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.

How the brains of domestic animals evolved under domestication remains poorly understood. We quantified brain shape variation in domestic dogs (n = 203, 111 breeds) and wolves (n = 40) using endocast-based 3D geometric morphometrics. Size, shape, and morphological integration were assessed on the whole brain, and in six morphofunctional subregions. Results demonstrate that domestication and artificial selection significantly restructured brain form and morphological integration patterns in dogs, reflecting mosaic evolution across brain subregions. Dogs exhibit a three-fold increase in brain shape variation relative to wolves, as well as expanded frontal lobes and areas putatively associated with social interaction behavior-these regions are also larger in cooperative vs. independent breeds. Morphological integration is higher in dogs than wolves, and in modern breeds compared to ancient breeds. Thus, rather than constrain, integration appears to facilitate neuroanatomical evolvability under domestication and breeding selection. Ancient dog breeds retain more wolf-like neuroanatomy. Breed function is a poor predictor of brain shape, but brain integration restructures according to breed function, with working breeds displaying the highest integration. These findings reveal the profound impact of domestication on neuroanatomical evolution, emphasizing neuroanatomical features linked to social behavior, and challenging prevailing assumptions about the role of structural integration on evolvability.

In North-western Mediterranean basin, from Southern France to North-eastern Iberia, the transition from the Iron Age to Antiquity is marked by significant political, economic, and cultural changes, as well as a major shift in the body size of livestock, particularly cattle. However, the evolution of suids and caprines during this period has been less thoroughly investigated in the area. This study aims to investigate the morphological variation of sheep, goats, and pigs from the Rhône to the Ebro rivers, from the First Iron Age to Late Antiquity (eighth century BCE to sixth century CE). To this end, 1,099 caprine and 384 suid third lower molars from 96 archaeological sites were analysed using a 2D landmark and sliding semi-landmark based geometric morphometric approach. The impact of a series of socio-economic and environmental factors on the morphometric variation was tested considering time, geography, altitude, topography and urban/rural categorisation of the sites. The results indicate that while sheep teeth increased in size and differ in shape between the Second Iron Age and the end of the Roman Empire, no variation was observed in goat teeth measurements, suggesting different selection patterns for the two species over time. For suids, no differences in teeth size were detected, but differences in shape were observed throughout the chronology, possibly reflecting zootechnical improvements. While little, or no effect of different factors was found for the teeth of suids and goats, the shape of sheep teeth exhibits clear geographical structuring, along with effects of altitude, topography and site type. Thus, changes in tooth shape and size in domestic species are not the result of a single explanatory factor, but rather reflect multifactorial influences including both environmental and anthropological factors. The importance of these influences may vary over time and between species.

Human mediated translocation of non-native pig species (genus Sus ) to the islands of Wallacea and Oceania has significantly 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 714 modern and ancient dental remains. Our analyses demonstrate that feral and domestic pigs in Wallacea and Oceania possess 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 possess a distinct tooth morphology, and a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ∼4,000-3,000 years ago via Taiwan and the Philippines. ### Competing Interest Statement The authors have declared no competing interest.

The identification of archaeological fruits and seeds is crucial for understanding the relationships between humans and plants within the cultural and biological history of both wild and cultivated species. We compared the relative performance of a deep learning approach, namely convolutional neural networks (CNN), and outline analyses via geometric morphometrics using elliptical Fourier transforms (EFT) at identifying pairs of plant taxa. We used their seeds and fruit stones that are the most abundant organs in archaeobotanical assemblages, and whose morphological identification, chiefly between wild and domesticated types, allows to document their domestication and biogeographical history. We used existing modern datasets of four plant taxa (barley, olive, date palm and grapevine) corresponding to photographs of two orthogonal views of their seeds that were analysed separately to offer a larger spectrum of shape diversity. Sample sizes ranged from 473 to 1,769 seeds per class, which constitute a relatively small dataset for training CNNs models yet typical within archaeobotanical research. On these eight datasets, we compared the performance of CNN and EFT coupled with linear discriminant analyses. Our objectives were twofold: i) to test whether CNN can beat geometric morphometrics in taxonomic identification and if so, ii) to test which minimal sample size is required. We ran simulations on the full datasets and also on subsets, starting from 50 images in each binary class. For the CNN network, we deliberately used a candid approach relying on preparameterised VGG19 network. For EFT, we used a state-of-the art morphometrical pipeline. The main difference rests in the data used by each model: our CNN used bare photographs where EFT used outline coordinates. This "pre-distilled" geometrical description of seed outlines is often the most time-consuming part of morphometric studies. Results show that our CNN beats EFT in most cases, even for very small datasets. We finally discuss the potential of CNNs for archaeobotany, and how bioarchaeological studies could embrace both approaches, used in a complementary way, to better assess and understand the past history of species.

