Investigating patterns of animal domestication using ancient DNA

Animal domestication is a continuous but nonlinear evolutionary process that follows different paths (trajectories) of human-animal relationships. These paths vary in structure and intensity over time and include processes like human intentionality (such as control and taming of wild animals), directed selection on behavioral and phenotypic traits and characters, human-mediated movement of domestic herds across space (migration), wild-domestic admixture, and adaptation. Because domestic animals are continuously shaped through complex interaction of these processes, gaining a better understanding of where, when and how these took place helps clarifying human prehistory and the practice and process of domestication. Studies of modern and ancient DNA (aDNA) have recently disentangled the history of several domestic species. These studies have often shown that domestication processes were far more complex than previously thought, often encompassing more than one independent domestication event, and continuously shaped by migration and admixture. Importantly, ancient DNA studies have convincingly demonstrated that inferring the past (for example, where, when and how domestication and selection took place) from the present (modern contemporary domesticates) is biased by comparatively recent events such as modern breed formation. Ancient DNA is therefore a key component in the reconstruction of where, when and how animal domestication took place. This thesis aims to shed new light on pig and chicken domestication by analysing ancient DNA extracted from archaeological specimens from Europe and the Near and Middle East. First, I find that pig domestication took place over a much wider temporal and geographical range than previously thought, and secondly that the current reference framework for inferring where and when pigs were domesticated (wild boar mitochondrial phylogeography) must be revised. In addition, I find that genetic variation in modern domestic chickens, to a great extent, is the result of recent rather than ancient events of admixture and strong human driven selection. Overall, these finds strengthen the presumption that genetic signatures in modern contemporary populations often provide misleading estimates of their ancient history. Across genes and species, therefore, this thesis demonstrates the effectiveness of using ancient DNA for resolving a range of different aspects of human prehistory and animal domestication

Genetic insight into an extinct population of Asian elephants (Elephas maximus) in the Near East

The current range of the Asian elephant is fragmented and restricted to southern Asia. Its historical range was far wider and extended from Anatolia and the Levant to Central China. The fossil record from these peripheral populations is scant and we know little of their relationship to modern Asian elephants. To gain a first insight to the genetic affinity of an E. maximus population that once inhabited Turkey we sequenced ca. 570 bp mtDNA from four individuals dating to ~3500 cal. BP. We show that these elephants carried a rare haplotype previously only observed in one modern elephant from Thailand. These results clarify the taxonomic identity of specimens with indeterminate morphologies and show that this ancient population groups within extant genetic variation. By placing the age of the common ancestor of this haplotype in the interval 3.7–58.7 kya (mean = 23.5 kya) we show that range-wide connectivity occurred at some time or times since the start of MIS 3, ~57 kya, probably reflecting range and population expansion during a favourable climatic episode. The genetic data do not distinguish natural versus anthropogenic origin of the Near Eastern Bronze Age population, but together with archaeological and paleoclimatic data they allow the possibility of a natural westward expansion around that time

New horizons at L’Anse aux Meadows

The UNESCO World Heritage site of L’Anse aux Meadows (LAM) in northern Newfoundland is the only undisputed site of pre-1492 presence of Europeans in the Americas. In August 2018, we undertook fieldwork at LAM to sample the peat bog 30 m east of the Norse ruins for a multiproxy paleoenvironmental assessment of Norse settlement. Instead, we encountered a new cultural horizon. Here we report our fieldwork at this iconic site and a Bayesian analysis of legacy radiocarbon data, which nuance previous conclusions and suggest Norse activity at LAM may have endured for a century. In light of these findings, we reflect on how the cultural horizon, containing nonnative ecofacts, may relate to indigenous or Norse activities

Establishing the validity of domestication genes using DNA from ancient chickens

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Elucidating recent history by tracing genetic affinity of three 16th century miners from Sweden.

