The archaeogenetics of european ancestry

The archaeogenetics of Europe remains deeply controversial. Advances in ancient deoxyribonucleic acid (DNA) analysis have suggested gene flow between Neanderthals and modern humans, who arrived in Europe <50 000 years ago, but have so far failed to support evolution of Neanderthals from a population of Homo heidelbergensis represented by remains in northern Spain. The extent to which European Mesolithic forager populations versus Neolithic pioneers from the Near East contributed to the extant gene pool of Europeans also continues to be contested. Whilst analyses of extant mitochondrial lineages have emphasised late Palaeolithic and Mesolithic expansions, ancient DNA (aDNA) results suggest significant Neolithic dispersals from the southern ‘refugial’ zone into the northern ‘bio-tidal’ zone. However, whether these had a primarily Near Eastern or North Mediterranean source remains a matter for debate. Meanwhile, aDNA has also begun to highlight an important role for later dispersals, especially during the late Neolithic, in shaping the European gene pool.

A genetic perspective on African prehistory

The various genetic systems (mitochondrial DNA, the Y-chromosome and the genome-wide autosomes) indicate that Africa is the most genetically diverse continent in the world and the most likely place of origin for anatomically modern humans. However, where in Africa modern humans arose and how the current genetic makeup within the continent was shaped is still open to debate. Here, we summarize the debate and focus especially on the maternally inherited mitochondrial DNA (mtDNA) and a recently revised chronology for the African mtDNA tree. We discuss the possible origin of modern humans in southern, eastern or Central Africa; the possibility of a migration from southern to eastern Africa more than 100 ka, carrying lineages within mtDNA haplogroup L0; the evidence for a climate-change-mediated population expansion in eastern Africa involving mtDNA haplogroup L3, leading to the “out-of-Africa” migration around 70–60 ka; the re-population of North Africa from the Near East around 40–30 ka suggested by mtDNA haplogroups U6 and M1; the evidence for population expansions and dispersals across the continent at the onset of the Holocene ; and the impact of the Bantu dispersals in Central, eastern and southern Africa within the last few millennia.

Ancient materials and techniques to improve the earthen building durability

A substantial part of the world building heritage has been performed by earthen building. The durability of this existing heritage and mainly of the new buildings built with earth is particularly conditioned by the erosion caused by water action, especially in countries with high levels of rainfall. This research aims to contribute to the increase of knowledge about the ancient building techniques that provide enhanced durability. It is possible to analyse the ancestral practices used to protect the earth material from the water action in order to understand how the old earthen buildings were preserved over the centuries, resisting to harsh weather conditions. Among these techniques are: the incorporation of biopolymers (such as oils or fats from animal or vegetable origin); the addition of some minerals; and the earth stabilization with lime. However, this knowledge seems to be forgotten, probably due to the prejudice related to earthen constructions, which several times are associated with a poor building. This research also focuses on the study of new methods of earth stabilization with lime and biopolymers, adapting the ancient knowledge to improve the durability related to the water action. Therefore, alternative solutions can be obtained to improve the performance of earthen buildings, mainly the resistance of the material in the presence of water, reducing its permeability to water. In addition, with the proposed solutions it is possible to obtain good levels of water vapour permeability, one of the major advantages of the construction with earth.

Application of near surface mounted (NSM) strengthening technique to traditional timber frame walls

Timber frame buildings are well known as an efficient seismic resistant structure popular all over the world not only due to their seismic performance, but also to their low cost and the strength they offer. These constructions still exist today and it is important to be able to preserve them, so a better knowledge on their behaviour is sought. Furthermore, historic technologies could be used even in modern constructions to build seismic resistant buildings using more natural materials with lesser costs. A great rehabilitation effort is being carried out on this type of buildings, as their neglect has led to decay or their change in use and alterations to the structure has led to the need to retrofit such buildings; only recently studies on their behaviour have become available and only a few of them address the issue of possible strengthening techniques for this kind of walls. In this scope, an innovative retrofitting technique (near surface mounted steel flat bars) is proposed and validated on traditional timber frame walls based on an extensive experimental program. The results of the static cyclic tests on distinct wall typologies retrofitted with the NSM technique are herein presented and discussed in detail. The main features on deformation, lateral stiffness, lateral resistance and seismic performance indexes are analysed

MixAR mobile prototype: visualizing virtually reconstructed ancient structures in situ

Archeology and related areas have a special interest on cultural heritage sites since they provide valuable information about past civilizations. However, the ancient buildings present in these sites are commonly found in an advanced state of degradation which difficult the professional/expert analysis. Virtual reconstructions of such buildings aim to provide a digital insight of how these historical places could have been in ancient times. Moreover, the visualization of such models has been explored by some Augmented Reality (AR) systems capable of providing support to experts. Their compelling and appealing environments have also been applied to promote the social and cultural participation of general public. The existing AR solutions regarding this thematic rarely explore the potential of realism, due to the following lacks: the exploration of mixed environments is usually only supported for indoors or outdoors, not both in the same system; the adaptation of the illumination conditions to the reconstructed structures is rarely addressed causing a decrease of credibility. MixAR [1] is a system concerned with those challenges, aiming to provide the visualization of virtual buildings augmented upon real ruins, allowing soft transitions among its interiors and exteriors and using relighting techniques for a faithful interior illumination, while the user freely moves in a given cultural heritage site, carrying a mobile unit. Regarding the focus of this paper, we intend to report the current state of MixAR mobile unit prototype, which allows visualizing virtual buildings – properly aligned with real-world structures – based on user's location, during outdoor navigation. In order to evaluate the prototype performance, a set of tests were made using virtual models with different complexities.

Indústria Transformadora em Timor-Leste: uma proposta para um setor industrial

Dissertação de mestrado em Engenharia Industrial

Mosaic maternal ancestry in the Great Lakes region of East Africa

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

Transmission and progression to disease of Mycobacterium tuberculosis phylogenetic lineages in The Netherlands

The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference, Mycobacterium africanum showed significantly lower infectivity and clustering indices in the foreign-born population, while Mycobacterium bovis showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on M. tuberculosis control efforts.