For several decades, the origin of domestic horses has been the focus of research across multiple disciplines, yet many aspects of the horse domestication process remain poorly understood. One of the reasons for the difficulty in establishing a coherent scenario of horse domestication is that archaeological, mtDNA, and Y chromosome data have yielded ambiguous results, possibly because each class of markers reflects different aspects of the domestication process. In this thesis, I use large autosomal genetic datasets from horses sampled across Eurasia to investigate the origin and spread of horse domestication. I begin by characterising genetic diversity of horses from the Eurasian steppes and neighbouring regions, thus laying the groundwork for a more thorough analysis into the demographic history of horses. I then investigate the origin and mode of spread of horse domestication in the Eurasian steppe region using a spatially explicit genetic model. I show that horse domestication was initiated in the western part of the steppes, and that the spread of horse domestication involved both movement of domestic herds and extensive recruitment of wild horses from across this vast region, a scenario which integrates both archaeological and molecular evidence. Having established the route of spread of early domestic horses out of their domestication origin in the western steppe, I go on to investigate the routes and levels of gene flow among Eastern Eurasian horse populations post-domestication. I show that the ancient Silk Roads have played an important role in shaping the genetic structure of Eastern Eurasian horses, facilitating gene flow across deserts and high mountain chains. Finally, I provide further compelling evidence for the persistence of wild horses in the Iberian Peninsula throughout the Holocene period, and the substantial contribution of these local populations to the gene pool of Iberian domestic horses. Together, my results provide a coherent picture of the origin and spread of horse domestication, integrating for the first time previous evidence from archaeology, mtDNA and Y chromosome sequence data.

Understanding the success of the human species is central to evolutionary anthropology. While we share many traits with our relatives the great apes, only humans migrated to all corners of the earth and domesticated other species, leading to the emergence of complex societies. Investigations into human genomes have shown that they are a rich source of information for insights into our past. However, for a complete understanding of human evolution it is necessary to look beyond our own genomes. This thesis is about using comparative genomics to place human evolution within a wider context by studying adaptation in our closest living relatives and in the species that we domesticated. In the first study, I investigate the genetic changes involved in the earliest stages of dog domestication. Using a global sample of dog and wolf genomes I identify regions that are highly diverged between these species. I find that selection in the initial stages of dog domestication likely involved genes involved in the fight-or-flight response, advancing our understanding of this process. In the second study, I look for commonalities in the genetic changes that occurred during animal domestication across species. I compare genome sequences from experimentally and historically domesticated species. I identify genes and variants that may underlie the phenotypic changes that occurred during domestication. I find evidence of biological pathways that appear to always be involved in the domestication process. In the third study, I characterise the signatures of natural selection in all major Hominidae lineages using population genomic data. I find that most signatures of positive selection are species specific, although some loci appear to be selected across several lineages. I determine that the efficacy of selection varies between species and is significantly correlated with long-term effective population size. These results contribute to a more complete understanding of human evolution. i This thesis is based on the following manuscripts: 1. Cagan A & Blass T. (2016) Identification of genomic variants putatively targeted by selection during dog domestication. BMC Evolutionary Biology,16:1. 2. Cagan A, Albert FW, Plyusnina I, Trut L, Renaud G, Romagné F, Wiebe V, Kozhemjakina R, Gulevich R, Trapezov O, Yudin N, Alekhina T, Aitnazarov R, Trapezova L, Herbeck Y, Schöneberg T, Pääbo S. Genes and pathways selected during animal domestication. Submitted to eLife. 3. Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. (2016). Natural Selection in the Great Apes. Molecular Biology and Evolution, 33:3268-3283.:Summary 1 Zusammenfassung 8 Chapter 1 Identification of genomic variants putatively targeted by selection during dog domestication 16 Chapter 2 Genes and pathways selected during animal domestication 38 Chapter 3 Natural Selection in the Great Apes 73 References 149 Acknowledgments 152 Curriculum Vitae 153 Declaration of Independence 156 Author Contribution Statements 157

