A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.

The domestic dog was probably the first domesticated animal, and the only one to spread to all continents in ancient times. The dog is one of the most phenotypically diverse animals, a result of human selection throughout dog history. Studies of the genetic origins and early spread of domestic dogs is important to gather information about biological and cultural mechanisms behind domestication but also to investigate early human history. The step from a hunter and gatherer lifestyle to farming is one of the most important steps in human history. In this thesis I will present work aimed at understanding both domestic dog origins and dispersal. In order to be able to investigate dog origins based on a second haploid chromosome we identified 14,437 bp of Y-chromosomal DNA sequence. Based on this we show that dogs in Asia south of Yangtze River (ASY) has the highest genetic diversity and was founded from a large number of wolf founders confirming earlier mtDNA results. Early dog dispersal is tightly coupled to human history with the dog brought along as a cultural item. We have for the first time investigated the dog dispersal into Polynesia and Australia and our data can be used as evidence for a more complex settlement of Polynesia than earlier indicated from archaeological and linguistic studies. Analysis of Y-chromosome SNPs in Australian dingoes confirms earlier mtDNA genetic studies that the dingo is part of the domestic dog phylogeny and was founded from a small population of domestic dogs. We have also for the first time investigated the dog population on Madagascar and our data strongly indicates a mainland African origin for the Madagascan dogs. Finally, we have investigated the American dog population sampled from throughout the continent and also for the first time included putative indigenous breed dogs such as Chihuahua and Pero Sín Pelo del Peru, and the free-ranging Carolina dogs from southern USA. Our data clearly indicates a primarily Old World origin for the indigenous breed dogs and also for the free-ranging Carolina dogs in USA. We can also for the first time present evidence for continuity between the ancient and extant dog population with e.g. exclusive sharing of a haplotype between a modern sample of Chihuahua and an ancient Mexican sample. / QC 20120510

The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock. In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones. Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.

Osteoporosis is a disease that leads to decreased bone mineral density (BMD), an altered bone micro-architecture and fragile bones. The disease is highly heritable and numerous genes are thought to be involved, making it difficult to identify the causative genetic elements. Animal models, mainly intercrosses between laboratory strains of mice, have been succesfully used to map genes affecting these traits, but may not mirror the multifactorial genetic etiology of highly complex traits such as osteoporosis. Over the course of tens of thousand years humans have kept domestic animals whose phenotypic repertoires have been tailored to meet our needs. Wild-type red junglefowl (RJ) and domestic White Leghorn (WL) chicken differ for several bone traits. In this thesis Quantitative Trait Loci (QTL) mapping was used to trace the inheritance of bone traits in two separate intercrosses between RJ and WL. In these studies we identified several QTL that contributed to differences in BMD, bone size and biomechanical strength of bone. In a comparison of QTL identified in the two intercrosses it was observed that nine QTL had overlapping genomic positions, implicating these loci as important to bone phenotypic variation in chicken. In two separate studies, microarray technology was used to compare global gene expression in bone tissue from RJ and WL. In these studies, differential expression was observed for 779 and 560 genes, respectively. Many differentially expressed genes were co-localized with QTL, which implicates them as QTL-candidates. Results presented in this thesis link several genomic regions and genes to variation in bone traits. Increased knowledge about these identified genes and regions will contribute to a better understanding of the mechanisms underlying inter-individual differences in bone metabolism, both in chicken and man.

