MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups. One such technocomplex where the maker is unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which covers an area in northwestern and central Europe from the UK to Poland. This paper presents the morphological and proteomic species identification, mitochondrial DNA analysis, and direct radiocarbon dating of human remains directly associated to an LRJ assemblage at the cave site of Ilsenhöhle in Ranis (Germany).  

Methods
DNA was extracted from skeletal remains identified as hominin from the site Ranis, Germany following the protocol described in Rohland et al., 2018 (buffer 'D') and then converted into single-stranded double-indexed libraries according to the automated protocol in Gansauge et al., 2020. Libraries from all specimens except R10873 were then enriched for human mitochondrial (mt) DNA via automated hybridization capture (Zavala et al., 2022). Enriched and non-enriched libraries were sequenced on Illumina platforms with paired-end sequencing. The ancient parameters for BWA (‘-n 0.01 –o 2 –l 16500’) were used for aligning reads to the revised Cambridge Reference Sequence (rCRS). Reads shorter than 35 basepairs or with mapping qualities less than 25 and PCR duplicates were removed. Consensus bases were called for positions with at least 5 reads and 80% support when masking C-to-T substitutions on the terminal seven positions of reads. The resulting sequences were realigned to the rCRS with previously published mtDNA genomes from 54 modern humans, 19 ancient humans, and two Neanderthals using MAFFT).