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This master thesis examined the scent marking behaviour by urine and faeces in four equid species, African wild ass (Equus africanus), Grevy?s zebra (Equus grevyi), Plain zebra (Equus quagga) and Mountain zebra (Equus zebra), in captivity. Data about scent marking were collected during two five-month seasons of behavioural observation of 15 equid herds in 5 Czech Zoos, Zoo Dvůr Králové, Zoo Liberec, Zoo Brno, Zoo Ostrava and Zoo Ústí nad Labem. The study focused mainly on testing several hypotheses explaining scent marking in stallions, mares and foals and also on interspecies differences in this behaviour.

付記する学位プログラム名: 霊長類学・ワイルドライフサイエンス・リーディング大学院 / 京都大学 / 新制・課程博士 / 博士(理学) / 甲第24876号 / 理博第4986号 / 新制||理||1712(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 平田 聡, 教授 三谷 曜子, 教授 松田 一希 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Domestic animals have rich phenotypic diversity that can be explored to advance our understanding of the relationship between molecular genetics and phenotypic variation. Since the advent of second generation sequencing, it has become easier to identify structural variants and associate them with phenotypic outcomes. This thesis details studies on three such variants associated with monogenic traits. The first studies on Rose-comb in the chicken were published over a century ago, seminally describing Mendelian inheritance and epistatic interaction in animals. Homozygosity for the otherwise dominant Rose-comb allele was later associated with reduced rooster fertility. We show that a 7.38 Mb inversion is causal for Rose-comb, and that two alleles exist for Rose-comb, R1 and R2. A novel genomic context for the gene MNR2 is causative for the comb phenotype, and the bisection of the gene CCDC108 is associated with fertility issues. The recombined R2 allele has intact CCDC108, and normal fertility. The dominant phenotype Greying with Age in horses was previously associated with an intronic duplication in STX17. By utilising second generation sequencing we have examined the genomic region surrounding the duplication in detail, and excluded all other discovered variants as causative for Grey. Dun is the ancestral coat colour of equids, where the individual is mostly pale in colour, but carries intensely pigmented primitive markings, most notably a dorsal stripe. Dun is a dominant trait, and yet most domestic horses are non-dun in colour and intensely pigmented. We show that Dun colour is established by radially asymmetric expression of the transcription factor TBX3 in hair follicles. This results in a microscopic spotting phenotype on the level of the individual hair, giving the impression of pigment dilution. Non-dun colour is caused by two different alleles, non-dun1 and non-dun2, both of which disrupt the TBX3-mediated regulation of pigmentation. Non-dun1 is associated with a SNP variant 5 kb downstream of TBX3, and non-dun2 with a 1.6 kb deletion that overlaps the non-dun1 SNP. Homozygotes for non-dun2 show a more intensely pigmented appearance than horses with one or two non-dun1 alleles. We have also shown by genotyping of ancient DNA that non-dun1 predates domestication.

The Hittite burial material consists of a very heterogeneous material. The material shows some shared aspects between the different cemeteries and their grave types. However, this material lacks previous extensive comparative studies in central Anatolia. This study aims to problematize this funerary material, by re-evaluating the previous interpretation and by creating links between the different types of material and the cemeteries it was found in. This will be achieved by analyzing four different categories of Hittite graves from the three cemeteries: Osmankayasi, Gordion and Ilica. The total material consists of 268 graves: 91 from Osmankayasi, 46 from Gordion and 131 from Ilica. The material was originally excavated and published during the fifties and sixties by the three archaeologists Kurt Bittel, Machteld Mellink and Winfried Orthmann. The burial material will be analyzed to establish parallels and differences between the three sites, their materials and grave categories. Literary sources and empirical data will be used to supplement previous research but also the new interpretations discussed in this thesis. Keywords: Hittite, cemeteries, mortuary practices, Osmankayasi, Gordion, Ilica, cremations, pithos burials, pit graves, cist-graves, ethnicity, status, equids / Det Hettitiska begravnings materialet består av ett väldigt heterogent material. Materialet visar ändå vissa delade aspekter mellan de olika gravfälten och gravtyperna. Dock saknar detta material tidigare omfattande komparativa studier i centrala Anatolien. Denna studie avser att problematisera detta gravmaterial, genom att skapa kopplingar mellan de olika typerna av materialet och mellan de utvalda platserna som det återfanns i. Detta mål avses att uppnås genom att analysera fyra olika typer av Hettitiska gravar från de tre platserna Osmankayasi, Gordion och Ilica. Det totala grav antalet består av 268 gravar: 91 från Osmankayasi, 46 från Gordion och 131 från Ilica. Materialet var ursprungligen utgrävt och publicerat under femtio och sextio-talet av de tre arkeologerna Kurt Bittel, Machteld Mellink och Winfried Orthmann. Gravmaterialet kommer att analyseras för att etablera paralleller mellan de tre platsernas material och dess gravkategorier. Litterära källor och empiriskdata kommer att användas för att komplettera den tidigare forskningen och de nya tolkningarna i denna studie.

