In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve sufficient amounts of ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1,686 per species) to characterize (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs, and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterize mitogenomes to an average depth-of-coverage of 19.4 to 2,003.7 -fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimize costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity change over space and time, including from environmental samples. Here we provide the fasta files of the probes.

Three soil profiles from the Eger floodplain in Nördlingen in southern Germany (NEP1, NEP2 and NEP3), were sampled and micropalaeontological data were collected. Samples were weighted, wet sieved through 125 µm, dried on a heating plate at <60°C, and studied under a stereomicroscope at the University of Jena, Germany. Some specific particles of interest (plant remains, charcoal, mollusc and brick fragments) were assessed in semiquantitative abundance classes for each sample, while all other particles of interest were picked and counted in absolute abundances. This includes Mollusca, Ostracoda, reworked microfossils, macrobotanical remains (seeds and fruits), and insect and bone fragments. Where possible, taxa were identified down to species level.The data allow to develop a palaeoenvironmental reconstruction through the soil profiles, and can provide information on fluvial activity, landscape development and the general hydrological situation through time. It can in combination with other data corroborate the correlation of the three profiles and the interpretation of the depositional history in the Eger floodplain.