The new possibilities offered by information & communication technologies (ICTs) within the work-place and elsewhere have attracted wide attention by economic and social actors. One outcome is the institutional ‘push’ for all businesses to embrace these technologies and ‘get online’. However, it is evident that take-up amongst businesses has been highly uneven with some cautious in their adoption and, thus, many have not fully exploited the possibilities offered. To understand this variety in the adoption and use of online technologies (which in some cases includes their nonadoption and non-use) it is necessary to examine practices and establish underlying dynamics surrounding new forms of ICTs. This thesis will investigate the practices associated with the adoption and use of ICTs in the hotel industry. Three basic questions are addressed. The first relates the online practices of hoteliers, including the use of online intermediary services, the nature of uptake and the implications for both practices and relations with customers. The second relates to any externalities which condition a hotelier’s practices. The third is concerned with how to conceptual explain observations – findings. Investigation of these questions has resulted in an empirically rich study. This has involved a multi-method approach that allows online practices to be viewed through different lenses and from an adapted Social Shaping of Technology perspective. The population of Scottish serviced accommodation providers was compiled and used to determine the uptake of online practice. Interviews revealed specific practices. Published material provided insight into contextual issues, particularly those relating to institutional developments. The research shows that there were three principle strategies for the adoption of the new technologies. First, they were embedded by the users themselves (‘internalisation’) – often through much effort and processes of configuration – into their ‘busy day’. The process of ‘learning’ (or learning by trying) was found to be an integral feature of uptake. Secondly, some users opted for an alternative solution where, rather than design their own website, they adopted the offerings of online intermediaries (such as online booking facilities) (‘intermediation’). However, the appropriation of online intermediation was found to be both costly and fraught with new kinds of risks (e.g. double bookings) and uncertainty (e.g. no guarantees of bookings). Thirdly, a further option (‘localisation’) was for local groups of hoteliers to collectively produce an online presence that promotes the locality and thereby indirectly provides benefits to their businesses. The analysis was performed using a modified version of Silverstone’s (1992) ‘domestication’ framework. However, ‘localisation’ questioned the assumptions underpinning ‘domestication’, suggesting the need for a more sophisticated analytical device, such as offered by the metaphor of ‘tailoring’. It is concluded that the apparently deterministic institutional view of the benefit of online technologies and the imperative that they are fully exploited to give competitive advantage, can be at odds with the locally contingent and diverse nature of online practices. The research found that the new online practices did not entirely replace traditional ones, but emerged as complementary to them.