O Vírus do Nilo Ocidental, do inglês West Nile virus (WNV) é um patógeno emergente que é amplamente distribuído na América do Norte e Central. A recente introdução na América do Sul chamou a atenção para a propagação do WNV em países Latino Americanos. O ciclo de transmissão envolve mosquitos, pássaros, cavalos e seres humanos. A avaliação sorológica realizada nestes estudo foi composta por 678 soros de equídeos e 478 soros de aves, realizada por meio do ensaio ELISA de bloqueio específico para WNV e somente as amostras com resultados positivos foram confirmadas por testes de neutralização por redução em placas (PRNTs). A análise molecular foi realizada em soros de 1.241 equídeos saudáveis e em 63 macerados de cérebros de equídeos que morreram de encefalite e obtiveram resultados previamente negativos para outros patógenos. Também testamos swabs de 3.445 aves pelo método molecular, além de amostras de 24 morcegos e 11 onças. As amostras analisadas foram coletadas em diferentes biomas do Brasil. Identificamos pelo ELISA anticorpos para o WNV em treze equídeos e cinco pássaros e o teste de PRNT90 confirmou positividade para o WNV em quatro amostras de equídeos coletadas em 2009 em uma região entre a Amazônia e o Pantanal. Nenhuma das amostras de aves positivas pelo ELISA foram confirmadas por PRNT90. Das 4.784 amostras testadas por RT-PCR, penas duas apresentaram resultados positivos para a detecção, sendo uma ave residente na região do Pantanal e um anatídeo na região do Maranhão, respectivamente. A circulação do WNV é confirmada pela presente pesquisa em larga escala, mesmo na ausência da detecção de casos clínicos. / West Nile virus (WNV) is an emergent pathogen that is widely distributed in North and Central America. The recent introduction in South America has focused attention on the spread of WNV across Southern American countries. The transmission network involves mosquitoes, birds, horses and humans. The serological evaluation of sera from 678 equids and 478 birds was performed using a WNV-specific blocking ELISA, and only the positive results were confirmed by plaque reduction neutralisation tests (PRNTs). Molecular analysis was performed on sera from 1241 healthy equids and on 63 macerates of brains from equids that died of encephalitis and had previously tested negative for other pathogens. We also tested swabs from 3.445 birds, 24 bats and 11 phanteras. The samples analysed were collected in different biomes of Brazil. We identified WNV antibodies by ELISA in thirteen equids and five birds, and PRNT90 confirmed WNV positivity in four equid samples collected in 2009 in an area between the Amazon and the Pantanal. None of the ELISA positive bird samples were confirmed by PRNT90. Of the 4.784 samples tested by RT-PCR, only two were positive for the detection, a resident bird in the Pantanal region and a duck in the region of Maranhão, respectively. WNV circulation is confirmed by this large scale survey even in the absence of detection of clinical cases.

