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Multidisciplinary investigation of a ‘British big cat’: a lynx killed in southern England c. 1903
No full textThe alleged presence of non-native felid species in the British countryside – popularly, though in part erroneously, known as ‘British big cats’ or ‘alien big cats’ – is a long-standing and controversial topic, perennially of interest to both the mass media and amateur naturalists, and with little apparent acceptance from the technical zoological community. Nevertheless, a number of carcasses and captured live specimens have demonstrated the occasional presence within the region of escapees that potentially explain at least some ‘British big cat’ eyewitness records. We report here the existence of a probable Canada lynx, Lynx canadensis, shot in Newton Abbot, Devon, England, in or prior to 1903, and then accessioned to Bristol Museum and Art Gallery. The specimen (represented by extensive skeletal material and a stuffed taxidermy mount) is Bobcat-like in some respects but is identified as a Canada lynx on the basis of skeletal morphology with a high degree of support; attempts to extract DNA were unsuccessful. Stable strontium isotope analysis supports either a recent introduction from western Canada or long-term acclimation to the local area of Devon where it was collected. Although the specimen was undoubtedly an ‘alien’ (an escapee or release from a collection), it is significant as material evidence in demonstrating, for the first time, the presence of a wild-caught, feral, exotic felid dating to the early years of the twentieth century
Rats, cats and hares: exploring natural and humanly-mediated dispersal through a genetic approach
Full text linkThe natural world has been largely shaped by climate fluctuations throughout time. However, more recently in the earth’s history this has changed. Humans have been manipulating the world around them for millennia, including moving a variety of species within and outside of their natural ranges. This can be deliberate: such as the raising of animals for subsistence, or accidental: such as stowaway animals on ships. In order to further our understanding of where and when people have moved animals in the past this thesis explores the movements of three understudied species. It begins with the study of a species whose range has been largely shaped by natural causes, the mountain hare. It’s distribution across Europe and Russia has been shaped by the changing climate, however even with these changes, it maintained its population structure throughout its vast range through time. This thesis focuses on the western edge of the mountain hare range where it was cut off from the rest of the continuum on the edge of the ice sheet with the last advance of ice, surviving in refugia and recolonising when conditions became favourable similarly to other possible Celtic fringe species in Britain and Ireland. This demonstrates the resilience of this cold adapted species over millennia of climate fluctuation. The other two species studied were translocated by people, one intentionally and one accidently. The domestic cat was at least initially intentionally moved for pest control. The domestic cat arrived in Britain in the Iron Age and became widespread in the Roman period. It was also an early arrival in the Orkneys of Scotland in the Scottish Late Iron Age, contemporary with Roman Britain. Domestic cats then became widespread in the Viking and Norse periods of Orkney. In Ireland only two of the three domestic cat lineages were found which may demonstrate that they missed the first wave of introduction of domestic cats. The black rat was the final species investigated; they were unintentionally transferred as stowaways on boats. This research explores their initial movements into Europe in the Roman period followed by their decline, re-emergence and later decline. Studying all three species together gives us a greater breadth of understanding of the movements of animals in the past, both naturally and anthropogenically. In addition, the results of this thesis will provide information that will be useful in the conservation management of each of these species in the future
What does a bear baiting assemblage look like?: Interdisciplinary analysis of an early modern “sport”
No full textBear baiting was a popular and culturally important form of entertainment in Shakespeare’s England. It occurred all over the country, but was most formalised in Bankside, London, a key early modern entertainment hub. Here, we bring together zooarchaeological, stable isotope and archival evidence from nine archaeological sites in Bankside to define features specific to bear baiting. We then provide a model for identifying bear baiting assemblages in the archaeological record of England and beyond
Ancient DNA perspectives on pathogen evolution in domestic animals
