Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.

Funder: Max-Planck SocietyFunder: St John’s College, CambridgeFunder: Fondation Raoul FollereauFunder: 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 TübingenBackgroundHansen'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

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

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

Morphé : análise das proporções entre os membros, dimorfismo sexual e estatura de uma amostra da colecção de esqueletos identificados do Museu Antropológico da Universidade de Coimbra

Dissertação de mestrado em Evolução Humana apresentada à Fac. Ciências e Tecnologia da Univ. Coimbr

Study of stafne's defects in Late Neolithic, Late Roman, Medieval and Modern skeletal samples from Portugal

Lingual mandibular cortical defects (Stafne’s defects) are relatively uncommon in recent as well as past populations, but while this condition is often discussed in clinical reports, they are rarely the subject of anthropological research. In this paper, the prevalence of Stafne’s bone defects in skeletal samples from Late Neolithic, Late Roman, Medieval and Modern Portugal is investigated (N = 704 complete mandibles and 111 incomplete mandibles). The aims of this paper are threefold: (1) to present and analyse for the first time in Portuguese osteological record prevalence data on Stafne’s bone defect, (2) to analyse variations in defect prevalence between skeletal samples from a wide temporal array, and (3) to verify if more tenuous lesions in which resorption of the lingual cortex was not yet extensive had the classic radiographic appearance described by Stafne in order to validate the hypothesis that lesions are present clinically in many more cases than published figures indicate. In all cases, differential diagnosis against other conditions that mimic Stafne’s defects, namely odontogenic lesions, cysts and neoplasms, was done. In all samples, the evidence of Stafne’s defect occurred in 12 individuals (1.7%), and males (2.84%) were more frequently affected than females (0.61%). When incomplete mandibles were considered, only one left fragment (0.90%) exhibited Stafne’s defect. Accurate identification of all examples of Stafne’s bone defects in antiquity is thought to represent an important contribution to elucidate which factors may be responsible for this trait’s cultural, ecological, temporal, and geographical patterning

Periodontal disease in a Portuguese identified skeletal sample from the late nineteenth and early Twentieth Centuries

Periodontal status was investigated in 600 adult dentitions belonging to the identified osteological collections curated at the University of Coimbra, Portugal. These collections date to a point temporally intermediate between the large epidemiological studies of the 20th century and archaeological collections that antedate the 19th century. The aim of this study is to compare periodontal data derived from contemporary samples with statistics compiled from epidemiological studies to determine if factors such as age-at-death, sex, and tooth type are essential or not to account for in future archaeological studies of periodontitis. Periodontal disease status was assessed based on the textural and architectural variations of the interdental septum and the extent of bone loss. Overall, the frequency of periodontitis within the Coimbra collections is 73.8%. Men were more susceptible to periodontal disease than women. Gingivitis was widespread in the younger age groups. Destructive periodontitis was observed early in adulthood, rising steadily with age. The most susceptible sites to periodontal breakdown were located in the posterior region of the upper jaw. Some variation in reported frequencies of periodontitis was found in epidemiological reports, which might result from variation in methods for identifying the pathology, differences in the age composition of the samples examined, variation in oral hygiene and/or diet, or some other factors. Regarding the pattern of distribution of periodontal disease, Coimbra results were similar to comparable modern epidemiological surveys, making clear the importance of considering sex, age, and oral distribution of periodontitis in future archaeological studies

Dental caries in a Portuguese identified skeletal sample from the late 19th and early 20th centuries

Dental caries was investigated in 600 adult dentitions belonging to the identified osteological collections of the Museum of Anthropology, University of Coimbra, Portugal (late 19th/early 20th centuries). The main advantage of this sample compared to an archaeological source is the presence of known demographic parameters such as age, sex, and occupation. The aim of this study is to investigate the issues involved in comparing caries data derived from archaeological death assemblages with statistics compiled from clinical studies of the living. When only the upper dentition was considered, higher rates were observed in females than in males. No differences were found between sexes for lower teeth. In both sexes, both the percentage of carious teeth and the severity of lesions were found to increase with age, demonstrating that caries activity continued throughout life. The slight decrease observed for the age group 70-79 years is probably due to the increased antemortem tooth loss in the elderly. Caries was most common at contact areas (32.9%) and rarest at smooth crown surfaces (6.5%). Root surface caries was graphed in relation to the exposure of roots, and it was confirmed that the degree of root exposure was not strongly related to the frequency of carious lesions on the exposed root surface, although both increased with age. Molars were attacked more frequently by caries as a whole than premolars, canines or incisors. The results are similar to studies of recent living populations with a limited access to professional dental care

Anatomical variation: analysis of non-metric traits of the postcranial skeleton in African slaves from the 15th–17th centuries (Lagos, Portugal)

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.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

Dental wear in the medieval necropolis of São João de Almedina (12th-16th centuries) and its relationship with eating habits

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

Como os chimpanzés (Pan troglodytes) em cativeiro direcionam a comunicação gestual de acordo com a faixa etária

Gestural communication among nonhuman primates evolved as a response to their complex social environment. In this scope, males and females, adults and nonadults employ different gestures, probably due to their distinct social roles. In this study, a within and between age group analysis of the gestures produced in different contexts was carried out. For this purpose, a community of 16 captive chimpanzees (Pan troglodytes) was observed during a 3-month period. Initially, data were collected through ad libitum sampling in order to identify their gestural repertoire. Subsequently, focal sampling was used to identify who gesticulated with whom and in what context. Overall, the results showed that juvenile chimpanzees tend to direct their gestures to different age groups according to the context; more specifically, juvenile chimpanzees frequently gesticulate within their age group in play contexts, and with older individuals in locomotion and affiliation contexts. Based on this, a certain degree of flexibility in juvenile chimpanzees gestural signalling is suggested, to the extent that they rather direct their gestural signs to chimpanzees of the same age group with the aim of involving themselves in the activities’ context in which the gestural sign is produced.A comunicação gestual nos primatas não-humanos evoluiu como uma resposta à complexidade social. Neste âmbito, machos e fêmeas tendem a usar diferentes tipos de gestos, provavelmente consequências das diferentes pressões sociais a que estão sujeitos. Neste estudo, realizou-se uma análise intra e interclasses etárias dos gestos produzidos em contextos distintos. Para tal, durante um período de 3 meses, observou-se uma colónia de chimpanzés (Pan troglodytes) em cativeiro. Inicialmente, os dados foram recolhidos através de uma amostragem ad libitum, para a elaboração do catálogo gestual. Posteriormente, a amostragem focal determinou quem gesticula com quem, e em que contexto. De um modo geral, os resultados mostraram que, em alguns casos, os chimpanzés juvenis tendem a gesticular para outros chimpanzés de reperclasses etárias semelhantes, tendo em conta o contexto; mais especificamente, estes direcionam gestos em contexto de brincadeira para outros chimpanzés juvenis, e comunicam com chimpanzés adultos em contexto de locomoção e afiliação. Com base nestas evidências, sugerimos a existência de um certo grau de flexibilidade na capacidade de comunicar por gestos dos chimpanzés juvenis, uma vez que estes tendem a direcionar os seus gestos para recetores de classes etárias aparentemente mais adequados, tendo em conta o contexto do sinal gestual