No / Four recently discovered frozen child mummies from two of the highest peaks in the south central Andes now yield tantalizing evidence of the preparatory stages leading to Inca ritual killing as represented by the unique capacocha rite. Our interdisciplinary study examined hair from the mummies to obtain detailed genetic and diachronic isotopic information. This approach has allowed us to reconstruct aspects of individual identity and diet, make inferences concerning social background, and gain insight on the hitherto unknown processes by which victims were selected, elevated in social status, prepared for a high-altitude pilgrimage, and killed. Such direct information amplifies, yet also partly contrasts with, Spanish historical accounts.

Yes / We examined six skeletons from mediaeval contexts from two sites in England for the presence of Mycobacterium leprae DNA, each of the skeletons displaying osteological indicators of leprosy. Polymerase chain reactions directed at the species-specific RLEP multicopy sequence produced positive results with three skeletons, these being among those with the clearest osteological signs of leprosy. Following in-solution hybridization capture, sufficient sequence reads were obtained to cover >70% of the M. leprae genomes from these three skeletons, with a mean read depth of 4–10×. Two skeletons from a mediaeval hospital in Chichester, UK, dating to the 14th–17th centuries AD, contained M. leprae strains of subtype 3I, which has previously been reported in mediaeval England. The third skeleton, from a churchyard cemetery at Raunds Furnells, UK, dating to the 10th to mid-12th centuries AD, carried subtype 3K, which has been recorded at 7th–13th century AD sites in Turkey, Hungary and Denmark, but not previously in Britain. We suggest that travellers to the Holy Land might have been responsible for the transmission of subtype 3K from southeast Europe to Britain. / Funded by a studentship awarded by Majlis Amanah Rakyat (MARA) to A.K. and by the University of Bradford and the University of Manchester.

Yes / DNA analysis demonstrates that all seven individuals buried in an Early Iron Age barrow at Dolge njive, southeast Slovenia, are close biological relatives. Although group composition does not suggest strict adherence to a patrilineal or matrilineal kinship system, the funerary tradition appears highly gendered, with family links through both the male and female line being important in structuring communities. We explore the implications for our understandings of kinship and funerary practices in Early Iron Age southeast Europe. / This research forms part of ENTRANS: a collaborative project involving the Universities of Bradford, Zagreb and Ljubljana, and the Institute for the Protection of Cultural Heritage of Slovenia. ENTRANS (PI: Armit) received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 291827. The project is financially supported by the HERA Joint Research Programme (www.heranet.info) which is co-funded by AHRC, AKA, BMBF via PT-DLR, DASTI, ETAG, FCT, FNR, FNRS, FWF, FWO, HAZU, IRC, LMT, MHEST, NWO, NCN, RANNÍS, RCN, VR and The European Community FP7 2007-2013, under the Socioeconomic Sciences and Humanities programme. Research for this paper also received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 834087 (COMMIOS). The ancient DNA work was supported by NIH grant GM100233, John Templeton Foundation grant 61220, the Howard Hughes Medical Institute, and the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation.

This study is an extension of the author's previous thesis (Theorell 2013) and focus on the analysed tibia, the humerus and the proximal and distal part of the radius of sheep bones from Gotland and goat bones from City of Falun. Methods for bone elements assessed in this study are compiled and evaluated by Zeder and Lapham (2010). The bones were then geneticallyspecies identified and the results were compared. Seven of thirteen criteria for both sheep and goat reached 100% of correct identification.Best performing criteria were on humerus and distal radius for both sheep and goats. The results for the complete bone assessments divided for the species showed best performance ongoats. Worst performing bone is the tibia. High performing criteria were found on all thetypes of bones used in this study which can be used to distinguish between sheep and goats. / Föreliggande studie är en utökning av författarens tidigare magisteruppsats (Theorell 2013) och fokuserar på att analysera skenben, överarmsben samt proximal och distal del av strålbenet från fårben från Gotland och getben från Falun. Metoder för benslagen som används i denna studie har samlats och utvärderats av Zeder och Lapham (2010). Efter osteologisk analys har benen genetiskt artidentifierats och resultaten från bägge analyser har jämförts. Sju av tretton kriterier för både får och getter visade 100% korrekt bedömning. Kriterier med bäst resultat fanns på överarmsben och distalt på strålben. Sett till bedömning av komplett benslag skilt mellan får och getter visade att metoderna presterade bäst på getter. Sämst resultat uppvisades på skenbenet. Generellt uppvisade samtliga benslag kriterier som är möjliga att använda för att särskilja mellan får och getter.

