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International Symposium on Biomolecular Archaeology (ISBA)  highlights the work of MHAAM

The growing prominence of the work of Harvard’s Initiative for the Science of the Human Past (SoHP) and MHAAM was hard to miss at the eighth biennial world gathering of biomolecular archaeologists in Jena, Germany, September 18-21, 2018. The International Symposium on Biomolecular Archaeology (ISBA) was hosted by Johannes Krause and the Max Planck Institute for the Science of Human History (MPISHH), SoHP’s collaborative partner in the creation of MHAAM.

The previous ISBA meeting, held at Oxford in 2016, attracted about 200 participants.  The explosive growth of the new discipline of archaeoscience was manifest this year in Jena: with more than 400 participants, attendance outstripped all predictions for a conference meeting in a lovely but somewhat out-of-the way corner of eastern Germany.

 

Harvard’s SoHP and MHAAM investigators and their projects were exceptionally well represented. After an opening lecture by Svante Pääbö, Wednesday’s papers included David Reich on the genomic formation of south and central Asia; Alissa Mittnik used archaeogenetics to discover household structure and marital patterns among Bronze Age farmsteads in Bavaria, while Eadaoin Harney presented on the mysterious skeletons of Roopkund and Iñigo Olalde sketched the genetic history of the Iberian peninsula over the last 8000 years from aDNA. On Friday Noreen Tuross reevaluated Neanderthal subsistence, current MHAAM post-doc Saskia E. Ryan explored changes in ancient diets from birth to toddling through novel uses of light stable isotopes in tooth dentin, and Nathan Nakatsuka estimated ancient nuclear DNA contamination from linkage disequilibrium patterns.

 

Harvard-authored posters kept up the pace: the two current holders of MHAAM graduate fellowships, second-year PhD candidates Aurora Allshouse (Archaeology/Anthropology) and Megan Michel (Human Evolutionary Biology), respectively, used isotopes to track movement around a busy Byzantine port city, and highlighted the aDNA search for markers of malaria among ancient Sardinians. Prof. Tuross presented recent questions on the microbiome and isotopic fractionation, Dr. Linda M. Reynard took a new look at fundamental methodological questions arising from light stable isotopes in archaeological contexts, and Alexander Kim examined Yeniseian hypotheses in light of genome-wide ancient DNA from historical Siberia.

 

Finally, two scientists working at MPISHH on the historical plague pandemics that are central to MHAAM’s transatlantic research program presented critical insights featuring new evidence from mass graves, three of which were identified by the Harvard MHAAM pandemic team.  In his poster “Ancient Yersinia pestis genomes from Britain, France, Germany and Spain reveal extensive strain diversity during the First Plague Pandemic (541-750 CE),” Marcel Keller presented the first robust molecular proof that the Justinianic Pandemic reached Britain, France and Anglo-Saxon England, and abundant new evidence from early medieval Bavaria.  Gunnar U. Neumann underlined plague persistence in Europe during the Second Pandemic thanks to a 16th century Yersinia pestis genome from particularly well-preserved individuals from Logroño, Spain. McCormick co-authored both papers. Alumni of the SoHP network also featured prominently in the meeting, including former Harvard post-docs Pontus Skoglund (Francis Crick Institute, London) who gave a paper on modelling early human lineages in Africa, and Michael Campana (Smithsonian Institution, Center for Conservation Genomics) who displayed evidence for Ancient DNA phylogenomics using DNA capture and maximal information (super)trees.

August 29, 2018

Ancient Peoples-Modern Names: Reconciling material cultures in archaeology with the new archaeogenetic data

A new study in Nature – Scientific Reports addresses the fundamental issue of identifying and naming genetic clusters in the new field of archaeogenetics. The first joint publication of the Max Planck – Harvard Research Center for the Archaeoscience of the Ancient Mediterranean lays the groundwork for resolving misunderstandings in the classification of ever growing libraries of ancient genetic data.

 

Ancient DNA analysis is a powerful new tool for investigating the human past that is transforming the traditional disciplines like archaeology and history. This new study tackles one of the fundamental obstacles in the collaboration between archaeogeneticists and archaeologists: the development of a common language for archaeological phenomena.

 

Recent methodological advances in the field of ancient DNA analysis have exponentially increased the number of ancient genomes published. This data can be analyzed to identify statistical groupings of individuals who share more genetic variants with each other. To name these “genetic clusters,” geneticists have frequently borrowed names from archaeological groupings, without considering the historically problematic nature of the concept of cultures and identities in archaeology. This has led to the misinterpretation of the genetic results in subsequent papers and by the public, or even a rejection of ancient DNA studies as a whole in parts of the archaeological community.

 

The nature of names is that they have or rather convey meanings. What we call a thing inevitably influences what we think it is. Naming is thus a double-edged sword that can to the same extent prevent and stir misunderstandings.

 

To address these issues the paper focuses on two aspects: 1. It explains the concept of “genetic clusters” in contrast to “archaeological cultures.” 2. It discusses naming conventions used in recent genetic publications and introduces two future possibilities for the nomenclature of genetic clusters: a system based exclusively on the combination of geographical terms and relative dates (e.g. Levant Middle Bronze Age), and a mixed nomenclature that additionally uses names of archaeological cultures (e.g. Yamnaya) and subsistence practices (like hunter-gatherer). The authors of the paper lay the groundwork for debate establishing a wider theoretical framework that allows more careful integration of genetic research into ancient studies.