Depuis leur domestication, les équidés sont étroitement associés aux activités humaines et ont, au fil des siècles, été façonnés au gré d’exigences morphologiques, esthétiques, d’allure ou de performance. Cette sélection artificielle a fortement impacté leurs traits phénotypiques et fonctionnels, produisant le large panel des races actuelles. Les sources historiques ont abondamment décrit l’importance des équidés et la diversité de leurs usages dans les sociétés passées. Ceci interroge donc sur la potentielle existence de types morphologiques spécialisés à des périodes antérieures à l’émergence des races. Dans ce contexte, les os présentent un intérêt particulier en tant que reflet des caractéristiques morphologiques et fonctionnelles des animaux du passé. En outre, les équidés étant fréquemment retrouvés sous la forme de squelettes complets en contexte archéologique,leurs restes offrent la possibilité d’étudier l’intégralité de la morphologie squelettique et notamment les interactions entre les os. Pourtant, les restes osseux d’équidés restent relativement peu exploités, probablement en raison des limites inhérentes aux méthodes d’étude actuelles. L’objectif de ce travail est de mieux comprendre la diversité phénotypique et fonctionnelle des équidés domestiques par des approches en morphométriegéométrique. La question de leur identification spécifique est tout d’abord abordée via la recherche de critères discriminants, qualitatifs et quantitatifs, applicables à du matériel archéologique. Les patterns de covariation entre les os sont ensuite explorés afin d’aborder des questions fonctionnelles. Les résultats révèlent une forte intégration morphologique entre les os des membres chez les équidés domestiques et mettent en évidence des différences entre les races selon un axe de covariation principalement porté par des interactions fonctionnelles. Ceci tend à montrer que la sélection artificielle, considérée comme le principal acteur de la diversification morphologique chez le cheval domestique, n’influence pas seulement le phénotype mais aussi les facteurs biologiques qui le sous-tendent. Enfin, une première application à des spécimens archéologiques permet dediscuter l’impact de potentielles formes de sélection artificielle et de standardisation morphologique sur des chevaux anciens. Les résultats démontrent l’intérêt d’étudier non seulement les variations de forme des os, mais aussi leurs covariations, afin d’enrichir nos connaissances concernant les traits morphologiques et fonctionnels des animaux passés, ainsi que les pratiques d’élevage qui y sont associées. L’étude des covariations contribueégalement à accroitre notre compréhension des processus micro-évolutifs, tels que la sélection artificielle, et à travers cela, permet de mieux documenter la manière dont la diversité phénotypique est produite. / Equids and humans share a long history of interaction from the first domestication to the standardization of modern breeds. In order to suit human activities, they have been molded through selection for conformation, harmony, gaits, or performance. This artificial selection is known to have largely impacted morphological and functional traits, producing the large range of current breeds. Historical sources extensively described the widepanel of equid usage in different human civilizations, raising the issue of the potential existence of specialized morphological types in the past, prior to the emergence of modern breeds. In this respect, bones prove to be of particular interest, as an image of the phenotypic and functional characteristics of past animals. Moreover, horses being often found as complete skeletons in archaeological contexts, their remains allow for the study of the complete skeletal morphology, especially concerning the interactions between bones. However, equid bone remains are largely under-explored, probably due to the recurrent limitations inherent to existing study methods. The objective of this work is to describe and understand the phenotypic and functional diversity of domestic equids, using geometric morphometrics approaches. Identification issues are firstly addressed through the research of qualitative and quantitative discrimination criteria, applicable to archaeological samples. Next, morphological and functional questions are addressed, especially investigating bone shape covariation. The obtained results reveal strong morphological integration within equid limb bones and evidenced breed specific differences along a covariation axis largely produced by functional interactions between bones. They show thatartificial selection, regarded as responsible of most of the modern diversification of horse breeds, not only targets the phenotype but also impacts the biological factors which underlie it. Finally, a first application to archaeological skeletons allows to question the influence of potential artificial selection and morphological standardization on past horses. The results demonstrate the interest of not only exploring bone shape variation,but also covariation, to increase our knowledge about the morphological and functional traits of past equids and about the related breeding practices. The study of morphological integration may also contribute to enhance our understanding of micro-evolutionary processes, such as artificial selection on domestic taxa, and through that, gain insights into how phenotypic diversity is produced.