Krebserkrankungen sind das Resultat komplexer Vorgänge und Veränderungen. Eine wichtige Variable in der Initialisierung ist die Interaktion zwischen Genotyp und Umwelt. Da Magenkarzinome zu den wenigen Krebserkrankungen gehören, bei denen im letzten Jahrhundert ein deutlicher Rückgang in der Inzidenz beobachtet werden konnte (Becker 2006), stellt sich die Frage, ob es Unterschiede in der genetischen Ausstattung von historischen Tumorgenomen im Vergleich zu rezenten gibt. Als typisches Zielgen für Tumormutationen wurde das Tumorsuppressorgen p53 untersucht. Au¬ßerdem wurde Helicobacter pylori (H. pylori) als Risikofaktor für die Entstehung von Magenkarzinomen in den historischen Proben identifiziert. Insgesamt standen 51 Gewebeproben von Magenkarzinompatienten aus den Medizinhistori¬schen Museen Berlin und Zürich, dem Pathologisch-anatomischen Bundesmuseum Wien sowie der anatomischen Sammlung der Universität Tartu zur Verfügung. Bei 47 Proben handelte es sich nach histologischer Diagnose um Magenkarzinome. Die Proben sind zwischen 50 und 180 Jahre alt und wurden in Konservierungsflüssigkeiten unbekannter Zusammensetzung gelagert. Von 45% der Proben konnten vollständige Sequenzen der Exons 5 bis 8 des p53-Gens generiert werden. Es konnten Veränderungen im Mutationsspektrum und in der Lokalisation der Mutationen in den historischen Proben im Vergleich zu rezenten Tumormutationen festgestellt werden. Die Mutationsfrequenz betrug 52%. Insgesamt wurden zehn verschiedene Mutationsereignisse in p53 bei elf verschiedenen Proben detektiert, wobei drei Proben von zwei Mutationen betroffen waren. Zwei Mutationen führen direkt (Q144X) bzw. indirekt (S166fs) zu der Entstehung von Stoppcodons. Zu einem Verlust des p53-Proteins bei gleichzeitiger Akquirierung onkogener Funktionen kommt es durch die Hotspot-Mutation R248W (Wang & El-Deiry 2007). Zu einer Zunahme der Funktionsfähigkeit (gain-of-function) kommt es außerdem durch die Mutation K291E. Die Mutation E271K ist an einer splice site lokalisiert, so dass das Exon nicht in die mRNA übernommen werden kann. Die Konsequenzen der anderen Mutationsereignisse sind nicht eindeutig belegt, scheinen aber einen geringeren Einfluss auf die Funktionalität von p53 zu haben. Abweichend zu rezenten Magenkarzinomen konnte die Mutation M246K als Hotspot der historischen Proben identifiziert werden. Insgesamt waren nur vier historische Mutationen bisher aus rezentem Magenkarzinomgewebe beschrieben, davon die Mehrheit in Studien mit asiatischen Patienten. Die veränderten Mutationen der historischen Magenkarzinome können als Hinweis auf Veränderungen in den karzinogen wirkenden Einflussfaktoren dienen, etwa eine veränderte Lebens- und Ernährungsweise durch die Einführung von Kühlmöglichkeiten für Lebensmittel. Der Risikofaktor H. pylori konnte in 70% der Gewebeproben sicher nachgewiesen werden. Der Anteil der Träger des Virulenzfaktors cag betrug 44%. 73% der Proben mit p53-Mutation waren nachweislich mit H. pylori und davon wiederum 63% mit einem cag-positiven Stamm infiziert. Die Infektion ermöglicht eine Teilerklärung für die untypische Lokalisation der Mutationen, da H. pylori-induzierte Mutationen seltener an Magenkarzinom-Hotspots vorkommen (Murakami et al. 1999). Es konnten keine resistenztypischen Mutationen gegen das Antibiotikum Clarithromycin in den historischen Geweben identifiziert werden. Die vorliegende Arbeit konnte p53-Mutationen und das Bakterium H. pylori in den historischen Gewebeproben identifizieren. Ein verändertes Mutationsspektrum und die veränderte Lokalisation der Mutationen geben den Hinweis, dass sich die Einflüsse auf die Entstehung der Magenkarzinome im letzten Jahrhundert verändert haben.