Cow cockle (Vaccaria hispanica [P. Mill.] Rauschert) is a summer annual species introduced to North America from Europe. It has been investigated as a potential crop for the Canadian prairies because of its ultra–fine starch, cyclo–peptides, and saponins. However, cow cockle has a long history of being a weed in Canada and may need additional scrutiny of its weediness potential before initiating commercial production. In addition, cultivating poorly domesticated species may lead to further environmental and weed management risks; hence, an understanding of the domestication status is required. The objectives of this research were to evaluate available cow cockle germplasm i) to identify populations that are best adapted to cultivation as well as the traits responsible for such adaptation, ii) to determine seed dormancy levels in cow cockle populations and to determine how temperature and light affect seed dormancy and germination, and iii) to determine whether cow cockle populations are persistent and form a seed bank. A total of 15 cultivated, weedy, and wild cow cockle populations from different parts of the world were compared for agro–morphological, seed dormancy and seed persistence characters from 2009 to 2011. In the field persistence study, two populations including weedy (Scott weedy) and cultivated (Scott) lines were included. Cluster analysis revealed three main groups among the populations based on the traits studied. Physiological maturity, seed size, plant height and seed yield differed most among populations. The cultivated populations, Pink Beauty, Turkey, PB–87, Scott and a weedy population, UMan–89 had higher seed yield, larger seeds, and greater biomass compared to the other populations. Although weedy populations showed some adaptation to cultivation, characters relating to plant architecture, seed size and yield suggested a weedy habit. Freshly matured seeds of all the populations showed high levels of primary conditional dormancy except “Mongolia”. At optimum temperature conditions for germination (10 C), the effect of temperature regime (alternating and constant) and light on seed dormancy were insignificant. The variation in optimum temperature, light, and their interactions among the cow cockle populations may be due to the plants evolving to adapt to their local environments. In the field persistence study, the weedy population had higher seedling emergence at two out of three locations and a larger residual seed bank at all the locations. Despite the differences in seed persistence between the populations, considerable numbers of seed of both weedy and cultivated lines were recovered from the soil seed bank at the end of the study. This concurs with the results of the laboratory persistence study, as both the populations had greater seed longevity (p50 values > 50 days) which suggests a field persistence of over three years. In conclusion, higher seed yield, larger seeds, and greater biomass in cultivated populations may result from certain pre–adaptation towards domestication, which may have been acquired during the process of pre–domestication cultivation. From a domestication perspective, if cow cockle were grown as a crop, the conditional dormancy may not be considered a barrier to domestication and can be viewed as a physiological mechanism to avoid germination at harvest. The major concern in cow cockle domestication would be seed persistence, as it can form a reasonably long–term seed bank. This may pose some concerns for the production of cow cockle as a crop in the Canadian Prairies. The current research suggests that cow cockle populations from Canada, although they showed some adaptation to cultivation; are largely weedy and can be considered as variants of an early introduced species which might have evolved to adapt to non–native conditions.

A suite of plants from the maize genus Zea L. (Poaceae) and the specialist herbivore Dalbulus maidis (DeLong and Wolcott, 1923) (Hemiptera: Cicadellidae) were used to test the hypotheses that anti-herbivore defenses are affected by plant life-history evolution and human intervention through domestication and breeding for high yield. The suite of plants included a commercial hybrid maize (Zea mays ssp. mays L.), a landrace maize, two populations of annual Balsas teosinte (Z. mays ssp. parviglumis Iltis & Doebley), and perennial teosinte (Z. diploperennis Iltis, Doebley & Guzman). Leaf toughness and pubescence, oviposition preference, and feeding and oviposition acceptance parameters were compared among the suite of host plants looking for effects of transitions in life history (perennial to annual teosinte), domestication (annual teosinte to landrace maize), and breeding (landrace maize to hybrid maize) on defenses against D. maidis. Observations on leaf toughness suggested that the life history and domestication transitions weakened the plant’s resistance to penetration by the herbivore’s mouthparts and ovipositor, as expected, while observations on pubescence suggested that the breeding transition led to stronger defense in hybrid maize compared to landrace maize, contrary to expectation. Observations on oviposition preference of D. maidis coincided with the expectations that life history and domestication transitions would lead to preference for Balsas teosinte over perennial teosinte, and of landrace maize over Balsas teosinte. A negative correlation suggested that oviposition preference is significantly influenced by leaf toughness. Observations on host plant feeding and iii oviposition acceptance under no-choice conditions suggested that D. maidis equally accepts all host plants considered in this study, thus these observations did not support the hypotheses associated with the life history, domestication, and breeding transitions evident in the herbivore’s host genus. Overall, the results of this study suggested that plant defenses against specialist herbivores are variably affected by plant life history evolution, domestication, and breeding. Additionally, the study’s results suggested that chemical defenses may play a role in Zea antiherbivore defense because the two physical defenses that were evaluated (i.e. leaf toughness and pubescence) only partially explained host preference of D. maidis