Objectives: Sala Silver Mine in central Sweden was an important manufacturer of silver from at least the 16th till the early 20th century, with production peaking in the 16th, mid 17th and 19th centuries. The job opportunities offered by the mine attracted people to the area resulting in the development of a small township with an associated cemetery in the vicinity of the mining center. People affiliated to the mine were buried on the cemetery for around 150 years. Written sources reveal that common criminal convicts from Sweden-Finland and war prisoners from the numerous wars fought by Sweden during the time were exploited in the mine, and some of them were likely buried on the cemetery. The cemetery has been excavated on several occasions and the recovered human remains were divided into two different groups based on burial custom, demography and biochemical results. One group was believed to contain war prisoners; the aim of this study was to produce and interpret genomic data from these individuals to test if their genetic ancestry is consistent with the hypothesis that they were non-locals. Materials: Teeth from seven different individuals were sampled for dentine. Results: Three of the analyzed teeth contained sufficient amounts of endogenous human DNA for the generation of genomic sequence data to a coverage of 0.04, 0.19 and 0.83, respectively. Discussion: The results show that despite seeming heterogeneity the three individuals grouped within the range of genetic variation of modern and contemporary Swedes, yielding no statistical support to the hypothesis that they were foreign captives. However, due to the lack of contemporary or modern Danish genomic data we cannot refute these individuals originated in Denmark which was suggested as one of possible sources of the 17th century Swedish prisoners of war

New zooarchaeological evidence from Pictish sites in Scotland : implications for early medieval economies and animal-human relationships

Funding This research was part of the Northern Picts Project (2009–2015), The Comparative Kingship Project (since 2017) funded by the Leverhulme Trust as part of a Research Leadership Award under Grant RL-2016-069, and Historic Environment Scotland Citadel project—code is RG15531-10. KB was supported by the Leverhulme Trust (PLP-2019–284). Acknowledgments We wish to thank the two reviewers for their constructive comments that have improved the original version of this paper. We thank the University of Aberdeen students and volunteer excavators who participated in the excavations and the onsite collection of samples as well as helping clean and sort the faunal material. We also wish to thank Zena Timmons and Jerry Herman (National Museum of Scotland) for access to NMS collections and for their time. Thanks to funding from Don and Elizabeth Cruickshank that allowed many of the excavations referenced here to take place and enabled publication of results.Peer reviewedPublisher PD

Exploring the complexity of domestication : a response to Rowley-Conwy and Zeder

Funding: This work was supported by Natural Environment Research Council [grant number NE/F003382/1]. Acknowledgements: We once again thank the many institutions and individuals that provided sample material and access to collections, especially the curators of the Museum für Haustierkunde, Halle; Museum für Naturkunde, Berlin; Zoologische Staatssammlung, Munich; Muséum National d’Histoire Naturelle, Paris; The American Museum of Natural History, New-York.Peer reviewedPostprin

New genetic and morphological evidence suggests a single hoaxer created ‘Piltdown man’

In 1912, palaeontologist Arthur Smith Woodward and amateur antiquarian and solicitor Charles Dawson announced the discovery of a fossil that supposedly provided a link between apes and humans: Eoanthropus dawsoni (Dawson's dawn man). The publication generated huge interest from scientists and the general public. However, ‘Piltdown man's’ initial celebrity has long been overshadowed by its subsequent infamy as one of the most famous scientific frauds in history. Our re-evaluation of the Piltdown fossils using the latest scientific methods (DNA analyses, high-precision measurements, spectroscopy and virtual anthropology) shows that it is highly likely that a single orang-utan specimen and at least two human specimens were used to create the fake fossils. The modus operandi was found consistent throughout the assemblage (specimens are stained brown, loaded with gravel fragments and restored using filling materials), linking all specimens from the Piltdown I and Piltdown II sites to a single forger—Charles Dawson. Whether Dawson acted alone is uncertain, but his hunger for acclaim may have driven him to risk his reputation and misdirect the course of anthropology for decades. The Piltdown hoax stands as a cautionary tale to scientists not to be led by preconceived ideas, but to use scientific integrity and rigour in the face of novel discoveries

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely-related, haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.Vicki A. Thomson, Ophélie Lebrasseur, Jeremy J. Austin, Terry Hunt, David Burney, Tim Denham, Nicolas J. Rawlence, Jamie R. Wood, Jaime Gongora, Linus Girdland Flink, Anna Linderholm, Keith Dobney, Greger Larson, Alan Cooper