The smooth scallop (Flexopecten glaber) is a seafood that was widely consumed in Gallia Narbonensis (Southern France) during Roman times. Harvested from lagoons along the Mediterranean coast, the species was transported to consumers up to a hundred kilometres from the seashore. However, the origins of this fresh produce supplied to the Gallo-Romans remain largely unknown. The variation in size and shape of 1149 shells originating from 27 archaeological sites in Southern France, dating from the 1st c. BC to the 12th c. AD, was quantified using Elliptic Fourier Transforms and analysed through geometric morphometrics. The morphometry of scallop shells is highly structured geographically, showing differences between lagoons of origin regardless of the period. This archaeobiogeographical pattern allows for the estimation of the geographical origin of valves discovered in the hinterland and the reconstruction of marine resource provisioning centres. While most valves were sourced as close as possible to the place of consumption, the exception of the smooth scallops from the city of Nemausus (Nimes) reveals a structured network dedicated to urban supply. Future research could extend these methodologies to a broader geographical scope, providing a more detailed analysis of trade and supply networks of Mediterranean shellfish.

The Ouled Djellal White Arab sheep is the predominant breed in the Algerian steppes and high plains, known for its adaptability and meat production. This study examines correlations between mandibular, body, and craniometric measurements in two age groups to establish a reference dataset for archaeozoological applications. Thirty female Ouled Djellal sheep, evenly divided into young adults (2–4 years) and adults (>4 years), were examined. Eight body measurements were recorded pre-slaughter, followed by eight mandibular and sixteen craniometric measurements after bone preparation, with four indices subsequently calculated. Significant correlations were observed between mandibular and body measurements, and between mandibular and craniometric parameters. Correlations were more numerous and stronger in adults (ranging from 0.47 to 0.70) than in young adults (from 0.41 to 0.67). While differences in covariation strength were observed between age groups, some correlations, such as those between thoracic perimeter (TP) and mental foramen length (ML6), and between head length (hL) and aboral height of the ascending branch (MH1) persisted across age groups. Dentition-related measurements correlated more frequently in adults, reflecting skeletal maturity, whereas variability in young adults indicated ongoing growth. These findings highlight the importance of age considerations in morphometric analysis and provide reference data for estimating body size and cranial dimensions from mandible measurements, contributing to archaeozoological studies of North African ancient specimens.

The opium poppy (Papaver somniferum L.) is one of the most important plants in human history. It is the main source of opiates used as analgesic medicines or psychotropic drugs, the latter related to addiction problems, illegal trafficking and geopolitical issues. Poppyseed is also used in cooking. The prehistoric origins, domestication and cultivation spread of the opium poppy remain unresolved. Traditionally, Papaver setigerum has been considered the wild ancestor with early cultivation presumed to have occurred in the Western Mediterranean region, where setigerum is autochthonous. Other theories suggest that somniferum may have been introduced by Southwest Asian early farmers as a weed. To investigate these hypotheses, we analysed 190 accessions from 15 Papaver species using genotype-by-sequencing and geometric morphometric (GMM) techniques. Our analysis revealed that setigerum is the only taxa genetically close to somniferum and can be better described as a subspecies. The domesticated plants are, however, distinct from setigerum. Additionally, GMM analysis of seeds also revealed morphological differences between setigerum and somniferum. Some phenotypically wild setigerum accessions exhibited intermediate genetic features, suggesting introgression events. Two major populations were found in somniferum and, to some extent, these correspond to differences in seed form. These two populations may reflect recent attempts to breed varieties rich in opiates, as opposed to varieties used for poppyseed production. This study supports the idea that opium poppy cultivation began in the Western Mediterranean, with setigerum as the wild progenitor, although some wild varieties are likely to be feral forms, which can confound domestication studies.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

Understanding how domestic mammal species evolved through time provides insight into the artificial and natural selection processes that have shaped the diversity of domestic animals. The focus of this article is the morphometric evolution of sheep, goats and suids in the Northwestern Mediterranean Basin over the last 8000 years, employing a 2D geometric morphometrics protocol applied to the third lower molars. Using a comprehensive dataset comprising 2798 archaeological specimens from 176 sites in Southern France and Spanish Catalonia, along with 1303 modern specimens, we aim to identify and contrast the environmental and anthropic factors influencing species evolution linked to past husbandry practices. Each of these three taxa follows its own evolutionary trajectory, exhibiting variations over time and across different regions. Notably, reduction in the centroid size of sheep molars between the Neolithic and the early Iron Age could potentially be associated with an increased demand for meat and/or shifts in male-to-female ratios. A clear geographical structuring of caprines between the Neolithic and Antiquity is observed, likely influenced by a combination of factors including artificial selection, environmental changes and socio-economic dynamics, as corroborated by previous studies. Moreover, a reduction in molar size during the Middle Ages is observed across all three species, possibly linked to extensive agropastoral practices. Furthermore, divergent processes of breed improvement and standardization are identified in pigs and caprines. This study highlights the complex nature of morphological variations in domestic species, emphasising the multifactorial influences involved. It underscores the importance of interdisciplinary approaches in understanding the factors contributing to morphological transformations over time.