Stories about aborigines in a settler society, especially stories about aboriginal maidens and settler men, tend to become national allegories. Initially, the aboriginal maiden is a figure for colonial landscapes and resources, while later, in her conversion in fact or fiction from aboriginal to settler, she helps build national identity. Yet after being romanced, the aboriginal maiden’s fate is to disappear from settler consciousness, because she is displaced by the national settler mother or because the settler loses interest in her, only to return in abjection to haunt the settler conscience. In her return as a prostitute, a commodified bride or a ghost, she disturbs the discourse of ‘national domestication’, the notion of nation as family. Though she returns in abjection, an Amazonian association tends to linger in the person of the aboriginal maiden, an association that suggests the kind of self-empowerment on which a healthy liberal society depends. In other words, the figure of the aboriginal maiden tends to be used in the construction, the contestation, and potentially the reconstruction of national identity in a settler society. While I discuss examples from settler societies around the world, particularly the story of Pocahontas, and try to contribute to ‘settler colonial discourse studies’, I focus on postwar Taiwan. This dissertation proposes the notions of the ‘settler society’ and the Habermasian public sphere as ‘frames’ for the study of Taiwanese literature. I show how the Formosan aboriginal maiden has been appropriated for the construction and critique of both Chinese and Taiwanese nationalisms. I argue that while nationalism is partly about social control and the advancement of particular interests, writers who have romanced the Formosan aborigine have been implicitly participating in a debate about national domestication, the telos of which is the democratic imagination of a good society, one in which the Formosan aborigines will feel in some sense ‘at home’, though perhaps not as members of the ‘national family’. Finally, under the rubric of ‘alternative aboriginal modernities’, I discuss stories that reread the romance of the Formosan aborigine by aboriginal writers who have entered the national debate.

Stories about aborigines in a settler society, especially stories about aboriginal maidens and settler men, tend to become national allegories. Initially, the aboriginal maiden is a figure for colonial landscapes and resources, while later, in her conversion in fact or fiction from aboriginal to settler, she helps build national identity. Yet after being romanced, the aboriginal maiden’s fate is to disappear from settler consciousness, because she is displaced by the national settler mother or because the settler loses interest in her, only to return in abjection to haunt the settler conscience. In her return as a prostitute, a commodified bride or a ghost, she disturbs the discourse of ‘national domestication’, the notion of nation as family. Though she returns in abjection, an Amazonian association tends to linger in the person of the aboriginal maiden, an association that suggests the kind of self-empowerment on which a healthy liberal society depends. In other words, the figure of the aboriginal maiden tends to be used in the construction, the contestation, and potentially the reconstruction of national identity in a settler society. While I discuss examples from settler societies around the world, particularly the story of Pocahontas, and try to contribute to ‘settler colonial discourse studies’, I focus on postwar Taiwan. This dissertation proposes the notions of the ‘settler society’ and the Habermasian public sphere as ‘frames’ for the study of Taiwanese literature. I show how the Formosan aboriginal maiden has been appropriated for the construction and critique of both Chinese and Taiwanese nationalisms. I argue that while nationalism is partly about social control and the advancement of particular interests, writers who have romanced the Formosan aborigine have been implicitly participating in a debate about national domestication, the telos of which is the democratic imagination of a good society, one in which the Formosan aborigines will feel in some sense ‘at home’, though perhaps not as members of the ‘national family’. Finally, under the rubric of ‘alternative aboriginal modernities’, I discuss stories that reread the romance of the Formosan aborigine by aboriginal writers who have entered the national debate.

"An ‘exponential growth of science’ throughout modern history has been frequently boasted by numerous narcissistic accounts of ‘modern humanity.’ Nonetheless, ‘modern science’ seems to have overwhelmingly compromised on its original promises by fitting into an ‘industrial scheme.’ With this concern, ‘molecular phylogeographics with conservational ambitions’ would look an intact ground for research efforts in a ‘school of biotechnology.’ The dog (Canis familiaris) as an earliest domestic animal has a history of conflicts over its origins and dispersal. Having those disputes addressed, valuable knowledge could be acquired on the nature and dynamics of domestication, and of human societies particularly of pre-agricultural ages. We employed two most widely-used genealogical markers, the mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome (NRY), to address dog demography. Through 582 bps of mtDNA Control Region, complemented with whole mitochondrial genomes, it was established that almost all maternal lineages of the domestic dog worldwide coalesce to a population of at least 51 and perhaps many more female wolves in Asia South of Yangtze River (ASY) approximately 16,000 years before present (BP). This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. A closer examination of this portrait in Southwest Asia (SwAsia) and the Fertile Crescent (FC), a region which has supplied persuasive evidence on early presence of the domestic dog, retrieved the same information, with implications for backbreeding with the local wolf population. Meanwhile, analyses of mtDNA dispersal showed that dogs took the long way via land to Madagascar Island, and not together with humans via sea. By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. Screening of NRY by a SNP assay in the dingoes of Australia Island as a population of feral dogs revealed restricted and similar dispersal patterns for sires and dams. Prospects of ancient, multilocus and whole genome assays with the emerging high-throughput technologies has still more to promise on finer elaborations of these issues." / <p>QC 20120529</p>

