Several millennia of human-mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.

Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.

To trace the history of human-cat interactions and the arrival of domestic cats (Felis catus) in East Asia, we analyzed 22 small felid bones excavated from 14 archaeological sites across China spanning 5,000 years. Genomic and radiocarbon evidence revealed that commensal leopard cats (Prionailurus bengalensis) appeared in anthropogenic environments at least 5,400 years ago and persisted until 150 CE. After a gap of several centuries, the earliest known domestic cat in China (c. 730 CE), reconstructed as a fully or partially white cat, was identified in Shaanxi during the Tang Dynasty. Genomic analysis combining 130 modern and ancient Eurasian cat specimens suggested an origin of Chinese domestic cats from the Levant and a likely merchant-mediated dispersal via the Silk Road. Commensal leopard cats and domestic cats once independently inhabited ancient human settlements in China but followed divergent sociocultural paths with only domestic cats becoming fully domesticated and globally introduced.

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries' gap of archeological feline remains, the first known domestic cat (706 to 883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions. ### Competing Interest Statement The authors have declared no competing interest.

During the colonization of the Americas, the Europeans have experienced multiple socioenvironmental contexts that lead them to develop different settlement strategies. The Spanish conquistadors’ spread toward the vast territories located north of the agrarian lands of Mesoamerica had to adapt to a new context. The resistance of seminomadic hunter-gatherer populations to the European advance challenged the establishment of permanent settlements and set up an agropastoral territory. Based on the analysis of archaeological (field archaeology, ceramics, zooarchaeology) and geohistorical data, this article presents the study of PA1-Cerrito de Tres Mezquites, a fortified and isolated building associated with the Spanish world and identified as a venta (inn) dated to the late sixteenth century. The construction system of this building can be linked to the warlike context that accompanied the process of advancement and colonization of the Chichimeca region. Our study indicates that this building was part of the larger mining socioeconomic system. It played a fundamental role as a commercial node that contributed to spread the Hispanic culture to rural areas far from the major urban centers, to include them in an intercontinental network of long-distance exchanges. But the shift of the frontier to more northerly latitudes in the early seventeenth century, and the limitations imposed by the marshy environment in which the site was established, likely led to a change in its function. In conclusion, this study shows the Spanish rapid adaptive behavior and reuse of the building inherent in getting to know a new space and taking possession of it.

Pigs are the most commercially important modern livestock animal in East Asia. Numerous aspects of their domestication history remain unclear, however, including the geographic center of their domestication, their subsequent dispersal routes, and the emergence of phenotypic traits specific to domestic pigs. To address these questions, we generated 21 nuclear genomes and 23 mitogenomes from ancient domestic pigs and wild boar from 5,800 BCE to 1,300 CE across China. Our analyses of newly generated and previously published Eurasian suid genomes confirmed Northern China and eliminated Southwestern China as the domestication origin of modern East Asian pigs. Following their association with people and the first appearance of black coat coloration, Northern Chinese domestic pigs dispersed alongside Yellow River millet farmers to the Yangtze River Basin and Southwestern China, which they admixed with local wild boar. A genome-wide loss of diversity and signatures of inbreeding in ancient Northern pigs may have been the result of intensified human management as early as 3,000 BCE. Our results reveal the geographic and temporal origins and subsequent dispersal and admixture of pigs in China, mirroring human migration and agricultural development history.

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwest Asian, North Asian and South Asian—each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin. An analysis of 38 ancient genomes from the aurochs, the extinct ancestor of modern cattle, provides insight into the population ancestry and domestication of this species.

Long considered on the margins, far from the major cultural traditions, the Sechura Desert is situated at the crossroads between the cultures of southern Ecuador and those of the northern Peruvian coast and preserves a large number of varied archaeological sites. Despite this evidence, little is known about the societies that inhabited this region during the Holocene. Exposed to natural hazards, including El Niño events, and to major climatic changes, they were able to adapt and exploit the scarce resources that this extreme environment offered them. Because of this rich history, we have been conducting archaeological research in this region since 2012 in order to clarify the dynamics of human occupation and their links with climate oscillations and environmental changes. This paper present the results of a multidisciplinary study of Huaca Grande, a mound located on Nunura Bay, 300 m from the Pacific Ocean. The nature of the human occupations at Huaca Grande was varied, and several adjustments occurred over time. The subsistence economy was based mainly on local marine resources and a continual use of terrestrial vegetal resources. However, a major change occurred in the more recent occupations, with the apparition of non-local resources (maize and cotton) indicating that Huaca Grande was connected to trade networks. The results show two main phases of occupation separated by a long abandonment (mid-5th century CE to mid-7th century CE and mid-13th century to mid-15th century CE). The occupation of the site appears to have been influenced by changes in the local climate and by extreme El Niño events. Our results highlight the great adaptability of these human groups over the span of a millennium and their capacity to react to the climatic changes and hazards that characterise this region.