Submitted by DANIEL ANTONIO VILLAMIL MONTERO null (dvillamontero@fca.unesp.br) on 2017-07-17T04:38:29Z No. of bitstreams: 1 TeseDAVM_julho.pdf: 9783024 bytes, checksum: 5e47b7548f0a031f8c1c3c3ddbc72902 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-07-19T16:34:48Z (GMT) No. of bitstreams: 1 villamilmontero_da_dr_bot.pdf: 9783024 bytes, checksum: 5e47b7548f0a031f8c1c3c3ddbc72902 (MD5) / Made available in DSpace on 2017-07-19T16:34:48Z (GMT). No. of bitstreams: 1 villamilmontero_da_dr_bot.pdf: 9783024 bytes, checksum: 5e47b7548f0a031f8c1c3c3ddbc72902 (MD5) Previous issue date: 2017-02-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / As relações e interações entre os seres humanos e as passifloras são múltiplas e complexas, incluindo casos como a domesticação, dispersão, aproveitamento e depredação de espécies (entre outras). Dada sua importância econômica, as passifloras constituem um recurso genético muito importante e a caracterização de populações silvestres e cultivadas é uma prioridade para os países neotropicais que albergam a maior diversidade do gênero. Mais de 80 espécies produzem frutos comestíveis e pelo menos 37 são cultivadas local e regionalmente. A implementação de estratégias para a conservação e o aproveitamento destes recursos fitogenéticos são necessárias, devido ao seu potencial para o desenvolvimento e diversificação de agricultura. O estudo aprofundado das relações humanas com as plantas cultivadas do gênero Passiflora pretende contribuir com delineamentos para programas de conservação da biodiversidade de passifloráceas. Neste trabalho são abordadas informações agroecológicas, biogeográficas e etnobotânicas correspondentes às espécies úteis de Passiflora. / Relationships and interactions between humans and passionflowers are multiple and complex, including cases such as domestication (among others). Due to their economic importance, passiflowers constitute a very important genetic resource and the characterization of wild and cultivated populations is a priority for Neotropical countries that have the greatest diversity of the genus. More than 80 species produce edible fruits and at least 37 are grown locally and regionally. The implementation of strategies for the conservation and utilization of these genetic resources are necessary due to their potential for the development and diversification of agriculture. A depth study of cultivated plants of the genus Passiflora intends to contribute with designs for programs of conservation of the biodiversity of Passifloracea. In this work the agroecological, biogeographic and ethnobotanical information corresponding to the useful species of Passiflora are presented and discussed.

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that colonize the roots of the majority of vascular land plants. These fungi have a unique nuclear organization, in which thousands of nuclei co-exist among an unsegmented fungal body. In individual strains these nuclei can all be genetically similar (homokaryotic) or be derived from two distinct parents (dikaryotic). In other fungal groups the presence of two distinct nuclei in one cell (fungal dikaryons) can change their fitness, function, and symbiotic relationship; begging the question, what impact does the presence of two parental genotypes have on the arbuscular mycorrhizal symbiosis? I am investigating this by measuring the mycorrhizal response (MR) of potato cultivars with different degrees of domestication using representative AMF homokaryons (4) and AMF dikaryons (4). I found that the genetic organization (dikaryotic vs homokaryotic) and domestication status of the host (modern vs old) are both significant factors in the mycorrhizal response of host plants. Specifically, biomass is significantly greater when inoculated with homokaryotic AMF compared to dikaryotic AMF. Dikaryotic strains have low arbuscule colonization in modern cultivars and higher in old, although there are not significant differences in other fungal responses between homokaryotic and dikaryotic AMF. Furthermore, nutrient uptake (N and P) is greater in old cultivars than modern cultivars, although the root:shoot ratio is lower in old cultivars. Analyses of single spores using digital droplet PCR (ddPCR) confirm that nucleotype ratio of dikaryotic spores shifts depending on the host identity. This research provides novel insights into the role of AMF genetic organization in the mycorrhizal symbiosis in greenhouse conditions. In particular, this work shows that the presence of two distinct nucleotypes results in the fungi being more readily adaptable to the host leading to a more stable MR and a potentially selfish strategy, when in symbiosis with potato cultivars.