Thyroid hormones are well known important to be in development and growth in birds and that signaling of thyrotropin (TSH) regulates the photo induced seasonal reproduction. A mutation at the thyroid stimulating hormone receptor (TSHR) gene in domestic breeds of chicken could be involved in the release of the photoperiodic regulation. Furthermore, TSH can affect a wide range of domestication related phenotypes, such as behaviour, growth rate and pigmentation. The aim of this study was to investigate the behaviours expressed in the different genotypes on the TSHR gene in chickens. Four standard tests were conducted, aerial predator, fear of human, social dominance and tonic immobility. An advanced intercross line of chickens between red junglefowl and White leghorn was used. Male domestic type chickens explored more, showed more less fear behaviours and showed least fear behaviours in the fear of human test. Increased activity and flight response has been interpreted as a lower fear response, which is in line with this study. The wild type chickens showed more social dominance than domestic type chickens which are in line with previous results. In tonic immobility there was a difference between the wild type male and heterozygous male chickens in latency until first head movement. The conclusion of this study is that there is a difference between the wild type and domestic type chickens. This indicates that the TSHR gene is involved in behavioural changes during domestication, but whether it is due to passive or active selection is the question.

Social support is thought to give animals benefits from social partners, such as improved coping with challenges. The aim of this study was to investigate differences in social support in the red junglefowl (RJF) and a domestic layer strain, the White Leghorn (WL). A runway test consisting of two compartments with unfamiliar and familiar stimulus animals was used to measure social motivation before and after a stressful experience. Total number of test animals was 56 divided into four groups; male and female WL as well as male and female RJF. Results showed that females preferred to stay close to familiar conspecifics after stress treatment. Before stress treatment there was little difference between either sex of WL while RJF males and females chose different zones. Females preferred familiar conspecifics, indicating that they rely more on familiar social stimuli for social support. Males of the two breeds behaved differently towards stimulus animals. WL males showed aggression towards familiar stimulus animals while RJF males directed aggression towards unfamiliar stimulus animals. Indication of sexual behavioural dimorphism was supported while further research is needed in domestication effects on social support in chickens.

Domestication has taken place over thousands of years and during that time we have bred animals on different traits. The red jungle fowl is the ancestor to all domesticated chicks, including the white leghorn which is used in egg production. The domestication of the red jungle fowl has resulted in behavioral changes between itself and domesticated breeds, such as white leghorn. In this study we examine how these two breeds handle stress and whether or not they use social support when coping and recovering from a stress experience. The study took place in a built arena with two stimuli animals on each side. There the animal was studied for 5 minutes, stressed for 3 minutes and studied again for 5 minutes. We found that the red jungle fowl males spent more time in the unfamiliar zone before stress than males of the white leghorn. Our results also showed that the females of white leghorn and red jungle fowl spent more time in the familiar zone than males after being stressed. This is an indication that they are more dependent on social support from familiar animals after stress than the males are. Aggressive behavior was also observed among the males. Red jungle fowl males acted aggressively towards the unfamiliar stimuli animals and the white leghorn towards the familiar stimuli animals. In conclusion, we found that the females where in greater need of social support than the males. / Biologi