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.

abstract: Although the Caribbean has been continuously inhabited for the last 7,000 years, European contact in the last 500 years dramatically reshaped the cultural and genetic makeup of island populations. Several recent studies have explored the genetic diversity of Caribbean Latinos and have characterized Native American variation present within their genomes. However, the difficulty of obtaining ancient DNA from pre-contact populations and the underrepresentation of non-Latino Caribbean islanders in current research have prevented a complete understanding of genetic variation over time and space in the Caribbean basin. This dissertation uses two approaches to characterize the role of migration and admixture in the demographic history of Caribbean islanders. First, autosomal variants were genotyped in a sample of 55 Afro-Caribbeans from five islands in the Lesser Antilles: Grenada, St. Kitts, St. Lucia, Trinidad, and St. Vincent. These data were used to characterize genetic structure, ancestry and signatures of selection in these populations. The results demonstrate a complex pattern of admixture since European contact, including a strong signature of sex-biased mating and inputs from at least five continental populations to the autosomal ancestry of Afro-Caribbean peoples. Second, ancient mitochondrial and nuclear DNA were obtained from 60 skeletal remains, dated between A.D. 500–1300, from three archaeological sites in Puerto Rico: Paso del Indio, Punta Candelero and Tibes. The ancient data were used to reassesses existing models for the peopling of Puerto Rico and the Caribbean and to examine the extent of genetic continuity between ancient and modern populations. Project findings support a largely South American origin for Ceramic Age Caribbean populations and identify some genetic continuity between pre and post contact islanders. The above study was aided by development and testing of extraction methods optimized for recovery of ancient DNA from tropical contexts. Overall, project findings characterize how ancient indigenous groups, European colonial regimes, the African Slave Trade and modern labor movements have shaped the genomic diversity of Caribbean islanders. In addition to its anthropological and historical importance, such knowledge is also essential for informing the identification of medically relevant genetic variation in these populations. / Dissertation/Thesis / Zipped file contains Appendices A-K. Supplemental tables, figures, protocols and spreadsheets associated with dissertation. / Doctoral Dissertation Anthropology 2017

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.

Current knowledge of past vegetation and faunal diversity has been based on pollen and macrofossil analysis from lake sediments. The innovative method of sedimentary ancient DNA (sedaDNA) is a promising, complementary proxy to reconstruct information about past environments. However, to what extent animal DNA can be extracted from old sediments and soils has not been frequently studied. This study explored if ancient DNA of moose (Alces alces), reindeer (Rangifer tarangus), goat (Capra aegagrus) and plants could be extracted from millennia old lake sediments of Lake Krigstjärn and archaeological soil samples in northern Sweden. SedaDNA was successfully extracted and detected from both reindeer and plants DNA, while goats sedaDNA was absent in all sediments. Moose ancient DNA (aDNA) was only detected in the archaeological soils. Yet, there were signs that the applied moose primer set was not optimal for heavily degraded DNA and the validity of this primer needs further research. Earliest detections of reindeer DNA can be dated to ~6500 c. years ago. Oldest sediments contained DNA, indicating sufficient DNA preservation conditions in the sediments of Lake Krigstjärn. Finds of plants DNA in pre-deglaciational sediments may indicate the existence of >9500 year old glacial vegetation. Altogether is sedaDNA a highly promising tool to reconstruct diversity, origin and immigration routes of mammals, but technical issues such as primer set specificity and its purpose should be considered and tested carefully in advance.

Ce travail s’est intéressé à la dynamique de peuplement du sud de la Sibérie et de l’Altaï à l’âge du Bronze (IIIème - Ier millénaire avant J.-C), période pendant laquelle les steppes eurasiennes auraient connues de nombreux mouvements de populations. Les analyses moléculaires ont portés sur 69 spécimens anciens. La stratégie adoptée a consisté, en plus de l’étude de l’ADN mitochondrial, à étudier les lignées paternelles de ces individus, ainsi que des marqueurs autosomaux, informatifs de leur origine biogéographique (AIM) et des caractères pigmentaires. L’ensemble des données moléculaires obtenues nous a permis de mettre en évidence une évolution du pool génique au sein de la région étudiée. Le faible effectif observé par groupe culturel ainsi que le processus de recrutement funéraire peut avoir biaisé une partie des analyses. Néanmoins, ces données moléculaires ont amené de nouveaux éléments pour la compréhension du peuplement de cette région qui apparaît comme un processus complexe. / The present work has focused on the settlement of the South Siberia and the Altai mountains during the Bronze Age (III-I millennium BC), period during which the Eurasian Steppes knew a lot of population movements. The molecular analyses were performed on 69 ancient samples. The used strategy consisted in the study of maternal and paternal lineages and autosomal markers informative of biogeographical ancestry (AIM) and physical appearance. Taken together, these results show an evolution of the genetic pool in this area during the Bronze Age. The low effective observed in each cultural group and the funeral recruitment could of course have induced a bias in some analyses. Nevertheless, these molecular data gave new elements to understand the settlement of this region which seems to be a complex process that it will be necessary to deepen with new paleogenetic even paleogenomic studies.