April 11, 2018

 

Death by Contact: Ancient Pathogen Genomes from Epidemics in Early Mexico," MHAAM Lecture by Johannes Krause (Director, Department of Archaeogenetics, MPISSH Jena, Univ. Tübingen), with comments by Edward T. Ryan, Director of Global Infectious Disease, Massachusetts General Hospital, Professor of Medicine, Harvard Medical School, Professor of Immunology and Infectious Diseases, Harvard School of Public Health, and Principal Investigator, Harvard collaboration with the International Centre for Diarrhoeal Disease Research in Dhaka, Bangladesh; and Noreen Tuross, Landon T. Clay Professor of Scientific Archaeology, Department of Human Evolutionary Biology, Harvard University.

Genome-wide data from ancient microbes may help to understand mechanisms of pathogen evolution and adaptation for today’s emerging and re-emerging infectious diseases. Ancient pathogen genomes provide, furthermore, the possibility to identify causative agents of past pandemics and therefore elucidate mortality crisis such as those that marked the early contact period in the New World. In order to identify the presence of pathogens in past populations our group used a novel high-throughput DNA sequence alignment and taxonomic assignment tool MALT (MEGAN ALignment

Tool) and were able to identify traces of Salmonella enterica DNA in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in Southern Mexico. This cemetery is linked to the 1545–1550 CE epidemic that affected large parts of Mexico, the pathogenic cause of which has been debated for more than a century. After application of a specifically designed targeted DNA enrichment procedure we generated genome-wide data from ten individuals for Salmonella enterica subsp. entericaserovar Paratyphi C, a bacterial cause of enteric fever. We propose S. Paratyphi C as a strong candidate for the epidemic population decline during the 1545 outbreak at Teposcolula-Yucundaa and provide evidence that it was likely introduced by Europeans.

 

See video of the talk on Youtube.

Read the article in "Nature," 15 January, 2018.

April 11, 2017

 

"Vectors, climate, economic conditions of epidemiology of historical plagues," (MHAAM Workshop, April 11, 2018).  

The Justinianic (541-ca. 750) and Black Death Pandemics (1347-1722) are among the largest-scale and persistently controverted disease events in human history. They have been viewed as causing enormous demographic, economic, and cultural changes resulting in the end of medieval civilization and the beginnings of modernity or, in the case of the Justinianic Pandemic, the destruction of the Roman economy and the civilization and polity built upon it. To verify and correctly assess these massive events, it is essential to reconstruct them at the highest level of detail possible, including their biology.  Until very recently, multiple theories argued that the pathogen was not Yersinia pestis.

Palaeogenetic work has confirmed historical evidence that Y.p. was in fact the main pathogen. Advancing technology is allowing the reconstruction of the complete genomes of these ancient bacteria, offering the possibility to track with precision the evolution of this lethal pathogen between and within pandemics going back at least to the Roman Empire. Controversial theories and hypotheses continue to be formulated re the vectors of bubonic plague (rats, not rats; other micromammals; rat fleas, human fleas, human lice), often in seeming disregard of the medical consensus (e.g., difficulty of inter-human transmission except for pneumonic plague), the zoological and entomological knowledge of the vectors and their behavior patterns, including under different climate scenarios, and how these might affect the epidemiology of Y.p. in ancient and medieval civilization. The workshop brought together specialists from Jena, Harvard, NIH, CDC and the University of York (UK) to discuss these questions, as well as ongoing archaeogenetic work in Jena and historical work at Harvard.

October 10, 2017

The new Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean was inaugurated at Harvard University on October 10, and featured a keynote lecture by Dr. Johannes Krause on his latest, unpublished research, as well as by Dr. Susan Alcock, Dr. David Reich and Dr. Iosif Lazaridis on new evidence for ancient migrations. The event included the signing of the agreement between the Max Planck Society and SoHP.

 

August 23-26, 2017

Professor Michael McCormick, SoHP Postoctoral Fellow Alexander More, and three Harvard-SoHP graduate students, Henry Gruber, Megan Michel and Jake Ransohoff, from the departments of History and of Human Evolutionary Biology traveled to Jena in July 2017, to meet with colleagues at the Max Planck Institute for the Science of Human History. During three active and exciting days, visitors from Harvard attended a lecture on new methods for analyzing and representing population genetics data; discussed new advances in genome data and prehistoric human migration with Dr. Stephan Schiffels and Dr. Wolfgang Haak; and joined a round-table discussion with doctoral students at Max Planck’s Historic Plague Project, led by Dr. Kirsten Bos and Dr. Alexander Herbig.

The Harvard team, in turn, shared their recent work on the philology of ancient plague sources, and discussed their findings in light of the new scientific vistas opened by the Historical Plague Project. The visit included a tour of exhibits and the conservation lab at the famous State Museum of Prehistory in Halle, and culminated with a trip to the Max Planck Institute’s labs in Jena. Group meals in Jena’s old town closed each busy day, during which senior scholars and graduate students alike renewed old collaborations and inaugurated new ones.