Submitted by Simone Souza (simonecgsouza@hotmail.com) on 2017-10-17T13:31:29Z No. of bitstreams: 1 DISS_2014_Alvair da Silva Alves.pdf: 1886387 bytes, checksum: 3e47dd34fe738b31c6e8fbbb7f127b27 (MD5) / Approved for entry into archive by Jordan (jordanbiblio@gmail.com) on 2017-11-07T15:02:07Z (GMT) No. of bitstreams: 1 DISS_2014_Alvair da Silva Alves.pdf: 1886387 bytes, checksum: 3e47dd34fe738b31c6e8fbbb7f127b27 (MD5) / Made available in DSpace on 2017-11-07T15:02:07Z (GMT). No. of bitstreams: 1 DISS_2014_Alvair da Silva Alves.pdf: 1886387 bytes, checksum: 3e47dd34fe738b31c6e8fbbb7f127b27 (MD5) Previous issue date: 2014-03-12 / CAPES / O objetivo do estudo foi estimar a infecção Rickettsial ( Rickettsia rickettsii , Rickettsia parkeri , ' Candidatus R. amblyommii ' , Rickettsia rhipicephali e Rickettsia bellii ) em eqüídeos , e carrapatos de uma região do Pantanal do Brasil. Amostras de 547 eqüídeos (500 cavalos e 47 asininos e muares ) foram avaliados pelo teste de imunofluorescência indireta (IFI ) . Um total de 665 adultos e 106 “pools” de ninfas de Amblyomma cajennense F.s1 , 10 carrapatos Dermacentor nitens Neumann, e 88 pools de larvas de Amblyomma sp. foram testadas por PCR . No geral 337 ( 61,6 % ) eram reactivos equídeos ( título ≥ 64 ) para pelo menos um antigénio de Rickettsia spp . Os valores de prevalência de Rickettsia foram 66%, e foram observados os maiores títulos de ponto final para 'Ca. R. amblyommii '. Na PCR, 3 ( 0,45% ) do fêmeas de A. cajennense s.l. foram positivos para 'Ca. R. amblyommii ' . Para os carrapatos imaturos foram observados uma taxa mínima de infecção de 0,75% e 0,34% para ninfas e larvas, respectivamente. As amostras positivas de carrapatos tiveram um fragmento do gene 16S rRNA sequenciados e as sequências apresentaram 99% de semelhança com Amblyomma sculptum Berlese . Este estudo relata uma ampla distribuição de Rickettsia entre equídeos, sugerindo o possível envolvimento, pela primeira vez, de A. sculptum na transmissão de 'Ca. R. amblyommii ' / The aim of the study was to estimate the rickettsial (Rickettsia rickettsii, Rickettsia parkeri, ‘Candidatus R. amblyommii’, Rickettsia rhipicephali, and Rickettsia bellii) infection in equids, and ticks of a Pantanal region of Brazil. Sera of 547 equids (500 horses and 47 mules, and donkeys) were evaluated by indirect immunofluorescence assay (IFA). A total of 665 adults and 106 nymphal pools of Amblyomma cajennense F. s.l., 10 Dermacentor nitens Neumann ticks, and 88 larval pools of Amblyomma sp. were tested by PCR. Overall 337 (61.6%) equids were reactive (titer ≥ 64) to at least one antigen of Rickettsia spp. The prevalence values for Rickettsia were 66%, and the highest endpoint titers were observed for ‘Ca. R. amblyommii’. In PCR 3 (0.45%) female of A. cajennense s.l. were positive for ‘Ca. R. amblyommii’. For the immature ticks were observed a minimum rate of infection of 0.75% and 0.34 % for nymphs and larvae, respectively. Positive samples of ticks have had a fragment of the 16S mitochondrial rRNA gene sequenced and sequences showed 99% similarity to Amblyomma sculptum Berlese. This study reports a wide distribution of Rickettsia among equids, suggesting the possible involvement, for the first time, of A. sculptum in transmitting ‘Ca. R. amblyommii’.

