Search

Additional file 1: Supplementary Information Supplementary Note 1 Archaeological information for the sites and samples. Radiocarbon dates. Supplementary Note 2 Radiocarbon Dating Supplemetary Note 3 Applied Methods. Fig. S1. Sample Processing and Genome-wide analyses Fig. S2. Combined damage profiles. Fig. S3. Phylogenetic trees of 1-fold covered genomes. Fig. S4. Phylogenetic trees of 3-fold covered genomes. Fig. S5. Bayesian Maximum Clade Credibility time-aware tree for the leprosy genomes. Fig. S6. Date Randomization Test for the M. leprae dataset. Fig. S7. TempEst analysis for the M. leprae dataset. Table S1. Sample information. Table S2. Eager Report. Table S3. SNP subtyping. Table S6. Unique SNPs and virulence factors.

In 2009, the skeletons of 158 individuals were recovered from an urban dump (15th–17th centuries) in Lagos (Portugal). The biological profile of the individuals, the intentional modifications of their teeth, as well as the funerary and historical context support the hypothesis of them being African slaves. The present study aims to evaluate the frequency of non-metric characters in the skeletons of these individuals by sex and side in order to identify specific characters of this sample. All of the adult individuals in the collection (N=101) were included in the study. A total of 29 anatomical variations were sought-after in eight bones of the postcranial skeleton (clavicle, scapulae, humerus, radius, ulna, femur, patellae and tibiae). Nine of these characters were not found whereas the remaining 20 were recorded with frequencies between 1.8% and 96.1%. Only one character (costoclavicular sulcus) showed statistically significant differences between sexes. Six characters (suprascapular bevel, septal aperture, medial trochlear bevel, hypotrocanterial fossa, vast external bevel and lateral squat facet) presented differences between the two sides of the skeleton. No specific character was found for this population sample., Em 2009, foram descobertos, em Lagos (Portugal), os esqueletos de 158 indivíduos inumados numa lixeira dos séculos XV–XVII. As condições de descarte dos indivíduos, o seu perfil biológico, as modificações intencionais dos seus dentes e o contexto histórico de Lagos suportam a hipótese de se ter tratado de escravos africanos. No presente estudo, pretendeuse avaliar a frequência de caracteres nãométricos nos esqueletos destes indivíduos, bem como diferenças entre sexos e lateralidades, de modo a identificar eventuais caracteres específicos desta amostra. Foram incluídos no estudo os 101 indivíduos adultos da coleção. Foram investigadas 29 variações anatómicas de oito pares de ossos do esqueleto pós-craniano (clavícula, escápula, úmero, rádio, ulna, fémur, patela e tíbia), das quais nove não foram encontradas. As restantes 20 foram registadas com frequências compreendidas entre 1,8% e 96,1%. Apenas um carácter (sulco costoclavicular) demonstrou diferenças significativas entre os dois sexos. As lateralidades revelaram-se diferentes em seis caracteres (chanfradura supraescapular, abertura septal, chanfradura troclear medial, fossa hipotrocanteriana, chanfradura do vasto external e faceta de agachamento lateral). Quando comparados com a literatura, os resultados obtidos não permitiram identificar qualquer carácter específico desta amostra populacional.

This paper presents the osteological analysis of a young adult exhumed from the cemetery associated to Igreja do Carmo, Lisbon, Portugal, during the second archaeological intervention in 2010/2011. Although the cemetery had been used between the beginning of the 15th century and 1755 A.D., the archaeological context of the burial allows us to gauge its dating between the 17th and the 18th centuries. The skeleton is distinguished by a cranial morphology suggestive of an African origin and intentional dental modifications. These consist of the removal of both incisal angles of the upper incisors, which corresponds to a practice related to culture, commonly made in sub-Saharan Africa since prehistoric times to the present. A periapical lesion was associated to the maxillary right central incisor that was apparently healthy but modified. The left clavicle showed bone remodelling along the shaft. Five ribs displayed new bone deposition, and the sternal end of the first left rib was deformed and destroyed. The differential diagnosis of the lesions gave rise to several possible pathological conditions, namely, treponematosis and chronic respiratory disease, particularly tuberculosis. Various macroscopic aspects and the geographical context lead us to consider venereal syphilis as the most probable diagnose. Considering that, during the 16th century, Lisbon has become a fundamental part of the intercontinental maritime routes it is not surprising that African people were buried in the cemeteries of Lisbon, allowing us to learn more about their lives and deaths.

O estudo do desgaste dentário em populações arqueológicas é importante para perceber como se vivia no passado já que uma vez erupcionados os dentes não sofrem remodelação. A localização, severidade e tipos de desgaste podem revelar hábitos culturais e dietéticos. O objetivo deste estudo é analisar o padrão de desgaste dentário, por sexo e classe etária, nos indivíduos de uma amostra medieval de São João de Almedina (Coimbra, Portugal) de modo a melhor conhecer os seus hábitos. A amostra em estudo é composta por 58 adultos (28 homens, 20 mulheres e 10 indivíduos do sexo desconhecido). Os níveis de desgaste oclusal e aproximal foram registados com os métodos de Smith (1984) e Hillson (2001), respetivamente. Registou-se um desgaste oclusal médio de 3,86±1,59, caraterizado por grande exposição da dentina. Os níveis de desgaste interproximais são baixos (1,38±0,72 e 1,36±0,75). Os resultados foram comparados com outras populações, nomeadamente com os dados de Wasterlain (2006), recolhidos com a mesma metodologia, numa amostra da mesma região geográfica, mas dos finais do século XIX/inícios do século XX. Notou-se uma clara atenuação do desgaste na época pós-industrial o que pode ser resultado de um menos eficiente processamento da comida em época medieval.

