Keith Dobney

• BA, MSc, PhD
• Research Associate at University of Liverpool

Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Clust...

Establishing a link between mandibular morphology and diet in extant primates has long been a goal in biological anthropology because it should provide important insight into the diets of extinct primates, including fossil hominins. To date, efforts to explore this question have produced mixed results, largely perhaps due to a reliance on the use o...

Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallh...

The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great...

Debate surrounds the identity of the Europeans who settled Iceland and Greenland in the early medieval period. Historical sources record settlers travelling from Norway to Iceland and then Greenland, but recent analyses of biological data suggest that some settlers had British and Irish ancestry. Here, the authors test these hypotheses with 3D-shap...

Many of the millions of animals dedicated to the deities in Ancient Egypt were canids. In contrast to the rare textual sources, the abundance of skeletal remains offers the opportunity to address the question of whether wild or domestic canids were mummified. However, species identification from osteological material remains problematic because it...

Virtual methods for studying human remains are becoming increasingly popular in bioarchaeology, and the rate of technological innovation in the last few years has been such that we now have multiple options to choose from when collecting data. This raises the question of whether datasets generated with different methods are transposable. In the stu...

We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age (‘Late Minoan’) period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to...

In 1923, Sir Arthur Keith proposed that many common back problems are due to the stresses caused by our evolutionarily novel form of locomotion, bipedalism. In this article, we introduce an updated version of Keith’s hypothesis with a focus on acquired spinal conditions. We begin by outlining the main ways in which the human spine differs from thos...

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population h...

The settlement of Great Britain by Germanic-speaking people from continental northwest Europe in the Early Medieval period (early 5th to mid 11th centuries CE) has long been recognised as an important event, but uncertainty remains about the number of settlers and the nature of their relationship with the preexisting inhabitants of the island. In t...

The distribution of the black rat ( Rattus rattus ) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population...

Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, callin...

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our res...

Dental calculus (calcified dental plaque) is a cross-cultural biological matrix that is emerging as a critical source of information for anthropologists and oral health professionals. It contains a multitude of diverse biomolecules, providing information about an individual’s culture, diet, ancestry, and health. Most researchers who study archaeolo...

The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore th...

Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, callin...

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,...

Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a...

1. Biologists often seek to geographically provenance organisms using their traits. This is typically achieved by defining spatial groups using distinct patterns of trait variation. 2. Here we present a new spatial provenancing and trait boundary identification methodology based on correlations between geographic and trait distances, which requir...

The reconstruction of diet, subsistence strategies and human-animal relationships are integral to understanding past human societies, adaptations and resilience - especially in the circumpolar Arctic. Even in relatively recent periods, climatic excursions may have posed specific challenges for hunter-gatherer groups living at latitudinal and climat...

Background and objectives: The study reported here focused on the aetiology of spondylolysis, a vertebral pathology usually caused by a fatigue fracture. The goal was to test the ‘Overshoot Hypothesis’, which proposes that people develop spondylolysis because their vertebral shape is at the highly derived end of the range of variation within Homo s...

Background: Recently we proposed an evolutionary explanation for a spinal pathology that afflicts many people, intervertebral disc herniation (Plomp et al. [2015] BMC Evolutionary Biology 15, 68). Using 2D data, we found that the bodies and pedicles of lower vertebrae of pathological humans were more similar in shape to those of chimpanzees than w...

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late...

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these...

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these...

The Rattini tribe comprises some of the most specious genera in the mammalian kingdom. Many of these species are also highly morphologically conserved. As a result, identifying Rattini tribe animals, particularly those of the Rattus genus, to species level is extremely difficult. Problems with identification of conservative morphologies, particular...

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disapp...

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disapp...

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disapp...

Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint st...

Dogs were the first domesticated animal and, according to the archaeological evidence, have had a close relationship with humans for at least 15,000 years. Today, dogs are common pets in our society and have been linked to increased well-being and improved health outcomes in their owners. A dog in the family during childhood is associated with owne...

The trillions of microorganisms that live in association with the human body (microbiota) are critical for human health and disease, but there is a limited understanding of how cultural and environmental factors shaped our microbiota diversity through time. However, biomolecular remnants of the human oral microbiota - recovered from the calcified d...

The modern domestic dog is behaviourally and morphologically far removed from its ancient counterpart. Increasingly, research has demonstrated that using modern comparative collections for identifying domestic animals in archaeological contexts is problematic. This is likely the result of the intensive breeding that modern animals have undergone in...

Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species...

