Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

Dogs in Lithuania from the 12th to 18th C AD: Diet and Health According to Stable Isotope, Zooarchaeological, and Historical Data.

This article presents the results of research that focused on the nutrition and related health issues of medieval and early modern dogs found in the territory of present-day Lithuania. In this study, we present bone collagen carbon (δ13C) and nitrogen (δ15N) isotope ratios for seventy-five dogs recovered from seven sites which were dated back to the between the 12th and 18th C AD. In addition, by studying the remains of almost 200 dogs, we were able to estimate changes in the sizes and morphotypes of canines across over 600 years. On the basis of stable isotope and historical data, as well as the osteometric analysis, we discuss the dietary patterns of different sizes and types of dogs from the sites related to different social strata and time periods. The results of our study demonstrate that the size, type, diet, and health of canines from different time periods and sociocultural environments varied. Overall, carbon isotopic signals indicate that dogs' diets were based on C3 plant environment foods (cereals and animals), while freshwater fish was more important for some individuals in coastal Klaipeda/Memelburg Castle. The stable isotope analysis supported the historical records, indicating that cereals were highly important in the diet of elite dogs. Meanwhile, urban dogs had a different nutrition. In the Middle Ages, the consumption of plant-based foods was likely higher compared to the early modern period. Our study also revealed that the diets of dogs did not correlate with individual size. Compared to pigs, dogs had a higher intake of animal foods in their diet. In general, the nutrition of the studied canines was similar to that of the rural human population of the same period.

Carbon, nitrogen and sulphur isotope data of archaeological fish and mammal bone collagen from Lithuania.

Until relatively recently, stable sulphur isotope analysis of bone collagen was seldom undertaken in bioarchaeological research. With increasing frequency, its application has proven useful in reconstructing palaeodiets and palaeoecologies, as well as identifying potential migration and mobility patterns. Here, sulphur (δ34S) isotope analysis, together with carbon (δ13C) and nitrogen (δ15N), was performed on six fish and 34 mammal bone collagen samples from 14 prehistoric sites in Lithuania dating from the Late Mesolithic (ca. 7000-5000 cal BC) to the Late Bronze Age (ca. 1100-500 cal BC). We present the first δ34S data from Lithuania, including coupled δ13C and δ15N data, offering a crucial dataset for future research to explore spatial and temporal variability in the region and beyond.

Horses in Lithuania in the Late Roman-Medieval Period (3rd-14th C AD) Burial Sites: Updates on Size, Age and Dating.

The tradition of burying horses in Lithuania lasted from the Early Roman period until the late 14th C AD. It was the longest-lasting custom in Europe, which has left about 2000 known horse burials. This paper publishes the osteometric data and age of horses found in Lithuanian cemeteries and castles of the 3rd-14th C AD, over 200 individuals in total. These are the remains of all the horses still stored in Lithuanian institutions. The paper discusses the dynamics of horse body size in order to test previously suggested hypotheses regarding the relationship between large horse body size and its military use, possibly non-local breed, and high social status of the owner. Moreover, we are publishing the AMS 14C dates of 13 horses previously assigned to the Migration period. The research results corrected the existing chronology. The abundant data also allowed an assessment of the development of the size and age of the horses in Lithuania between the 3rd and 14th C AD. Osteometric analyses have shown that Late Roman-post-Migration-period horses were unusually large compared to the Viking and medieval horses in Lithuania. Meanwhile, we suggest that the semi-slender-legged 118-125-cm-tall horse, which predominated in the Viking period, is the most consistent with the local horse type. In general, the horses in Lithuania in the 3rd-11th C AD were small compared to those in Central and Western Europe or Scandinavia. More significant changes can be observed in the Middle Ages. In the 12-14th C AD, there was a much greater variety of horses and the expansion of taller (140-150 cm) individuals. However, the continued abundance of small horses in the medieval times, found buried with saddles and other equipment, allows one to renew the debate on the formation of the cavalry, the tactics of combat, and the social composition of horsemen in Lithuania.

Diet patterns in medieval to early modern (14th-early 20th c.) coastal communities in Lithuania.