Funder: Max-Planck Society, Funder: St John���s College, Cambridge, Funder: Fondation Raoul Follereau, Funder: University of Zurich���s University Research Priority Program ���Evolution in Action: From Genomes to Ecosystems���, Funder: the Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP) at the University of T��bingen, BackgroundHansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.ResultsHere, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.ConclusionsOur findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

Dissertação de Mestrado em Evolução e Biologia Humanas, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra Com este trabalho pertendeu-se aceder ao perfil biológico e paleopatológico duma amostra composta exclusivamente por indivíduos não adultos oriunda de uma de três fases de utilização da necrópole moderno-contemporânea, localizada na Santa Casa da Misericórdia de Faro (séculos XVI a XIX) e associada ao orfanato que recebia recém-nascidos através do mecanismo da roda, e, deste modo, identificar as características e qualidade das condições ambientais reunidas em torno do crescimento dos não adultos abandonados nesta Instituição. Procedeu-se, então, à obtenção e registo das dimensões de variadas peças ósseas e das fases de formação do material esquelético e dentário; à estimativa da idade à morte, segundo as vias metodológicas mais reconhecidas no meio científico; e à análise de evidências de origem patológica. Através dos resultados alcançados foi possível identificar um atraso no desenvolvimento esquelético dos não adultos, sendo os membros inferiores os mais afetados, facto concordante com a fase de aprendizagem da função locomotora. Destes dados adveio a confirmação da sujeição dos indivíduos a fortes restrições circundantes, nomeadamente a nível de nutrição e de proteção contra agentes patogénicos, sendo estas duas fontes de stresse dificilmente separadas num estudo antropológico. Porém, ambas são esperadas em ambiente de orfanato, onde as condições alimentares e higiénicas necessárias para um correto desenvolvimento infantil decerto escasseariam. A elevada frequência de lesões poróticas, deposição de osso novo e cribra, típicos de processos infeciosos de baixa complexidade ou curto tempo de formação e/ou de um estado fisiológico de subnutrição, vem corroborar estes dados, sobretudo quando presentes nos esqueletos imaturos previamente identificados como pequenos para a idade. Na análise de remanescentes osteológicos e odontológicos de indivíduos imaturos comprova-se, no entanto, que a aplicação dos métodos tradicionais de estimativa da idade à morte fica diversas vezes comprometida pelas más condições de preservação do material, sendo este caso agravado pela baixa faixa etária da maioria dos indivíduos, extremamente condicionante, nomeadamente no momento de identificação dos elementos dentários em campo. Tal restringiu a estimativa da idade dentária a 45% da amostra total, que conjuntamente com a impossibilidade de obtenção de uma porção elevada de medidas osteológicas, condicionou o estabelecimento do perfil de crescimento da amostra. Consequentemente foi eliminado o desejado passo seguinte de comparação com outras amostras esqueléticas, de diferentes proveniências. The aim of the present study was to access the biological and paleopathological profile of an osteological sample made up exclusively by non adult individuals. This sample comes from one of the three-phases of a modern-contemporary necropolis, located in Santa Casa da Misericórdia de Faro (16th-19th centuries) and associated with an orphanage which received newborns through the mechanism of the wheel. Furthermore, a second goal was to use those data to identify the characteristics and quality of the environmental conditions around the growth of the abandoned non adults in the institution. The dimensions of various osteological elements and the formation stages of skeletal and dental materials was obtained and recorded; age-at-death estimation was made according to the methodologies most recognized in the scientific community; and, finally, the paleopathological analysis of the specimens was performed. The obtained results suggest a delay in skeletal development, with the lower limbs being the most affected, which is consistent with the learning phase of the locomotor function. Such results are in accordance with severe environmental restrictions, particularly with regard to nutrition and pathogens protection, being these two stress sources hardly separated in an anthropological study. Both are expected in an orphanage environment, where food and hygienic conditions essential to a correct child development were certainly scarce. The high frequency of porotic injuries, new bone deposition and cribra, typical of low complexity and short formation infectious processes and/or physiological state of malnutrition, corroborate these facts, especially in the immature skeletons previously identified as small for their age. The osteological and dental remains analysis of immature individuals indicates, however, that the application of traditional methods for age-at-death estimation is repeatedly compromised by the sample poor preservation. The low age of most individuals aggravated this situation, particularly during teeth identification in the field. As so, dental age estimation was limited to 45% of the total sample, which combined with the unacess to some osteological measures, restricted the establishment of the sample’s growth profile. This lack excluded the next step of comparison with other skeletal samples.