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.

Sheep were domesticated ~10 000 years ago from Asiatic Mouflon. They then spread to Europe via the migration of farming human populations and had reached Scandinavia by ~6000 years ago. Another migration of humans stemming from the Pontic-Caspian steppe reached Scandinavia around ~5000 years ago, possibly with new types of sheep. Ancient sheep have mostly been studied using mitochondrial DNA. The few examples to date that have applied genome wide sequencing have shown that modern northern European sheep are most closely related to ~9000-year-old Anatolian sheep. Northern European Short Tailed sheep are a group known for their “rustic” phenotype. Their visual appearance together with mitochondrial DNA studies has led to the hypothesis that these sheep are a relict of early migrations. In this study I present five new ancient domestic sheep genomes, from the islands Gotland and Åland in the Baltic Sea, covering the timespan ~4000-500 years ago. Most samples show exceptionally good preservation, with four having over 1x nuclear coverage, ranging up to 11.6x. I use these genomes together with two large panels of Eurasian genome wide SNPs, which includes the three Norther European Short Tailed breeds from these islands, Gotland- Gute-, and Åland sheep. I study how these ancient sheep relate to modern populations. I also evaluate their wool phenotype based on two genetic markers and find that these ancient sheep probably had medium-coarse wool fiber thickness. The results also show that sheep in the Baltic Sea area show a remarkable degree of continuity between 4000 and 500 years ago, and that these ancient sheep are closely related to modern breeds from the area, Åland sheep being the closest extant population.

The Scandinavian brown bear went through a severe bottleneck due to human actions in the early 1900’s that reduced the population to low numbers. After protective measures were taken, the population recovered and today it consists of around 3000 individuals. Such loss of genetic variation can have long-lasting effects on population viability even as populations recover, and is therefore important to consider in the management and conservation of species. Previous studies investigating the genetic effects of the bottleneck based on genetic markers, such as microsatellites and mitochondrial DNA, have rendered inconclusive results. Here, whole-genome sequencing of historical and contemporary bears was used to estimate heterozygosity, inbreeding and mutational load in the pre- and post- bottleneck population. Surprisingly, a significant increase in heterozygosity was found in the contemporary population and no significant increase in inbreeding over time was found. However, mutational load was higher in the contemporary subpopulation in the south of Sweden compared to the subpopulation in the north, and the southern subpopulation seems to have lost unique genetic variation after the bottleneck. The results indicate that although the population was negatively affected by the bottleneck, a following increase in gene flow could have contributed to successful recovery of the population.

Archaeological dental calculus represents a depositional environment that entraps oral microbes, and debris of dietary, environmental, and cultural material that entered the mouth throughout the host’s life. Hence, they represent valuable archives of information about the host’s lifestyle, health, and environment. The aim of this study was to identify if the farming transition and its’ associated change in diet composition, may have influenced species composition in the oral cavity. To shed some light into the evolution of ancient oral microbiomes from Africa, 3 novel Iron Age dental calculus metagenomes together with a comparative dataset of 18 archaeological dental calculus metagenomes from North African Upper Palaeolithic, Later Stone Age, Iron Age, and 18th-19th century populations where analysed. Shotgun sequencing data was used to reconstruct 21 oral metagenomes from the past 15,000 years. This study found an oral microbiome that has been maintained from the Upper Palaeolithic (North Africa) to the 19th Century. However, closer examination to the relative abundance of three keystone species of the subgingival plaque, portray a chronological evolution that reflects that of its host during the major dietary and cultural transition that occurred during the farming revolution in the Iron Age.

<p>Mammoths (<em>Mammuthus</em>) have been studied extensively at the genetic level. However due to both taphonomic and technological limitations, only one of several late Pleistocene mammoth species, the woolly mammoth (<em>M. primigenius</em>), has been investigated. This limits our impression of mammoth population history to the the northern latitudes, just one of several environments in which mammoths lived and went extinct. It also obscures their evolutionary chronology, which prevents proper climatic and biogeographic contextualization of their history. Fortunately recent technological advances in high-throughput sequencing and targeted enrichment promise to expand Pleistocene faunal population phylogeography to non-permafrost, non-cave burial contexts. However the capacity and behavior of these combined technologies for characterizing ancient DNA is largely unexplored, preventing efficient and routine use for population-level studies. In this thesis I test and apply these technologies to remains of mammoth species from throughout North America. I first demonstrate their potential for poorly-preserved DNA, and then I evaluate their efficient application to large sample sets, as well as for capturing complete nuclear genomes. I then use these technologies to sequence dozens of mitochondrial genomes from Columbian (<em>M. columbi</em>)<em> </em>and other non-woolly mammoths, reconstructing their matrilineal phylogeography south of the ice. The revealed patterns not only imply a deep chronology for mammoth matrilineal diversity, but also that North American mammoth evolution was occurred via separate episodes of interbreeding between resident and invading populations, and between ecotypes. Overall the biological and methodological discoveries afforded by this body of work outline future research avenues on mammoth evolution, behavior, and extinction.</p> / Doctor of Philosophy (PhD)