Linear enamel hypoplasia (LEH) produces abnormal incremental lines or depressions in teeth enamel caused by a deficiency in the growth of calcified tissue. The depth and width of the LEH events can indicate the severity and duration of a stressful life event. LEH can be used to investigate developmental stress, as it will occur when the individual...

Ancient human migrations provide the critical genetic background to historical and contemporary human demographic patterns. However, our ability to infer past human migration events, especially those that occurred over rapid timescales, is often limited. A key example is the peopling of Polynesia, where the timing is relatively well defined, but th...

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 5(th) century BCE [1-3], it remains unclear how many t...

Domestic animals are often described as paedomorphic, meaning that they retain juvenile characteristics into adulthood. Through a three-dimensional landmark-based geometric morphometric analysis of cranial morphology at three growth stages, we demonstrate that wild boar (n = 138) and domestic pigs (n = 106) (Sus scrofa) follow distinct ontogenetic...

SI Figure 2: Results of analyses performed on the three ontogenetic series for which specimens in the three classes of age were available.

SI Table 1: List of all specimens included in the study. Juvenile: 0-3 months, before the eruption of all deciduous teeth, sub-adult: 3-15 months, and adult: over 15months, after deciduous teeth being replaced by permanent teeth.

SI Figure 1: A depiction of the location and number of homologous landmarks used in the analysis.

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...

Tooth crowding is one of several criteria used to infer the process of domestication in the zooarchaeo-logical record. It has been primarily used to support claims of early animal domestication, perhaps most contentiously in claims for the existence of so-called " proto-domestic " dogs as early as the Middle-Upper Palaeolithic. Tooth crowding studi...

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...

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of reg...

The domestic pig is among the first animal to have been domesticated. Its domestication dates from the beginning of the Holocene - when so-called Neolithic cultures across the Old World began to farm and a period that saw the domestication of the principal farmyard animals (i.e. sheep, goat and cattle). Domestic pigs have a peculiar place among dom...

Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs....

Close-range photographic techniques-including photogrammetry-are becoming common tools for constructing three-dimensional (3D) models of artifacts, particularly in archaeological research. Whether models obtained through photogrammetry can be used for zooarchaeological studies requires a systematic examination. In the context of research into dog d...

The Orkney Vole offers a window into 130 years of British natural history and an island mystery that involves ecologists, archaeologists and geneticists. These interdisciplinary endeavours are providing striking insights into the potential pace of evolution and the role of human history in shaping our wildlife today. Here, the authors tell a tale o...

Commensalism within anthropogenic environments has not been extensively discussed, despite its impact on humans, and there is no formal framework for assessing this ecological relationship in its varied forms. Here, we examine commensalism in anthropogenic environments in detail, considering both ecological and evolutionary drivers. The many assump...

A dogged investigation of domestication The history of how wolves became our pampered pooches of today has remained controversial. Frantz et al. describe high-coverage sequencing of the genome of an Irish dog from the Bronze Age as well as ancient dog mitochondrial DNA sequences. Comparing ancient dogs to a modern worldwide panel of dogs shows an o...

In south-eastern Romania, a prominent place was given to pigs in the Gumelniţa culture (Late Chalcolithic, second half of 5th millennium BC); as was the highly prized wild boar, one of a variety of species targeted for hunting. The wild boars’ ecological niche and the scale of pig husbandry were investigated during a stable isotope study of the Gum...

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The...

Measurements of the complete skeleton of a small felid found in the H3 refuse pit at Wuzhuangguoliang (Jingbian county, Shaanxi prov.), and dated to 5267–4871 cal BP. Measurements are in millimetres (or millilitres for the volume of the brain case) and they have been recorded according to von den Driesch (1976, A guide to the measurement of animal...

Permission from the Redlist UICN for the open-access journal PLOS ONE to publish the map of Fig 1 under the Creative Commons Attribution License (CCAL) CC BY 4.0. (PDF)

Drawing of the «ash pit» H3 at Wuzhuangguoliang (Jinghian county, Shaanxi prov.), with the animal deposits comprising 5 hare skeletons, a weasel mandible and the almost complete cat skeleton, and, below, enlargement on the cat skeleton dated to 5267–4871 cal BP (Table 1) (redrawn after the drawings and photos of Hu and Sun, 2005). (PDF)

Results of the Linear discriminant analysis between P. bengalensis and F. silvestris. Distribution of the specimens, visualization of the mandible shape between the two species along the discriminant axis, and lateral views of mandibles of the two species (photo A. E.). (PDF)