ZooMS confirms geometric morphometrics species identification of ancient sheep and goat.

Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.

Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.

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.

Mass animal sacrifice at casas del Turuñuelo (Guareña, Spain): A unique Tartessian (Iron Age) site in the southwest of the Iberian Peninsula.

Zooarchaeological analyses of the skeletal remains of 52 animals unearthed in the courtyard of an Iron Age Tartessian building known as Casas del Turuñuelo (Badajoz, Spain) shed light on a massive sacrifice forming part of a series of rituals linked to the site's last period of activity and final abandonment. The rites took place towards the end of the 5th century BCE when both the building (intentionally destroyed) and the sacrificed animals were intentionally buried under a tumulus 90 m in diameter and 6 m high. The main objective of the zooarchaeological and microstratigraphic analyses was to determine the phasing of the sacrificial depositions. Evidence gathered from taphonomic assessments and a series of radiocarbon datings indicate that the sacrifices fall into three consecutive phases spanning several years. The findings of the zooarchaeological analyses clearly point to a selection of equid and cattle males. Adult equids predominate (MNI = 41) followed by adult and sub-adult cattle (MNI = 6). Pigs, in turn, are only represented by a few adults and sub-adult females (MNI = 4). Among the animals is a single dog of undetermined sex between 3 and 4 years of age. The fact that the animals are mostly adults discards the likelihood that they died from natural causes or an epidemic. In addition, the scenographic deposition of certain equids in pairs, as well as evidence of the burning of plant offerings, suggest an intentional ritualistic sacrifice. Nine of the initial depositions of Phase 1 in the SE quadrant were scattered and certain of their bones bear marks characteristic of both prolonged open air exposure and scavengers. Another 31 animals from Phases 1 and 2 are represented by almost complete, articulated skeletons, indicating they were promptly covered. Phase 3, by contrast, reveals both almost complete and partial animals bearing clear signs of processing for human consumption. This study thus sheds light on both the sequence of the animal sacrifices and the protocols linked to rites accompanied by the celebration of banquets. Certain features associated with the sealing of this building under a tumulus offer evidence of the decline of the Tartessian Culture. This study thus advances notions serving to contextualize ritual animal sacrifices in the framework of practice observed at other Iron Age sites in the Iberian Peninsula and elsewhere throughout Europe.

Performance and automation of ancient DNA capture with RNA hyRAD probes.

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history.

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.

Resilience and livestock adaptations to demographic growth and technological change: A diachronic perspective from the Late Bronze Age to Late Antiquity in NE Iberia.

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.

New trajectories or accelerating change? Zooarchaeological evidence for Roman transformation of animal husbandry in Northern Italy.

Throughout the Western provinces of the Roman Empire, greater economic and political connectivity had a major impact on agricultural production, which grew in scale and specialisation after integration with the Roman state. However, uniquely in Western Europe, farming strategies in Italy began to evolve centuries before the Roman conquest, and many 'Roman' patterns associated with livestock size and the relative proportions of different taxa first emerged during the early and middle centuries of the first millennium BC. These changes imply a significant reorganisation of production strategies well before Roman hegemony, even in relatively marginal areas of Italy. Zooarchaeological studies have documented further significant changes to livestock production in Roman times, but the relationship between these developments and earlier trends remains unclear. Through analysis of zooarchaeological data for species representation and livestock biometry from lowland northern Italy (Po-Friulian Plain), this study investigates animal exploitation between the Bronze Age and Late Antiquity in order to characterise the influence of Roman political and economic organisation on animal husbandry. Results demonstrated subregional variation in species representation, and different trajectories in the biometric evolution of cattle, sheep and goats, compared to pigs. Initial steps established in the Iron Age towards a more complex and dynamic livestock economy were accelerated and further reconfigured in Roman times, facilitated by Roman economic organisation and the specialised and large-scale production systems within it. Zooarchaeological trends continued to progress over the Roman period, until further changes at the very end of the chronology considered here-around the sixth century AD-suggest another wave of change. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12520-020-01251-7.

Pre-Roman improvements to agricultural production: Evidence from livestock husbandry in late prehistoric Italy.

Domestication of wild cattle, sheep, and pigs began a process of body size diminution. In most of Western Europe this process continued across prehistory and was not reversed until the Roman period. However, in Italy, an increase in livestock body size occurred during the Iron Age, earlier than the Western provinces. In order to better understand the nature and timing of this early increase in animal size, this paper presents a detailed regional study of taxonomic abundance and biometric data from zooarchaeological assemblages recovered from the Po and Venetian-Friulian Plains in northern Italy. Our results demonstrate a high level of regionality in the choice of species exploited, with husbandry systems focused on different domesticates, as well as regional differences in animal size. However, despite significant variation in species frequencies, settlement structure, and epigraphic tradition, all areas with sufficient data demonstrate similar significant changes in livestock body size. Cattle and sheep increased incrementally in size prior to the Roman conquest in all regions considered; surprisingly, pigs continued to decrease in size throughout later prehistory. The incremental pace and pan-regional character of the size change in cattle and sheep suggests an internally motivated phenomenon rather than herd replacement with a new larger population, as might follow colonisation or conquest. The divergence in size trends for bovids and suids suggests a noteworthy change in cattle and sheep herding practices during the Iron Age or final centuries of the Bronze Age, in contrast with greater continuity in pig management. Our analysis provides a thorough zooarchaeological synthesis for northern Italy and, for the first time, demonstrates that both cattle and sheep increased in size outside of Roman territory well before the conquest of this area. This study offers a basis for future chemical analyses (DNA, isotopes), which will further investigate the cause(s) of livestock size changes in northern Italy.

Shipping amphorae and shipping sheep? Livestock mobility in the north-east Iberian peninsula during the Iron Age based on strontium isotopic analyses of sheep and goat tooth enamel.

Animal mobility is a common strategy to overcome scarcity of food and the related over-grazing of pastures. It is also essential to reduce the inbreeding rate of animal populations, which is known to have a negative impact on fertility and productivity. The present paper shows the geographic range of sheep provisioning in different phases of occupation at the Iron Age site of Turó de la Font de la Canya (7th to 3rd centuries BC). Strontium isotope ratios from 34 archaeological sheep and goat enamel, two archaeological bones and 14 modern tree leaves are presented. The isotopic results suggest that sheep and goats consumed at the site were reared locally (within a few kilometres radius) during the whole period of occupation. The paper discusses the isotopic results in light of the socio-political structure of this period, as complex, strongly territorial societies developed during the Iron Age in the north-east Iberian Peninsula.