Il a été démontré que la pulpe dentaire pouvait constituer un matériel de choix pour la paléomicrobiologie. Au début de ce travail de thèse, nous avons envisagé de rechercher les bactéries bactériémiques chez les mammifères à partir de la pulpe dentaire de dents contemporaines et anciennes. Au préalable, il était nécessaire de classer les dents modernes et anciennes mises à notre disposition par les zoologues et en particulier de déterminer l’espèce à laquelle les dents anciennes appartenaient car il est souvent difficile de différencier morphologiquement des dents appartenant à des espèces proches. Deux méthodes ont été utilisées pour réaliser cette partie de notre travail: la première méthode moléculaire avec comme outil, le gène séquençage du cytochrome b et la seconde protéomique par analyse des profils peptidiques de la pulpe dentaire. Les résultats obtenus ont confirmé que la pulpe dentaire peut constituer une source d’ADN ancien et de protéines anciennes.Dans un deuxième travail, faisant suite aux travaux effectués dans le laboratoire, en collaboration avec différentes équipes d’anthropologues, nous avons mis en place une technique de détection simultanée à haut débit d’ADN bactérien ancien combinée à une PCR «suicide». Cette technique appliquée à la pulpe dentaire de dents humaines anciennes a été utilisée pour détecter sept pathogènes. Les résultats obtenus par cette technique moléculaire attestent de la présence simultanée d’ADN de Y. pestis et de B. quintana dans la pulpe dentaire de dents prélevées sur des restes humains dans les sépultures de Bondy, France (XIème - XVème) et de Venise, Italie (XIVème - XVIème). Ces données suggèrent la transmission de Y. pestis par le pou de corps, vecteur connu de B. quintana, au cours des épidémies de peste ancienne. Les résultats obtenus ont confirmé ceux obtenus par cinq autres équipes que Y. pestis est l'agent responsable de la «Peste Noire». Les résultats de notre travail de Thèse contribuent à la paléomicrobiologie. / The dental pulp has been demonstrated to be a suitable specimen on which to base paleomicrobiology studies. At the initiation of this Thesis work, we aimed to detect bacteria in the dental pulp extracted from contemporary and ancient mammals’ teeth. In mammals, the first task was the classification of species to which the teeth belong. In a first work, we have accomplished this task by two methods used in parallel: the molecular method based on cytochrome b gene sequencing and proteomic method by the dental pulp MALDI TOF mass spectrometry peptide profiling. The results of this work demonstrated that dental pulp is a source for studying both ancient DNA and ancient proteins. In a second work, following previous publications, we detected bacterial DNA from dental pulp of ancient human teeth using a multiplex high-throughput “suicide” PCR to detect seven pathogens (Yersinia pestis, Bacillus anthracis, Borrelia recurrentis, Bartonella quintana, Rickettsia prowazekii, Salmonella enterica Typhi and Poxvirus). We demonstrated the simultaneous presence of Y. pestis DNA and B. quintana DNA in dental pulp specimens collected from burials in Bondy, France dating 11th-15th and burials in Venice, Italy dating 14th-16th. This result may suggest the transmission of Y. pestis by the body louse, the known vector of B. quintana. Also, these results reinforce the large corpus of data produced by five different teams (Pusch et al., 2004 ; Cerutti et al., 2007 ; Bianucci et al., 2009 ; Haensch et al. 2010 ; Wiechmann et al. 2010) that the agent of the Black Death is Y. pestis. Our results herein contributed to the works in paleomicrobiology.