O Vírus do Nilo Ocidental, do inglês West Nile virus (WNV) é um patógeno emergente que é amplamente distribuído na América do Norte e Central. A recente introdução na América do Sul chamou a atenção para a propagação do WNV em países Latino Americanos. O ciclo de transmissão envolve mosquitos, pássaros, cavalos e seres humanos. A avaliação sorológica realizada nestes estudo foi composta por 678 soros de equídeos e 478 soros de aves, realizada por meio do ensaio ELISA de bloqueio específico para WNV e somente as amostras com resultados positivos foram confirmadas por testes de neutralização por redução em placas (PRNTs). A análise molecular foi realizada em soros de 1.241 equídeos saudáveis e em 63 macerados de cérebros de equídeos que morreram de encefalite e obtiveram resultados previamente negativos para outros patógenos. Também testamos swabs de 3.445 aves pelo método molecular, além de amostras de 24 morcegos e 11 onças. As amostras analisadas foram coletadas em diferentes biomas do Brasil. Identificamos pelo ELISA anticorpos para o WNV em treze equídeos e cinco pássaros e o teste de PRNT90 confirmou positividade para o WNV em quatro amostras de equídeos coletadas em 2009 em uma região entre a Amazônia e o Pantanal. Nenhuma das amostras de aves positivas pelo ELISA foram confirmadas por PRNT90. Das 4.784 amostras testadas por RT-PCR, penas duas apresentaram resultados positivos para a detecção, sendo uma ave residente na região do Pantanal e um anatídeo na região do Maranhão, respectivamente. A circulação do WNV é confirmada pela presente pesquisa em larga escala, mesmo na ausência da detecção de casos clínicos. / West Nile virus (WNV) is an emergent pathogen that is widely distributed in North and Central America. The recent introduction in South America has focused attention on the spread of WNV across Southern American countries. The transmission network involves mosquitoes, birds, horses and humans. The serological evaluation of sera from 678 equids and 478 birds was performed using a WNV-specific blocking ELISA, and only the positive results were confirmed by plaque reduction neutralisation tests (PRNTs). Molecular analysis was performed on sera from 1241 healthy equids and on 63 macerates of brains from equids that died of encephalitis and had previously tested negative for other pathogens. We also tested swabs from 3.445 birds, 24 bats and 11 phanteras. The samples analysed were collected in different biomes of Brazil. We identified WNV antibodies by ELISA in thirteen equids and five birds, and PRNT90 confirmed WNV positivity in four equid samples collected in 2009 in an area between the Amazon and the Pantanal. None of the ELISA positive bird samples were confirmed by PRNT90. Of the 4.784 samples tested by RT-PCR, only two were positive for the detection, a resident bird in the Pantanal region and a duck in the region of Maranhão, respectively. WNV circulation is confirmed by this large scale survey even in the absence of detection of clinical cases.

Les restes fossiles des grands herbivores (genres Bos, Bison, Equus, Coelodonta et Stephanorhinus) sont abondants dans les séquences archéo-paléontologiques du Pléistocène moyen et supérieur du Sud de la France. L’étude biométrique des restes osseux et dentaires à partir de 11 sites (Camp-de-peyre, La Micoque, Igue des Rameaux, Payre, Lunel-Viel, Rigabe, Suard, Combe-Grenal, Pech de l’Azé II, Coudoulous II, Peyre) et 22 ensembles/niveaux, contrôlée par des analyses statistiques factorielles, permet de caractériser les adaptations contextuelles de chaque taxon et leurs tendances évolutives, et d’affiner leurs apports biochronologiques. Les analyses de méso- et micro-usure dentaire détaillent les comportements alimentaires de ces taxons et les environnements locaux dans lequel ils vivaient, intégrant les variations saisonnières. L’utilisation des deux approches, biométriques et écométriques, augmente significativement notre résolution des contextes paléo-environnementaux, pour chacun des sites étudiés. Notre étude apporte de nouvelles données sur les modes d’adaptation tant anatomiques qu’éco-éthologiques des grands ongulés. Des conclusions sur la gestion des territoires par ces herbivores mais aussi sur leurs exploitations par leurs prédateurs, humains et non-humains, ont également été possibles. Nous avons ainsi mis en évidence des stratégies de prédation et d’acquisition originales, notamment centrées sur certains taxons (Equus) pour les groupes de Pré-Néandertaliens du Sud de la France opérant dans un rayon d’action plus important que celui d’autres prédateurs (en particulier hyènes). / The fossil remains of large herbivores (genus Bos, Bison, Equus, Coelodonta and Stephanorhinus) are frequent in the archaeo-paleontological record in the South of France during the Middle and Late Pleistocene. The biometrical study of bones and teeth remains from 11 sites (Camp-de-peyre, La Micoque, Igue des Rameaux, Payre, Lunel-Viel, Rigabe, Suard, Combe-Grenal, Pech de l’Azé II, Coudoulous II, Peyre) and 22 bone ensembles/layers, consolidates by factorial statistical analysis, allow us to define the degree of contextual adaptation and the evolutionary trend of each taxon which in turn refine their biochronological contribution. Diet habit of each taxon, local environments and seasonal variations are documented by dental meso- and micro-wear studies. Thanks to these two combined approaches, biometrical and ecometrical, we were able to significantly increase our knowledge about the paleoenvironmental context of each studied site. Our study brings new data about anatomical and ethological studied of large ungulates. We also display new results about the territory management by herbivores and then on their relationships with predators, human and non-human. Thus, we highlight Pre-Neandertalian original predation and acquisition strategies in South of France focusing on one species (Equus) in a territorial range larger than other carnivores’ (such as hyenids).