Full text linkPathogens, animals (domesticated or not) and humans have intertwined evolutionary trajectories for millennia now, with this relationship intensifying after the Neolithic Demographic Transition and its subsequent epidemiological transition that increased the exposure of animal populations to pathogenic reservoirs. Incorporating the temporal dimension in the study of disease evolution requires the incorporation of ancient pathogen DNA data in phylogenetic and population genetic analyses, which is not a simple task. Limited DNA survival and DNA damage, however, have hindered the search for ancient pathogens. For these reasons the accurate identification of microbial species from archaeological samples is integral and has the potential to provide an unprecedented perspective on the evolutionary history of major diseases that have affected humans and domestic animals. In the first chapter of this thesis I propose a novel analytical method for metagenomic identifications, HAYSTAC, which can also be applied for direct hypothesis testing regarding the presence of pathogens in metagenomic samples. By employing a clear probabilistic model for species identification from shotgun sequencing DNA data, along with incorporating additional algorithmic steps for taxonomic result validation, robust metagenomic identifications from sequencing data generated from archaeological samples become possible, with a significantly lower false positive rate when compared to pre-existing and established methods. In the second chapter of this thesis I used HAYSTAC to screen more than one thousand archaeological and modern chicken samples for Marek’s Disease Virus (MDV), a devastatingly virulent virus threatening the modern poultry industry. Following the DNA sequencing of archaeological chicken samples positive for MDV, I reconstructed the genomes of these ancient strains and compared them to modern ones. Through a time dependent phylogenetic reconstruction approach, I identified the possibility that modern MDV strains are evolving at an accelerated rate compared to ancient ones, with modern highly virulent strains possibly evolving from a potentially non-virulent (ancient) form (prior to 1907) of MDV, a finding that can have a significant impact on improving the health status of domestic chicken population globally. In the third chapter of this thesis, I examine if the process of domestication has had an impact on the disease burden of domestic pigs and dogs, by applying HAYSTAC. By applying hypothesis-driven species identification methods, I focused on screening animal derived metagenomes for zoonotic bacterial pathogens. Since many of the causative agents of these zoonotic diseases became prevalent in a post-industrial context, the results of this approach will be able to offer insights into how human activity has reshaped the landscapes of both the natural environment and animal diseases
Interpreting patterns in transcriptomes and ancient DNA from Next Generation Sequencing data
Full text linkA goal of biological research is to understand the implications of the evolutionary process. Efforts using direct analysis of nucleotide sequences have had a tremendous impact in achieving this goal. The revolution in palaeogenomics and transcriptomics research over the past decade is inextricably intertwined with the power of next generation sequencing platforms and the ability to target and sequence short DNA molecules at a high resolution. In palaeogenomics, archaeological specimens that were previously unsuitable for DNA analyses due to extensive postmortem sequence damage can now be used successfully as source material. The increasing availability of ancient DNA allows for greater precision and accuracy in the molecular dating of phylogenetic trees, and provides invaluable insights into the timing, location, mechanisms, and dynamics of important evolutionary processes such as domestication. In gene expression data, the sensitivity of RNA-seq allows for the potential detection of alternative splice isoforms of transcripts as well as rare and context-specific transcripts, such as those seen in complex tumour environments. In this thesis, I use bioinformatic techniques to 1) evaluate the expression of endogenous retrovirus-encoded putative oncogenes np9 and rec in RNA-seq data, and find that these gene products are upregulated in many cancers, and in specific stages of early embryonic development; 2) find that np9 and rec are positively and negatively correlated with the upregulation and downregulation of many cancer stem cell and epithelial-mesenchymal transition biomarkers; 3) utilise ancient and modern animal mitochondrial genomes to find evidence of time-dependence evolutionary rate estimates, showing that the degree of this effect varies among parts of the mitochondrial genome and with the estimation method being used; 4) reconstruct early animal domestication processes of pigs in Europe
Human influences on animals from an ancient DNA perspective: case studies on Chinese domestic cats (felis catus), Chinese leopard cats (prionailurus bengalensis), fallow deer (dama dama), and Chinese domestic pigs (sus scrofa)
No full textHuman-animal interactions since the late Pleistocene have exerted long-lasting and significant influences on animals. With the advance of ancient DNA techniques, the availability of genomic data from ancient samples has profoundly increased, and now with great possibilities we are able to investigate the past and gain knowledge of the phased genetic changes in history. Applying predominantly ancient genomic methods, I have conducted case studies on four different species under the states of domestication, semi-domestication, and commensalism respectively to explore how the anthropogenic exercises have affected the evolutionary trajectories of animals.