Assessing population diversity in southern Italy has traditionally relied on archaeological and historic evidence. Although informative, these lines of evidence do not establish specific instances of within lifetime mobility, nor track population diversity over time. In order to investigate the population structure of ancient South Italy I sequenced the mitochondrial DNA (mtDNA) from 15 Iron Age (7th – 4th c. BCE) and 30 Roman period (1st – 4th c. BCE) individuals buried at Iron Age Botromagno and Roman period Vagnari, in southern Italy, and analyzed δ18O and 87Sr/86Sr values from a subset of the Vagnari skeletal assemblage. Phylogenetic analysis of 15 Iron Age mtDNAs together with 231 mtDNAs spanning European prehistory suggest that southern Italian Iapygians share close genetic affinities to Neolithic populations from eastern Europe and the Near East. Population pairwise analysis of Iron Age, Roman, and mtDNA datasets spanning the pan-Mediterranean region (n=357), indicate that Roman maternal genetic diversity is more similar to Neolithic and Bronze Age populations from central Europe and the eastern Mediterranean, respectively, than to Iron Age Italians. Genetic distance between population age categories imply moderate mtDNA turnover and constant population size during the Roman conquest of South Italy in the 3rd century BCE. In order to determine the local versus non-local demographic at Vagnari, I measured the 87Sr/86Sr and 18O/16O of composition of 43 molars, and the 87Sr/86Sr composition of an additional 13 molars, and constructed a preliminary 87Sr/86Sr variation map of the Italian peninsula using disparate 87Sr/86Sr datasets. The relationship between 87Sr/86Sr and previously published δ18O data suggest a relatively low proportion of migrants lived at Vagnari (7%). This research is the first to generate whole-mitochondrial DNA sequences from Iron Age and Roman period necropoleis, and demonstrates the ability to gain valuable information from the integration of aDNA, stable isotope, archaeological and historic evidence. / Thesis / Doctor of Philosophy (PhD) / With biochemical information obtained from teeth, this study examines the population structure and geographic origins in two archaeological communities located in southern Italy. Analysis of classical remains has traditionally been the subject of historical and archaeological inquiry. However, new applications evaluate these population changes with integrated stable isotope and ancient DNA techniques. Overall, the biochemical results suggest that the pre-Roman communities harbor deep maternal ancestry originating from eastern Europe and the eastern Mediterannean. These results, when compared to the genetic diversity of Roman and broader Mediterranean populations, indicate that the Romans share closer genetic similarity with ancient Stone and Bronze Age communites from Europe and the eastern Mediterranean, than with the pre-Roman community studied here. Furthermore, tooth chemistry results indicate a predominantly local population buried in the Roman period cemetery.

The use of complete mitochondrial DNA to carry out phylogenetic and population genomics analyses on ancient species has shown to be successful. The relationship between modern elephants and mammoths has been elucidated thanks to analyses of genetic material coming from mammoth fossils. Similar to that here we used newly assembled complete mitogenomes from Alaskan mammoth populations from the Late Pleistocene, and publicly available mammoth mitogenome data, to assess their position within the three mitochondrial lineages previously described in the literature in a BEAST and RAxML phylogenetic tree.  The studied bone fragments underwent drilling and DNA extractions before the construction of the libraries and sequencing was carried out. A novel DNA extraction method using a 96 sample plate was implemented alongside standard extraction methods.  The mapping of raw reads was implemented using two BWA v0.7.18 algorithms, “aln” and “mem”. After the results of both mappings were compared, the analysis continued with the output generated by BWA aln, which had a better overall performance.  The resulting phylogenetic trees had similar morphologies and placed our 10 newly assembled mitogenomes within Clade 1, a clade that was distributed throughout Eurasia and North America. Clade 1 was further divided into three subclades named Clade 1C1-C2 and 1DE. Clade 1C1 was made up of Columbian, Jeffersonian and woolly mammoth mitogenomes. One of our mitogenomes (called OG002) was placed outside of Clade 1C1, possibly due to its low coverage. Clade 1C2 was made out of North American woolly mammoths and unidentified mammoth specimens. Most of our mitogenomes (8 out of 10) were placed within this clade in the RAxML tree, and 7 out of 10 were placed within this clade in the BEAST tree. OG001 was placed outside Clade 1C2 in the BEAST tree, possibly due to its low coverage (0.9X). Clade 1DE was made up of Eurasian woolly mammoth specimens and unidentified mammoth specimens. OG020 was placed within this subclade in both trees. The current phylogenetic results were not sufficient to identify the species of our new mitogenomes, but further analysis in samples with high coverage may elucidate this matter.

No / Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear and mitochondrial DNA appear to be present in almost all hair and nail samples, the quality of DNA, both in quantity and length of amplifiable DNA fragments, vary considerably not just by species, but by individual, and even within individual between hair types.

Yes / Doggerland was a landmass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British landmass from the rest of Europe. The Storegga Event, which triggered a tsunami reflected in sediment deposits in the northern North Sea, northeast coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed as, to date, no direct evidence for the event has been recovered from the southern North Sea. We present evidence of a tsunami deposit in the southern North Sea at the head of a palaeo-river system that has been identified using seismic survey. The evidence, based on lithostratigraphy, geochemical signatures, macro and microfossils and sedimentary ancient DNA (sedaDNA), supported by optical stimulated luminescence (OSL) and radiocarbon dating, suggests that these deposits were a result of the tsunami. Seismic identification of this stratum and analysis of adjacent cores showed diminished traces of the tsunami which was largely removed by subsequent erosional processes. Our results confirm previous modelling of the impact of the tsunami within this area of the southern North Sea, and also indicate that these effects were temporary, localized, and mitigated by the dense woodland and topography of the area. We conclude that clear physical remnants of the wave in these areas are likely to be restricted to now buried, palaeo-inland basins and incised river valley systems.

No description available.