No description available.

The domestication of animals is a process of great interest to many scientific fields, including genetics. Differences in coat colour between wild and domesticated animals have been of scientific interest for a long time. Coat colours are easily recognizable phenotypes and so have been studied since the dawn of modern genetics. Many phenotypes that are similar across species have the same genetic basis, but there are numerous exceptions. Similar phenotypes within a species can also have different genetic backgrounds. The progressive advances in genetic research methodology have given new insights into both the molecular basis for coat colours and the history of domestication over the last decades. The variation in coat colours seen today is believed to be caused mainly by human selection. Similarities in morphological changes between different species during domestication, including colour phenotypes such as white spotting, have long been noted. This is known as the domestication syndrome and two major hypotheses for this have been suggested: the neural crest hypothesis and the thyroid hormone hypothesis. This thesis gives an overview of the current knowledge about the genetic basis of coat colours in mammals, the genetic aspects of domestication of animals, and how the two are related.

Les objectifs de ce travail visent à appréhender l'histoire évolutive et biogéographique du palmier dattier (Phoenix dactylifera L.), espèce d'une importance capitale pour les populations humaines des régions chaudes et arides d'Afrique du Nord et du Moyen-Orient, au moyen d'analyses génétiques et morphométriques. En effet, les origines de la domestication du dattier demeurent peu connues malgré les données archéologiques qui semblent attester de sa culture à partir de la fin du 4ème millénaire avant notre ère. L'analyse phylogénétique du genre Phoenix réalisée à partir de séquences chloroplastiques a permis d'identifier les parents proches du dattier. Des populations de dattiers sauvages sont reconnues pour la première fois grâce à des analyses de diversité et de structuration génétiques. De manière congruente, l'analyse morphométrique de contours de la graines s'appuyant sur la méthode des transformées elliptiques de Fourier met en évidence une nette différenciation entre les individus sauvages et cultivés. La caractérisation des changements de traits morphologiques de la graine liés à la domestication est exploitée pour définir le statut sauvage ou domestiqué de matériel mis au jour dans différents sites archéologiques du Pakistan et d'Egypte. En outre, l'étude génétique de dattiers d'origine diverses semble démontrer qu'au moins deux évènements de domestication ont eu lieu : l'un en Afrique et l'autre au Moyen-Orient. Finalement, les études génétiques et morphométriques, menées séparément ou conjointement selon le type et l'ancienneté du matériel analysé, permettent pour la première fois de discuter des origines, de l'histoire biogéographique et de la dynamique de l'agrobiodiversité du palmier dattier, dans le temps et dans l'espace. / The objectives of this work are to understand the evolutionary history and biogeography of the date palm (Phoenix dactylifera L.), a species of importance to human populations in hot, arid regions of North Africa and the Middle East using genetic and morphometric analyzes. Indeed, the origins of the domestication of the date palm remain poorly understood despite the archaeological data that seem to attest its culture from the late 4th millennium BCE.Phylogenetic analysis of the genus Phoenix made ​​from chloroplast sequences identified close relatives of the date palm. Populations of wild date palms are recognized for the first time through analyses of genetic diversity and structure. Congruently, morphometric analysis of the seed outline based on the method of elliptic Fourier transform highlights a clear differentiation between wild and cultivated individuals. Characterization of changes in seed morphological traits related to domestication is used to define the status of wild or domesticated material excavated from various archaeological sites in Pakistan and Egypt. In addition, the date palm genetic study of various origins seems to indicate that at least two domestication events took place: one in Africa and one in the Middle East. Finally, genetic and morphometric studies, conducted separately or together depending on the type and age of the material analyzed, allow for the first time to discuss the origins, history and biogeographic dynamics of date palm agrobiodiversity, in time and space.