The first case involves Chinese domestic cats (Felis silvestris catus) by examining 4 nuclear genomes and 22 mitochondrial genomes from 22 ancient Chinese samples spanning 5,500 years. Chinese domestic cats are descended from African wild cats (Felis silvestris lybica) and were likely brought to China via the Silk Road during the 7th and 9th centuries AD. Leopard cats (Prionailurus bengalensis) might have been enjoying a commensal relationship alongside humans in the Late Neolithic before domestic cats arrived in China (6,000-5,500 BP). However, this commensal link did not survive the Han Dynasty (202 BC - 220 AD). Small felids and humans did not cohabit again until the Tang Dynasty (618-907 AD) when domestic cats were imported. Since then, domestic cats have not mixed with any Chinese native wild cat species, including the Chinese mountain cat (Felis silvestries bieti) and Asiatic wild cat (Felis silvestries ornata).
The second case involves the Chinese leopard cat (Prionailurus bengalensis), who were in a commensal relationship with humans since the Chinese Neolithic period (5,500 BP). This study collected seven ancient leopard cats from the Middle Reach of the Yellow River Basin. Ancient genome study shows that the leopard cats from the Middle Reach of the Yellow River Basin and Far East Russia were closely related, albeit the former was receiving introgression with Indochina leopard cats. According to archaeological, chronological, and literary analysis, leopard cats and humans ceased their commensal connection when the Han Dynasty (202 BC - 220 AD) fell, and never recovered. Domestic cats replaced leopard cats in the human niche, when they were introduced around the Tang Dynasty (618-907 AD).
The third case involves the Persian and European fallow deer (Dama dama mesopotamica and Dama dama dama). The post-glacial dispersal of the fallow deer was nearly entirely mediated by people. We generated and analysed 29 partial or mitochondrial genomes of ancient fallow deer to gain insights into their evolution and range changing. Ancient DNA analysis indicates that the two fallow deer subspecies diverged 0.57 million years ago and might have interbred in Southwestern Anatolia. An ancient maritime commercial route brought Persian fallow deer from the Levant to Cyprus and westward to the Mediterranean, while European fallow deer from Anatolia were dispersed to continental Europe.
The fourth case involves the Chinese domestic pigs (Sus domesticus). The Middle Reach of the Yellow River Basin was one of the domestication hubs of pigs. We have conducted ancient genomic investigation of five nuclear and nine mitochondrial genomes of ancient domestic pigs from two archaeological sites in the Middle Reach of the Yellow River Basin spanning at least 3,000 years, and zooarchaeological analysis on 1,400 pieces faunal remains excavated from the Zheng-Han City (2,500 BP). I suggest that the populations represented by the ancient domestic pigs from the Middle Reach of the Yellow River Basin had contributed to the formation of modern Chinese breeds and issued new hypothesis of the origin of the Chinese domestic pigs. Zooarchaeological approaches showed a reduction in pigs' prominence in archaeological sites and potential intensified pig husbandry in the MYR from the late Neolithic to the Iron Age.