AbstractIn the US Southwest and Northwest Mexico, people and turkeys (Meleagris gallopavo) have had a reciprocal relationship for millennia; turkeys supplied feathers, meat, and other resources, whereas people provided food, shelter, and care. To investigate how turkeys fit within subsistence, economic production, sociopolitical organization, and religious and ritual practice in the Mimbres Valley of southwestern New Mexico, we report on genetic (mtDNA) and stable isotope (δ13C, δ15N) data from turkeys recovered from Mimbres Classic period (AD 1000–1130) sites. Results indicate that Mimbres aviculturists had haplogroup H1 and H2 turkeys, and most ate maize-based diets similar to humans, but some ate nonmaize and mixed diets. We contextualize these data to other turkey studies from the northern Southwest and discuss how the human-turkey relationship began, the evidence for pens and restricting turkey movement, and the socioecological factors related to turkey management during the Classic period, particularly the challenges associated with providing maize to turkeys during times of environmental stress. This study has broad relevance to places where people managed wild, tame, and domestic animals, and we offer new insights into how prehispanic, small-scale, middle-range agricultural societies managed turkeys for ritual and utilitarian purposes.

Process philosophy offers a metaphysical foundation for domestication studies. This grounding is especially important given the European colonialist origin of 'domestication' as a term and 19th century cultural project. We explore the potential of process archaeology for deep-time investigation of domestication relationships, drawing attention to the variable pace of domestication as an ongoing process within and across taxa; the nature of domestication 'syndromes' and 'pathways' as general hypotheses about process; the importance of cooperation as well as competition among humans and other organisms; the significance of non-human agency; and the ubiquity of hybrid communities that resist the simple wild/domestic dichotomy.

The domestication of animals is a complex process that has been going on for the past 15,000 years. The association between humans and certain animal species has been so successful that the total biomass of domesticates today surpasses the biomass of all other terrestrial vertebrates. This entry reviews the definition of a domestic animal and the main principles underlying the process of animal domestication. It concludes with some final thoughts regarding the limits and future of animal domestication.

The last decade has seen important technological and methodological advances in the field of palaeogenomics, constantly pushing back the time boundary and broadening our understanding of past human-animal interactions. As well as the development of sequencing technologies, a variety of organic material is being (re)evaluated as potential substrates for DNA analyses. The authors here review a selection of these, including collagenous (leather and parchment), keratinous (hair and feather) and calcified (shell and eggshell) material, and environmental DNA including coprolite. The authors focus on the biological structure of these materials in relation to DNA preservation, highlighting their singularity in comparison to bones and teeth, and inform on some of their direct applications. Finally, the authors consider some of the new perspectives these substrates can bring to our understanding of the past, notably surrounding manufacturing practices and health.

People living in Mesoamerica and what is now the eastern and southwestern United States used turkeys ( Meleagris gallopavo ) as sources of meat, eggs, bones, and feathers. Turkey husbandry and domestication are confirmed in two of these regions (Mesoamerica and the American Southwest), but human-turkey interactions in Eastern North American (eastern United States and Canada) are not fully explored. We apply stable isotope (δ 13 C, δ 15 N) and ancient mitochondrial DNA analyses to archaeofaunal samples from seven sites in the southeastern United States to test whether turkeys were managed or captively reared. These combined data do not support prolonged or intensive captive rearing of turkeys, and evidence for less intensive management is ambiguous. More research is warranted to determine whether people managed turkeys in these areas, and whether this is generalizable. Determining whether turkeys were managed or reared in the southeastern United States helps define cultural and environmental factors related to turkey management or husbandry throughout North America. This inquiry contributes to discussion of the roles of intensified human-animal interactions in animal domestication.

Ancient DNA (aDNA) analyses from archaeological animal remains is well suited to many of the objectives investigated through zooarchaeological analyses. This paper aims at presenting the field of palaeogenomics, particularly in its application to zooarchaeological questions. While it does not seek for exhaustivity, it focuses on practical issues, hoping to promote trans-disciplinary dialogues. The authors begin with a presentation of the nature of aDNA and the main taphonomic pathways leading to its differential preservation. Then the authors offer a brief historical review of the aDNA techniques, from the early discoveries of 1984–1985 to the advent of next generation sequencing and high throughput approaches at the beginning of the 21st century. The aurhors describe the main challenges of aDNA research in recent years as it needs to adapt to a new range of methods and how the study of animal remains has been impacted. Finally, the authors highlight the main outcomes of the application of aDNA to describe animals and their populations and future lines of research that could be explored.