Since their domestication about 10 500 years ago, sheep and goats have been central to human subsistence economies. Despite shared traits and frequent co-herding, these species are biologically distinct, with their uses reflecting diverse cultural practices. Advances in geometric morphometrics enable detailed analyses of their phenotypic evolution, shaped by natural and artificial selection, genetic drift and gene flow. These evolutionary mechanisms are often challenging to disentangle in archaeozoology, but patterns of morphometric variation can reveal evolutionary parallels and divergences. This study investigates the morphometric evolution of sheep and goat teeth in the northwestern Mediterranean basin over 8000 years. Dental remains, which preserve well in archaeological contexts, provide rich data for evolutionary studies, including species-level identifications. Using two-dimensional geometric morphometrics, third lower molars from 1602 sheep and 635 goats, spanning archaeological and modern specimens, were analysed. Molar size, shape and variance were compared across six chrono-cultural phases, tracing diachronic morphological changes. Distinct patterns emerge: sheep exhibit greater variability likely reflecting selective breeding for diverse purposes. Goats, in contrast, show greater uniformity. These findings underscore unique evolutionary trajectories for sheep and goats, offering new perspectives on their biocultural evolution within the dynamic environmental and anthropic contexts that shaped their current diversity. This article is part of the theme issue ‘Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future’.

Despite the domestic cat's (Felis catus) close association with humans, the timing and circumstances of its domestication and subsequent introduction to Europe are unresolved. Domestication of its wild progenitor, the African wildcat (F. lybica), is widely attributed to the emergence of farming. Wildcats are said to have been attracted to settled communities by the rodent populations that were thriving within this new agricultural niche. Some claim the African wildcat even reached Europe during the Neolithic, though many credit the Romans with their dispersal. Through a program of zooarchaeological analysis, genetic identification and radiocarbon dating, we redefine the established chronology for the cat's domestication and dispersal across Europe. We argue that early human-cat relationships were more complex than the commensal and mutualistic pathways that have been proposed, and that both the domestication and translocation of cats were linked to its association with deities. Our results suggest domestic cats first arrived in Europe prior to Roman expansion during the early first millennium BCE, and that successive populations of domestic cats with unique mitochondrial signatures were introduced during the Roman, Late Antique and Viking periods. Lastly, by characterising the spatiotemporal representation of both domestic cats and the native European wildcat (F. silvestris), we argue that the introduction of domestic cats precipitated a decline in native European wildcat populations. ### Competing Interest Statement The authors have declared no competing interest.

Dogs exhibit an exceptional range of morphological diversity as a result of their long-term association with humans. Attempts to identify when dog morphological variation began to expand have been constrained by the limited number of Pleistocene specimens, the fragmentary nature of remains, and difficulties in distinguishing early dogs from wolves on the basis of skeletal morphology. In this study, we used three-dimensional geometric morphometrics to analyze the size and shape of 643 canid crania spanning the past 50,000 years. Our analyses show that a distinctive dog morphology first appeared at about 11,000 calibrated years before present, and substantial phenotypic diversity already existed in early Holocene dogs. Thus, this variation emerged many millennia before the intense human-mediated selection shaping modern dog breeds beginning in the 19th century.

The transition from hunter-gatherer communities to farming societies is a pivotal shift in human history, hinging on the emergence, selection and diffusion of domestic plants and animals. However, the sequence and order of these steps remain only partially understood. In this study, we used a possibilistic formalism to model the emergence and development of farming. This first attempt, based on an intentionally limited number of qualitative and discrete rules, represents the interactions between domestic and wild plants and animals, and human societies. This initial case study focuses on the emergence of farming in Southwest Asia. We constructed a theoretical model including a minimum number of five components and 18 processes. We explored three models representing increasing exploitation of resources from no overexploitation, to overexploitation of both wild and domestic resources. Our findings revealed possible scenarios for the emergence and development of farming, where animal domestication possibly emerged before plant domestication, contradicting the most accepted temporality. We also generated alternative hypotheses concerning the initiation of plant and animal domestications. The possible ecosystem development with resource overexploitation underscores the importance of wild resources for sustainable societies. This initial attempt at possibilistic modelling can be further developed and expanded to address a broad range of archaeological questions. This article is part of the theme issue ‘Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future’.