L'esturgeon européen Acipenser sturio (Linnaeus, 1758) était un poisson commun de nos fleuves jusqu'au début du 20e siècle. Toutes ses populations sont maintenant éteintes sauf une qui survit dans le bassin Gironde-Garonne-Dordogne en France. Les données disponibles sur l'espèce restent très partielles car elles proviennent quasi exclusivement de cette population relictuelle. Au cours de cette thèse, plus d'une centaine d'échantillons anciens d'esturgeons restes archéologiques ou spécimens naturalisés conservés dans les muséums d'histoire naturelle ont été analysé grâce aux méthodes de la paléogénétique. Ces analyses génétiques ont été réalisées sur l'ADN mitochondrial (surtout la Dloop) ainsi que sur cinq loci microsatellites qu'il a été nécessaire d'adapter aux méthodes d'étude de l'ADN ancien. Les données paléogénétiques obtenues ont permis d'étudier : 1) les relations de l'esturgeon européen avec les autres espèces d'esturgeons vivant ou ayant vécu en Europe, en particulier l'esturgeon de l'Adriatique A. naccarii et l'esturgeon atlantique A. oxyrinchus. 2) la diversité génétique de l'esturgeon européen sur l'ensemble de son ancienne aire de répartition. 3) la diversité génétique d'une population d'esturgeon européen au cours du temps la population du Rhône, d'une période où elle était florissante jusqu'à son extinction. L'ensemble de ces données ont été discuté à la lumière de la conservation de l'espèce, qui est aujourd'hui en danger critique d'extinction. / The European sturgeon Acipenser sturio (Linnaeus, 1758) was a common fish of our rivers until the beginning of the 20th century. All populations are now extinct except one which survives in the Gironde-Garonne-Dordogne basin in France. Data available on this species are only partial because they only stem from this relictual population. During this thesis, more than one hundred ancient sturgeon samples archaeological remains or naturalized museum specimens were analysed by paleogenetics means. These genetics anlyses were carried out on mitochondrial DNA (mainly the Dloop) and five microsatellites loci which were adapted to ancient DNA methodologies. Paleogenetics data that we obtained were used to study : 1) A. sturio interactions with other sturgeon species which live or lived in Europe, especially the Adriatic sturgeon A. naccarii and the atlantic sturgeon A. oxyrinchus. 2) the genetic diversity of A. sturio all over its former geographical range. 3) genetic diversity of a population of the European sturgeon through time the Rhone River population from a period it was flourishing until its extinction. All these data were considered in the light of the species conservation, since A. sturio is now critically endangered.

This thesis explores the potential of new substrates for ancient DNA studies and addresses novel questions that can now be asked. It also highlights an additional use of ancient DNA extracted from a traditional source.

O objetivo principal deste trabalho foi realizar a reconstrução das relações filogenéticas das espécies do gênero Deuterodon, testando suas possíveis relações com espécies de outros gêneros de Characidae que possuem um arranjo similar de dentes do dentário, como em Astyanax, Jupiaba e Myxiops. Na análise filogenética foi utilizada uma matriz previamente publicada e com o acréscimo de 49 táxons, totalizando 233 espécies de Characidae. Vinte novos caracteres foram adicionados a esta matriz com o intuito de entender as relações dos gêneros e espécies de interesse com os demais Characidae. Um total de 219 espécimes tiveram o DNA extraído e 4 genes foram amplificados. Análises moleculares e morfológicas recuperaram um clado mais inclusivo nomeado de Probolodini, composto pelos gêneros Deuterodon, Probolodus, Myxiops, Hyphessobrycon luetkenii, espécies de Astyanax da região costeira do Brasil e parte das espécies de Jupiaba. Deuterodon é redefinido sustentado por 9 sinapomorfias e composto por 7 espécies. Myxiops é outro gênero válido sustentado por 22 autapomorfias. Probolodus heterostomus apresentou 10 autapomorfias na análise, e que podem eventualmente representar sinapomorfias para o gênero após a análise das demais espécies. Astyanax é um gênero polifilético e as espécies de Astyanax da região costeiras estão mais estreitamente relacionadas a espécies de outros gêneros (Probolodus, Deuterodon e Myxiops) do que à espécie tipo do gênero, Astyanax mexicanus. Jupiaba também é um gênero polifilético com espécies distribuídas em vários clados na árvore filogenética. Deuterodon pedri é mais relacionado à Astyanax pelecus e a duas outras espécies de caracídeos não descritos do que ao gênero Deuterodon. Paralelamente, como uma etapa necessária à resolução de alguns problemas taxonômicos envolvendo as espécies trabalhadas neste estudo, técnicas para recuperação de DNA antigo de espécimes coletados nos séculos passados foram aprimoradas, tornando possível a extração e amplificação de DNA de espécimes tipos. Através da aplicação destas técnicas, a identidade de Deuterodon pedri foi esclarecida com a extração do DNA do lectótipo, que junto com a análise morfológica possibilitou o reconhecimento da espécie em material recentemente coletado e sua redescrição. Outro resultado paralelo foi a descoberta do holótipo de Tetragonopterus vittatus em uma visita à coleção do Muséum national d'Histoire naturelle de Paris, considerado como desconhecido até então. O exame desse material permitiu a revalidação da espécie em combinação nova, como Moenkhausia vittata, sendo retirada da sinonímia de Astyanax bimaulatus. O uso de técnicas tradicionais tais como estudo osteológico e taxonomia em conjunto com técnicas de biologia molecular possibilitaram o esclarecimento de relações filogenéticas neste grupo complexo e a resolução de dúvidas taxonômicas históricas. / The main objective of this work was to reconstruct the phylogenetic relationships of the species of the genus Deuterodon, testing their possible relationships with species of other characid genera that have similar teeth arrangement, as in Astyanax, Jupiaba, and Myxiops. In the phylogenetic analysis, a previously published matrix was used, with the addition of 49 taxa, totaling 233 Characidae species. Twenty new characters were added to this matrix in order to better understand the relationships of the genera and species of interest with the other Characidae. A total of 219 specimens had the DNA extracted and 4 genes were amplified. Molecular and morphological analyzes recovered a larger clade named Probolodini which is composed by the genera Deuterodon, Probolodus, Myxiops, Hyphessobrycon luetkenii and by species of Astyanax from the coastal region of Brazil and some species of Jupiaba. Deuterodon is redefined based on nine synapomorphies and composed of seven species. Myxiops is another valid genus supported by 22 autapomorphies. Probolodus heterostomus showed 10 autapomorphies that may constitute synapomorphies for the genus if proved to occur in the remaining species. Astyanax is polyphyletic and most of the Astyanax species of the Atlantic coastal Rivers are more closely related to other genera than to Astyanax mexicanus, the type species of the genus. Jupiaba is also a polyphyletic genus with species distributed in several clades in the phylogenetic tree. Deuterodon pedri is more related to Astyanax pelecus and to two other undescribed characid species than to the genus Deuterodon. In parallel, as a necessary step to solve some taxonomic problems involving the species in this study, techniques for recovering ancient DNA from specimens collected in the past centuries have been improved, making possible the extraction and amplification of DNA from type specimens of taxonomically complex species of Characidae. Through the application of these techniques, the identity of Deuterodon pedri was clarified with the aid of the DNA of the lectotype, which together with the morphological analysis allowed the recognition of the species in recently collected material and consequently its redescription. Another parallel result was the discovery of the holotype of Tetragonopterus vittatus in a visit to the collection of the Muséum national d'Histoire naturelle in Paris, considered as unknown until then. The examination of this specimen allowed the revalidation of the species in a new combination as Moenkhausia vittata removing from the synonym of Astanax bimaculatus. The use of traditional techniques such as osteological studies in conjunction with techniques of molecular biology allowed the clarification of phylogenetic relationships in these complex groups and the resolution of historical taxonomic problems as exemplified in this study.

