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

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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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

The genetic history of Scandinavia from the Roman Iron Age to the present

The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We used resources from projects SNIC 2022/23-132, SNIC 2022/22-117, SNIC 2022/23-163, SNIC 2022/22-299, and SNIC 2021-2-17. This research was supported by the Swedish Research Council project ID 2019-00849_VR and ATLAS (Riksbankens Jubileumsfond). Part of the modern dataset was supported by a research grant from Science Foundation Ireland (SFI), grant number 16/RC/3948, and co-funded under the European Regional Development Fund and by FutureNeuro industry partners.Peer reviewedPublisher PD

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans

The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE, it remains unclear how many times, and by whom, the islands were first settled. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th–11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%–31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the frst species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of diferentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fxation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, refecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located