Tuberculosis has been an important disease throughout human history, shaping countless past populations. The archaeological study of the causative agents of tuberculosis, members of the Mycobacterium tuberculosis Complex (MTBC), is hindered by the non-diagnostic nature of tuberculosis-associated skeletal changes. As such, ancient DNA (aDNA) or palaeogenetic analyses have become an important tool for identifying tuberculosis in past populations. However, due to the age and variable preservation of aDNA, there are often issues with sporadic results and false negatives. The overall aim of the work presented here was to use different methods, including traditional target-specific PCR, to identify and detect tuberculosis aDNA in archaeological remains. The main objectives within this overarching aim were to first test a method called whole genome amplification (WGA), used to non-specifically amplify all the DNA within a sample, and its potential to improve the yield of aDNA from skeletal remains (Chapters 3 and 4). To determine the extent of its impact, WGA was used in a comparative context, where each archaeological sample analysed was separately subjected to two methods of MTBC detection - the traditional targeted PCR method and the same method assisted by the initial application of WGA. The results show that applying WGA before the traditional targeted PCR methodology to detect the presence of MTBC pathogens in skeletal remains is only useful and viable in some cases, likely depending on the age and preservation of the sample. The second objective was to use next generation sequencing to obtain more information on the aDNA composition of certain archaeological samples and answer questions beyond the scope of traditional target-specific PCR techniques (Chapter 5). Although most of the sequencing runs were variably unsuccessful, the composition of two samples, both known to probably contain tuberculosis aDNA, could be analysed. The samples both contained similar amounts of mycobacterial aDNA and varying amounts of both human and even potentially human intestinal flora DNA. Finally, the third objective was to determine if MTBC aDNA could be detected in a rib sample from Private William Braine of the lost Franklin Expedition using standard target-specific PCR (Chapter 6). In this case study, no evidence of tuberculosis ancient DNA was found. The work done through-out highlights the difficulties of ancient DNA research and, in Chapter 4, shows the importance of using more than a single sample to evaluate methods for application in palaeogenetic contexts.

Denisova Cave is located in the Altai mountains of Russia. Excavations from this cave have yielded two large hominin molars and three hominin phalanxes from the Pleistocene. One of the phalanxes (Denisova 3) had extraordinary DNA preservation allowing the sequencing of high quality nuclear and mitochondrial DNA (mtDNA) genomes and has been shown to belong to a young girl from hereto unknown sister group of Neandertals, called Denisovans. The mtDNA of Denisova 3 surprisingly split from the mtDNA ancestor of modern humans and Neandertals twice as long ago as the split of modern humans and Neandertals. The mtDNA of one of the molars (Denisova 4) was also sequenced and differs at only two positions from the mtDNA of Denisova 3. A second phalanx (Altai 1) also yielded a high quality genome, and was a Neandertal. While Neandertals show an admixture signal of 1-4% into present-day non-Africans, Denisovans show an admixture of up to 5% in present-day Oceanians, and to a much lesser extent East Asians. This thesis encompasses two studies. In the first study, we sequenced the complete mtDNA genome of the additional molar (Denisova 8), as well as a few megabases of nuclear DNA from Denisova 4 and Denisova 8. While the mtDNA of Denisova 8 is clearly of the Denisova type, its branch to the most recent common ancestor of Denisovans is half as long as the branch leading to Denisova 3 or Denisova 4, indicating that Denisova 8 lived many millenia before the other two. Both Denisova 4 and 8 fall together with Denisova 3 based on nuclear DNA, bringing the number of known Denisovans from one to three. In the second study, we sequenced an almost complete mtDNA and a few megabases of nuclear DNA from the third hominin phalanx from Denisova Cave, Altai 2. Both the mtDNA and the nuclear DNA show Altai 2 to be a Neandertal. The mtDNA also showed the presence of substantial Pleistocene spotted hyena contamination. Low levels of spotted hyena contamination were also found in Altai 1, Denisova 3 and Denisova 4. Partial mtDNA genomes of the contaminating spotted hyenas from these four hominins were compared to mtDNA genomes of other extant and extinct spotted hyenas. We show that the spotted hyenas that contaminated the two Denisovans come from a population of spotted hyenas found in Pleistocene Europe as well as present-day Africa, while the spotted hyenas that contaminated Altai 2, and possibly Altai 1, come from a population of spotted hyenas found in Pleisticene eastern Russia and northern China. This indicates that Denisova Cave was a meeting point of eastern and western hominins as well as eastern and western spotted hyena populations.

No description available.

Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history. Extant sloths are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms of the Ice Age. By sequencing ten mitogenomes from extinct sloths, Delsuc et al. present a new molecular phylogeny revealing widespread morphological convergence with major implications for reinterpreting sloth evolutionary history.