The 10,000-year biocultural history of fallow deer and its implications for conservation policy.

Over the last 10,000 y, humans have manipulated fallow deer populations with varying outcomes. Persian fallow deer (Dama mesopotamica) are now endangered. European fallow deer (Dama dama) are globally widespread and are simultaneously considered wild, domestic, endangered, invasive and are even the national animal of Barbuda and Antigua. Despite their close association with people, there is no consensus regarding their natural ranges or the timing and circumstances of their human-mediated translocations and extirpations. Our mitochondrial analyses of modern and archaeological specimens revealed two distinct clades of European fallow deer present in Anatolia and the Balkans. Zooarchaeological evidence suggests these regions were their sole glacial refugia. By combining biomolecular analyses with archaeological and textual evidence, we chart the declining distribution of Persian fallow deer and demonstrate that humans repeatedly translocated European fallow deer, sourced from the most geographically distant populations. Deer taken to Neolithic Chios and Rhodes derived not from nearby Anatolia, but from the Balkans. Though fallow deer were translocated throughout the Mediterranean as part of their association with the Greco-Roman goddesses Artemis and Diana, deer taken to Roman Mallorca were not locally available Dama dama, but Dama mesopotamica. Romans also initially introduced fallow deer to Northern Europe but the species became extinct and was reintroduced in the medieval period, this time from Anatolia. European colonial powers then transported deer populations across the globe. The biocultural histories of fallow deer challenge preconceptions about the divisions between wild and domestic species and provide information that should underpin modern management strategies.

Ancient chicken remains reveal the origins of virulence in Marek's disease virus.

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

The biocultural origins and dispersal of domestic chickens.

Though chickens are the most numerous and ubiquitous domestic bird, their origins, the circumstances of their initial association with people, and the routes along which they dispersed across the world remain controversial. In order to establish a robust spatial and temporal framework for their origins and dispersal, we assessed archaeological occurrences and the domestic status of chickens from ∼600 sites in 89 countries by combining zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Our results suggest that the first unambiguous domestic chicken bones are found at Neolithic Ban Non Wat in central Thailand dated to ∼1650 to 1250 BCE, and that chickens were not domesticated in the Indian Subcontinent. Chickens did not arrive in Central China, South Asia, or Mesopotamia until the late second millennium BCE, and in Ethiopia and Mediterranean Europe by ∼800 BCE. To investigate the circumstances of their initial domestication, we correlated the temporal spread of rice and millet cultivation with the first appearance of chickens within the range of red junglefowl species. Our results suggest that agricultural practices focused on the production and storage of cereal staples served to draw arboreal red junglefowl into the human niche. Thus, the arrival of rice agriculture may have first facilitated the initiation of the chicken domestication process, and then, following their integration within human communities, allowed for their dispersal across the globe.

Humanity's Best Friend: A Dog-Centric Approach to Addressing Global Challenges.

No other animal has a closer mutualistic relationship with humans than the dog (Canis familiaris). Domesticated from the Eurasian grey wolf (Canis lupus), dogs have evolved alongside humans over millennia in a relationship that has transformed dogs and the environments in which humans and dogs have co-inhabited. The story of the dog is the story of recent humanity, in all its biological and cultural complexity. By exploring human-dog-environment interactions throughout time and space, it is possible not only to understand vital elements of global history, but also to critically assess our present-day relationship with the natural world, and to begin to mitigate future global challenges. In this paper, co-authored by researchers from across the natural and social sciences, arts and humanities, we argue that a dog-centric approach provides a new model for future academic enquiry and engagement with both the public and the global environmental agenda.

The relationship between the phosphate and structural carbonate fractionation of fallow deer bioapatite in tooth enamel.

RATIONALE: The species-specific relationship between phosphate (δ18 OP values) and structural carbonate (δ18 OC values) oxygen isotope ratios has been established for several modern and fossil animal species but until now it has not been investigated in European fallow deer (Dama dama dama). This study describes the relationship between phosphate and structural carbonate bioapatite in tooth enamel of extant fallow deer, which will help us further understand the species' unique environmental and cultural history. METHODS: The oxygen isotope composition of phosphate (δ18 OP value) and structural carbonate (δ18 OC value) of hydroxylapatite was determined in 51 modern fallow deer tooth enamel samples from across Europe and West Asia. The δ18 OC values were measured on a GV IsoPrime dual-inlet mass spectrometer and the δ18 OP values on a temperature-controlled elemental analyser (TC/EA) coupled to a DeltaPlus XL isotope ratio mass spectrometer via a ConFlo III interface. RESULTS: This study establishes a direct and linear relationship between the δ18 OC and δ18 OP values from fallow deer tooth enamel (δ18 OC = +9.244(±0.216) + 0.958 * δ18 OP (±0.013)). Despite the successful regression, the variation in δ18 O values from samples collected in the same geographical area is greater than expected, although the results cluster in broad climatic groupings when Koppen-Geiger classifications are taken into account for the individuals' locations. CONCLUSIONS: This is the first comprehensive study of the relationship between ionic forms of oxygen (phosphate oxygen and structural carbonate) in fallow deer dental enamel. The new equation will allow direct comparison with other herbivore data. Variable δ18 O values within populations of fallow deer broadly reflect the ecological zones they are found in which may explain this pattern of results in other euryphagic species.

Ring depressions in cattle horncores as indicators of traction use - a cautionary note.

In this short communication we call attention to the discovery of a ring depression (a circumferential constriction) in the horncore of a feral bull. This discovery casts doubt on the attribution of similar lesions in archaeological deposits as conclusive evidence of 'cord impressions' resulting from yoking or reining cattle for traction. Drawing upon evidence of horncore depressions in other species, we suggest that they reflect metabolic problems following horn development; additional research is required to test this hypothesis.

Rabbits and the Specious Origins of Domestication.

Rabbits are commonly thought to have been domesticated in ∼AD600 by French monks. Using historical and archaeological records, and genetic methods, we demonstrate that this is a misconception and the general inability to date domestication stems from both methodological biases and the lack of appreciation of domestication as a continuum.

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.

Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.