Coastal residents are quite often expected to consume a significant amount of aquatic resources, though historical evidence often reveals a rather complex diet. To better understand the actual consumption and the distribution of various foods, stable isotope (δ13C and δ15N) analyses were employed to skeletal remains from three coastal communities, Palanga, Kretinga and Smelte, ranging in date from the medieval period to the early modern ages (14th-early 20th c.) near the Curonian Lagoon and the Baltic Sea in Lithuania. Animal bones from the region, covering the same time periods, were also analysed. Stable isotope results were compared with historical records. According to historical sources different types of diet were prevalent during that period of time: Medieval Prussian-Lithuanian peasant, Lithuanian fisherman, German urban, and religious-based. Elevated δ15N values for Smelte samples suggest a diet consisting of considerable amounts of freshwater fish protein, which is in contrast to historical sources. There were no significant differences in stable isotope values between males and females, while subadult δ15N values were significantly higher than adult ones, indicating that those children were breastfed for an extended period. Meanwhile, Palanga and Kretinga samples had isotope values suggesting a high reliance on terrestrial resources and a peasant type of diet.

Diet, cuisine and consumption practices of the first farmers in the southeastern Baltic.

With the arrival of the Early Neolithic Globular Amphora and Corded Ware cultures into the southeastern Baltic, ca. 2900/2800-2400 cal BC, a new type of economy was introduced, animal husbandry. However, the degree to which this transformed the subsistence economy is unknown. Here, we conducted organic residue analyses of 64 ceramic vessels to identify their contents. The vessels were sampled from 10 Lithuanian archaeological sites dating across the Subneolithic-Neolithic transition to the Early Bronze Age (ca. 2900/2800-1300 cal BC). Our results demonstrate that regardless of location or vessel type, many ceramics were used to process aquatic resources. Against our expectations, this association continued even after marked economic change concurrent with the migration of pastoralists from central and southeastern Europe, as evidenced by recent ancient DNA analysis of human remains. Moreover, we observed dairy fats in pottery from all cultures of the Early Neolithic (i.e. Rzucewo, Globular Amphora and Corded Ware) but unlike other regions of Europe, it seems that these were incorporated into indigenous culinary practices. Furthermore, some vessels were used to process plant foods, and others may have been used for the production and/or storage of birch bark tar. However, evidence for domesticated plant processing, for example millet, was absent. We show that organic residue analysis of pottery provides a different picture of past consumption patterns compared to the stable isotope analysis of human remains from isolated burials where a clear dietary shift is evident.

Adapt or die-Response of large herbivores to environmental changes in Europe during the Holocene.

Climate warming and human landscape transformation during the Holocene resulted in environmental changes for wild animals. The last remnants of the European Pleistocene megafauna that survived into the Holocene were particularly vulnerable to changes in habitat. To track the response of habitat use and foraging of large herbivores to natural and anthropogenic changes in environmental conditions during the Holocene, we investigated carbon (δ13 C) and nitrogen (δ15 N) stable isotope composition in bone collagen of moose (Alces alces), European bison (Bison bonasus) and aurochs (Bos primigenius) in Central and Eastern Europe. We found strong variations in isotope compositions in the studied species throughout the Holocene and diverse responses to changing environmental conditions. All three species showed significant changes in their δ13 C values reflecting a shift of foraging habitats from more open in the Early and pre-Neolithic Holocene to more forest during the Neolithic and Late Holocene. This shift was strongest in European bison, suggesting higher plasticity, more limited in moose, and the least in aurochs. Significant increases of δ15 N values in European bison and moose are evidence of a diet change towards more grazing, but may also reflect increased nitrogen in soils following deglaciation and global temperature increases. Among the factors explaining the observed isotope variations were time (age of samples), longitude and elevation in European bison, and time, longitude and forest cover in aurochs. None of the analysed factors explained isotope variations in moose. Our results demonstrate the strong influence of natural (forest expansion) and anthropogenic (deforestation and human pressure) changes on the foraging ecology of large herbivores, with forests playing a major role as a refugial habitat since the Neolithic, particularly for European bison and aurochs. We propose that high flexibility in foraging strategy was the key for survival of large herbivores in the changing environmental conditions of the Holocene.