All contemporary taurine cattle originated some 10,000 years ago when their wild ancestor, the aurochs, was domesticated in the Near East. Although the aurochs was widespread also in Europe, there is no evidence for a local domestication. The aurochs has been extinct since 1627 and therefore little is known about its biology. Following domestication, cattle were selected for traits of interest to humans. All modern cattle breeds were developed in the 19th century and the only sources of information about prehistoric breeding practices, and breeds, come from a few ancient Roman Empire and medieval European written accounts. The aim for this thesis was to investigate the effects early selection may have had on the cattle genome and to investigate genetic variation in European aurochs. Using second-generation sequencing and coalescent simulation analyses of aurochs Y chromosomal DNA, I estimated effective population size to between 20,000-80,000 aurochs bulls, indicating that a large population was present when domestic cattle entered Europe. A Y chromosomal SNP revealed that the two male lineages present in modern cattle were also present in European aurochs, and that the frequency of these lineages in domestic cattle fluctuated over time. This indicates that cattle were mobile and that bottlenecks, possibly due to selective breeding, occurred. I used nuclear SNPs to trace genetic variation in North European cattle through time and show that when genetics is combined with archaeology and osteology, even small but notable changes in the use of cattle can be detected. There has been a significant decrease in genetic variation over time, with the most dramatic changes associated with the formation of breeds during the 19th century.

Ancient DNA analysis of archaeological wheat remains may serve to clarify unknown or controversial points in the history of wheat. In the first part of this study, extraction and amplification of DNA from Anatolian charred ancient wheat seeds obtained from different locations and ages was attempted. None of the our extraction samples yielded any PCR amplification. The possible reasons for this result were investigated by constructing an artificial charring experiment. The results suggest that the chances of obtaining DNA from the charred archaeological samples used in this study by the methods used are very low. Moreover, strong PCR inhibition by these charred seed extracts was observed. The second part of the study aimed to develop new DNA based markers for ancient wheat DNA analysis. Markers linked to the brittle rachis character exhibiting domestication status were sought, but no result was obtained. Primers targeting plasmon sequences were developed and tested. A primer pair amplifying a 400 bp portion of the chloroplast TrnLTrnF intergenic region was focused upon. A short piece of this region was amplified using ancient wheat DNA extracted in another study. This short piece appeared non-polymorphicupon sequencing. The sequence spanning a wider portion of this region contained a number of length polymorphisms. Phylogenetic reconstruction using maximum parsimony showed that these polymorphisms were able to distinguish wheat taxa at the maternal ancestor level.