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Log Size Indexes (LSI) allow the increase of the number of data and have been used in a number of zooarchaeological studies since 1950. However, some standards to calculate the log ratios remain unpublished, the calculation of the indexes can be tedious, and it is further hindered by the diversity of data recording practices. The R package ‘zoolog’ enables calculation of thousands of log-ratios in seconds, with the advantage that the users can choose between different public references, which increases the repeatability and comparability of the results, allowing the smooth integration of references and databases with heterogeneous nomenclatures. Alternatively, the users may use their own references. This paper presents the main functionalities and procedures enabled by the package ‘zoolog’, together with some examples of use. A real dataset and several examples with R code are provided with the aim of facilitating osteometrical analyses in zooarchaeology.

The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.

Animal management is shaped by its environmental and landscape context, but these factors are rarely investigated quantitatively in zooarchaeological studies. Here we aim to examine the relationship between trends in zooarchaeological data and environmental and climatic dynamics between the Middle Bronze Age and Late Antiquity in lowland northern Italy (Po–Friulian Plain). This region provides an ideal test case to investigate the impact of landscape variables (precipitation, solar irradiance, elevation, soil characteristics) and climate evolution due to the area's relatively homogenous topography and climatic conditions. This study presents a new elaboration and visualisation of zooarchaeological data from northern Italy, investigates correlations between these data and landscape variables, and contextualises trends in relation to regional environmental and climate proxies at two scales. This analysis reveals a shift towards more heterogeneous livestock on a regional level during the Late Iron Age and Roman period, and strong evidence for a correlation between cattle representation and local soil characteristics at a site-level during the Bronze Age. Consideration of climate data shows little relationship between species representation, livestock body size, and climate proxies, indicating that human social dynamics rather than climate change were the primary driver to changes in animal management on the regional macro-scale.

The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint.

Domesticated dogs have been present in the Iberian Peninsula long before other domesticated species, back to the late Palaeolithic period. Their origin is still uncertain, but dogs were already well established during the Chalcolithic period (ca. 5000–4000 BP). This study employed a multidisciplinary approach comprising osteometric, radiographic and palaeogenomic analyses to characterize Chalcolithic Iberian Canis remains. Two Chalcolithic archaeological sites – Leceia, Oeiras, in Portugal, and El Casetón de la Era, Villalba de los Alcores, Valladolid, in Spain – were the main focus of this study. Osteometric and odontometric data from eleven other sites in Iberia were also included. Osteometric results show signs of phenotypic variability, likely the result of human-driven selective pressure. Dental radiographic and dental wear analyses allowed age at death estimation for four individuals (two juvenile and two adults). Three Chalcolithic Iberian dogs had their mitogenomes resequenced and the mitochondrial DNA analysis allowed to assign each individual to two of the major known haplogroups – A and C. Molecular sex infered by the chromosomeX/chromosome1 coverage ratio allowed to identify one female and two males. This study unveils some aspects of the Iberian Chalcolithic dogs: these dogs already exhibited various morphotypes whose profiles might be associated to the performance of certain tasks, as well as mitogenomes of two distinct lineages that help tracking the evolutionary paths of Iberian dogs.

Roman conquest is known to have had a significant impact on animal husbandry across the Western provinces. Northern Italy is no exception, and zooarchaeological studies have demonstrated a variety of developments to livestock exploitation during Roman times. However, several of these developments have origins in later prehistory, well before Roman political hegemony in the region. In particular, significant size increases in cattle and sheep during the Iron Age point to an early re-organisation of livestock management, which was further impacted in Roman times. This presentation explores zooarchaeological evidence for changes in husbandry strategies in northern Italy over later prehistory and the Roman period through NISP, biometry, and age data, attempting to characterise similarities and differences in these two waves of change. Results are contextualised with historical evidence for Roman farming in Italy and environmental/landscape data in order to better understand the role of livestock in the regional agricultural economy and its development through the Roman period.

This paper explores changes in cattle size in the North-East (NE) and South-West (SW) of the Iberian Peninsula from Chalcolithic to Roman times. Zooarchaeological data are contextualised with the ecological characteristics and settlement pattern of both areas. Results reveal significant differences in cattle size and morphology between the two areas, as well as changes through time. Integration of zooarchaeological, ecological and settlement data suggest that orography played a significant role both in the changes in settlement pattern and in the evolution of cattle morphology in the two regions. In this sense, the flatter orography and higher solar irradiation in the SW would have provided better ecological conditions for cattle husbandry. In addition, exchanges of animals were probably easier in the SW compared with the hillier orography of the NE. The Roman conquest had a different impact on cattle size as well: a clear size change was visible in the NE (where Iron Age cattle were very small), whereas size increase was more subtle in the SW. In both areas, cattle remained smaller compared to the large animals attested in North-Western Europe in Roman times (e.g. the Netherlands and France). These results provide a diachronic and wide territorial perspective to better assess what were the factors (ecological and/ or social) that contributed to the changes observed on cattle size at two opposite sides of the Iberian Peninsula.

Cattle played a major role in the Roman economy. The zooarchaeological record indicates a general size increase across Europe, and many urban sites display higher cattle frequency remains compared to previous and later periods. The reasons for this size increase remains unknown: was it the result of the import of new lineages, related to wider mobility and trade networks? Or a consequence of selection and improvement of local stock using new breeding strategies? Or both? While morphological changes such as size increase, as detected in bone measurements, indicate improvement for larger animals, ancient DNA enables tracking changes in genomic diversity associated with mobility and animal selection traits. We aim to understand whether the Roman state enhanced cattle genetic diversity in the Western periphery using genomics. We generated whole-genome shotgun resequencing data (Illumina HiSeqX) to analyze around 100 cattle remains dating from the Roman period collected at archaeological sites in Portugal, Spain and Italy. Here we present and discuss the preliminary results of our analysis. For example, cattle mitochondrial DNA is geographically structured and it is, therefore, possible to associate maternal lineages to specific regions. Mitochondrial genome coverages for these specimens were between 1x and 100x, which allowed to determine the distribution of major haplogroups. Endogenous DNA content ranged between 0.5% and 50%. We will briefly discuss nuclear whole-genome data and their use to model genomic variation over time and investigate genetic relationships between past and extant cattle from these regions.

There are strong interactions between an economic system and its ecological context. In this sense, livestock have been an integral part of human economies since the Neolithic, contributing significantly to the creation and maintenance of agricultural anthropized landscapes. For this reason, in the frame of the ERC-StG project ’ZooMWest’ we collected and analyzed thousands of zooarchaeological data from NE Iberia. By considering these data in comparison with ecological indicators (archaeobotanical remains) and archaeological evidence (settlement characteristics and their distribution) this paper seeks to characterize changes in animal production and the relationship between people, livestock, and their environment. These methods allow for an investigation of the topic at different scales (site, zone, territory) with a broad diachronic perspective, and for consideration of orography and cultural traditions alongside climatic factors. Through this integration of various streams of evidence, we aim to better understand the structure of ancient economic systems and the way they conditioned human decision-making on animal production. Results show a shifting relationship with the territory between the Bronze Age and Late Antiquity, in which market requirements and an economic model with a higher degree of integration increasingly influenced husbandry strategies. These processes are reflected in changes in land use and forms of territorial occupation, although along different rhythms and trajectories.

Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.