Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression.

The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in South-east Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity. We found 1725 polymorphic sites (810 singletons, 853 parsimony-informative sites and 57 indels), 701 unique haplotypes, a haplotype diversity of 0.9995 and a nucleotide diversity of 0.0015. In addition to the dominant T3 and several rare haplogroups (Q, T5, T4, T2 and T1), we have identified maternal line in Austrian Murbodner cattle that possess surviving aurochs' mitochondria haplotype P1 that diverged prior to the Neolithization process. This is convincing evidence for rare female-mediated adaptive introgression of wild aurochs into domesticated cattle in Europe. We revalidated the existing haplogroup classification and provided Bayesian phylogenetic inference with a more precise estimated divergence time than previously available. Occasionally, classification based on partial mitogenomes was not reliable; for example, some individuals with haplogroups P and T5 were not recognized based on D-loop information. Bayesian skyline plot estimates (median) show that the earliest population growth began before domestication in cattle with haplogroup T2, followed by Q (~10.0-9.5 kyBP), whereas cattle with T3 (~7.5 kyBP) and T1 (~3.0-2.5 kyBP) expanded later. Overall, our results support the existence of interactions between aurochs and cattle during domestication and dispersal of cattle in the past, contribute to the conservation of maternal cattle diversity and enable functional analyses of the surviving aurochs P1 mitogenome.

Radiographic analysis and virtual cleaning of a bioarchaeological remain enclosed in mineral deposits from a limestone cave.

In limestone caves, environmental processes often cause alterations of human or animal skeletal remains, complicating classical analytical methods. Exemplary, a proximal femoral skeletal fragment, enclosed by a thick layer of speleothemic calcite deposits, was discovered during the exploration of the Bedara cave in Zumberak, Croatia. An examination without removal of the surrounding mineral deposits, possibly leading to damage of the specimen, was, therefore, desirable.We describe and discuss the applied techniques, including clinical computed tomography, virtual cleaning by a specially developed segmentation protocol using an open-source DICOM viewer, and virtual visualisation and dimensioning using computer-aided design software, so that this "hidden" specimen could be non-invasively examined in great detail. We also report on the circumstances and origin of the find, the results of radiocarbon dating, and its anatomical and taxonomic identification, according to which, the bone fragment belonged to a wild boar (Sus scrofa) from the timeframe of the Middle Eneolithic Retz-Gajary culture in the region (4,781 ± 35 years before present). This study provides a reference for future paleontological and anthropological analyses, seeking to unlock the enormous potential of anatomical studies of comparable skeletal remains that are either petrified or enclosed in speleothemic deposits.

Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition.

Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000-29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1-G3 These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.

Diet at the Roman Village of Virovitica Kiskorija South, Croatia.

The Virovitica Kiskorija South site was a Roman village. In this paper archaeological, archaeobotanical, and archaeo-zoological finds are presented and interpreted, then compared with similar sites and information available from ancient sources. The site was divided into complexes that made a whole. The finds within each complex are presented and compared to similar archaeological sites, as well as data from ancient written sources. The goal of the paper is to determine which kind of diet was present at this Roman village in Pannonia, and to analyze the differences and similarities between this village and analogous sites.