Combining the results of the four case studies, we have addressed the importance of anthropogenic forces in altering the evolutionary trajectories of animals: 1) The human-mediated dispersal can dramatically change the range of the species, even for the animals who had lost most of their genetic diversities, accompanying the migration of human, they were still able to be spread globally. 2) By establishing affinities or cultural connections with human, the population dynamics of animals would closely correlate with the development of human societies. 3) Importing new species would lead to the admixtures between exotic animals and its related local counterparts. Such admixtures could in one hand introduce new genetic diversities, while in another hand, offset the adaptability of the native species to local environment
Formal methods for evolutionary inference using ancient DNA
Full text linkAncient DNA has revolutionised our ability to study past evolutionary processes by enabling direct observation of genetic variation in past populations. However, current formal methods for evolutionary inference are challenged by the sparse and heterogeneous distribution of data in space and in time, typical of ancient DNA datasets, as well as sample age uncertainty. In this thesis, I introduce analytical approaches that explicitly address these problems and show how inference from ancient DNA can greatly benefit from analysis that formally compares different evolutionary and demographic scenarios. I apply these approaches to three different cases that represent a range of demographic histories and evolutionary questions spanning different time- scales, species and types of data. The first approach combines space and time into a single matrix that can be used to estimate levels of past within population mobility. I apply this method to human ancient DNA data spanning the last 35 thousand years to recover changes in mobility over this time period. The second approach combines spatially and temporally explicit simulations with ancient mitochondrial genome data, spanning the Northern hemisphere and the last 50 thousand years to reconstruct large- scale population dynamics in Grey wolves over this time period. The third approach uses likelihood-based analysis to reconstruct episodes of past selection from time series of ancient DNA data. I apply this method to genotype data spanning two thousand years from two loci in domestic chicken to estimate a number of selection parameters including the starting time of the selection. These case studies all illustrate how formal hypothesis testing in spatially and temporally explicit frameworks make it possible to directly link evolutionary histories to the climatic and archaeological records as well as historical sources and show how identifying potential drivers of evolution allow building a more detailed and complete picture of the past.</p
Palaeogenomics of animal domestication: computational modelling of ancestry, demography and selection
Full text linkThe study of animal domestication is in the midst of a genomic revolution, as technological advances dramatically increase the availability of DNA sequence data from ancient and modern domestic populations. For the first time, palaeogenomic datasets are being produced of sufficient size and scope to directly observe anthropological and evolutionary processes through time; from the emergence of domestic animals in the Neolithic, to the formation of modern breeds in the Victorian era.
This thesis applies computational modelling of ancient and modern DNA to infer ancestry, demography, and selection in domestic cattle (Bos taurus), horses (Equus ferus caballus), and dogs (Canis familiaris).
Chapter 1 reviews the substantial contribution palaeogenomics has made to the study of animal domestication, and details the latest theoretical and empirical advances, alongside individual profiles of sixteen major domestic species.
Chapter 2 reconstructs the allele frequency trajectories of genetic variants linked to quantitative traits in genome-wide associations studies (GWAS) of cattle and horses. Using a Bayesian modelling approach, and a dataset of more than 350 ancient genomes spread across the last 10,000 years, the age of the allele under selection for thousands of GWAS variants is inferred, along with the selection coefficients for hundreds of polygenic traits.
Chapter 3 analyses the first ancient genome-wide DNA from pre-contact North American dogs. Admixture analyses show that the earliest American dogs were not independently domesticated, and originated from a population of arctic dogs in Eastern Siberia. These dogs likely accompanied humans during the peopling of the continent, and rapidly diversified after their arrival, until their sudden replacement following the arrival of European colonists. Remarkably, their most closely related living relatives are now an 8,000-year-old contagious cancer clone known as Canine Transmissible Venereal Tumour (CTVT).
Chapter 4 presents an ancestry analysis of a rare breed of humpless, dwarf shorthorn cattle from the remote island of Socotra, in the Arabian Sea. Admixture analyses show that contrary to published hypotheses, these cattle are predominantly Eurasian taurine (Bos taurus) in ancestry, with only minimal African taurine heritage, and preliminary results indicate possible admixture with a basal clade of zebu cattle (Bos indicus)
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