapping reads. Complete mitochondrial genome of P. antiquus (Genbank No: KY499558) was used as mapping references using the ‘aln’ algorithm in BWA v0.7.17. Reads with minimum mapping quality score below 30 were discarded by running ‘view’ and the remaining ones were sorted from 5' mapping position by using ‘sort’ in SAMtools v1.9. Potential PCR duplicates were removed using “rmdup”, and a final bam format file was obtained by merging all libraries using “merge” in SAMtools v1.9.

The data files will be required to be opened and edited using software GENEIOUS v.10 (http://www.geneious.com/).