With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

There have been various explanations in archaeological literature about whether the earliest Bronze Age stone-cist graves and the first Pre-Roman Iron Age tarand graves in Estonia were built by locals or non-locals. As to possible immigrations, the stone-cist graves have been often related to Scandinavian populations, whilst early tarand graves allegedly had roots in eastern directions. The oldest known examples of these cemetery types are at Jõelähtme and Muuksi for stone-cist graves, and at Ilmandu and Kunda for early tarand graves, in the coastal zone of northern Estonia. In order to test the migration hypothesis we carried out a bioarchaeological study, measuring and mapping local biologically available Sr and O isotope ratios and analysing stable isotope signals of altogether eight individuals from these early stone-cist and tarand graves. The study material was chosen on the basis of the oldest AMS dates of skeletons available so far, or according to the earliest burial constructions in the cemeteries. Based on the comparison of local biologically available Sr and O isotopic baseline results and the results obtained from the individuals, we can talk about migrants in the case of two persons from Kunda and perhaps one from Muuksi, whilst most of the individuals analysed are of local origin. Thus, the idea of Early Metal Period migrations to Estonia from the surrounding regions is supported to some extent. However, the discussion of these migrations might turn out to be surprisingly different from what is expected on the basis of material culture. We also emphasise the importance of further analysis, especially mapping isotopic baseline data in the eastern Baltics, in order to draw further conclusions about the directions and extent of prehistoric migration in this region.

Although sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mitochondrial hypervariable region in 115 ancient sheep from 71 sites in Estonia (c. 1200 BC–AD 1900s), 19 ancient samples from Latvia, Russia, Poland and Greece (6800 BC–AD 1700), as well as 44 samples of modern Kihnu native sheep breed. Our analyses revealed: (1) 49 mitochondrial haplotypes, associated with sheep haplogroups A and B; (2) high haplotype diversity in Estonian ancient sheep; (3) continuity in mtDNA haplotypes through time; (4) possible population expansion during the first centuries of the Middle Ages (associated with the establishment of the new power regime related to 13^th century crusades); (5) significant difference in genetic diversity between ancient populations and modern native sheep, in agreement with the beginning of large-scale breeding in the 19^th century and population decline in local sheep. Overall, our results suggest that in spite of the observed fluctuations in ancient sheep populations, and changes in the natural and historical conditions, the utilisation of local sheep has been constant in the territory of Estonia, displaying matrilineal continuity from the Middle Bronze Age through the Modern Period, and into modern native sheep.