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1. The evolution and changing ecology of the African hominid oral microbiome

Author

Yates, James A. Fellows, Velsko, Irina M., Aron, Franziska, Posth, Cosimo, Hofman, Courtney A., Austin, Rita M., Parker, Cody E., Mann, Allison E., Nägele, Kathrin, Arthur, Kathryn Weedman, Arthur, John W., Bauer, Catherine C., Crevecoeur, Isabelle, Cupillard, Christophe, Curtis, Matthew C., Dalén, Love, Bonilla, Marta Díaz-Zorita, Fernández-Lomana, J. Carlos Díez, Drucker, Dorothée G., Escrivá, Elena Escribano, Francken, Michael, Gibbon, Victoria E., Morales, Manuel R. González, Mateu, Ana Grande, Harvati, Katerina, Henry, Amanda G., Humphrey, Louise, Menéndez, Mario, Mihailovic, Dušan, Peresani, Marco, Morodera, Sofía Rodríguez, Roksandic, Mirjana, Rougier, Hélène, Sázelová, Sandra, Stock, Jay T., Straus, Lawrence Guy, Svoboda, Jiří, Teßmann, Barbara, Walker, Michael J., Power, Robert C., Lewis, Cecil M., Sankaranarayanan, Krithivasan, Guschanski, Katerina, Wrangham, Richard W., Dewhirst, Floyd E., Salazar-García, Domingo C., Krause, Johannes, Herbig, Alexander, and Warinner, Christina

Published
2021

2. 14th century Yersinia pestis genomes support emergence of pestis secunda within Europe

Author

Parker, Cody E., primary, Hiss, Alina N., additional, Spyrou, Maria A., additional, Neumann, Gunnar U., additional, Slavin, Philip, additional, Nelson, Elizabeth A., additional, Nagel, Sarah, additional, Dalidowski, Xandra, additional, Friederich, Susanne, additional, Krause, Johannes, additional, Herbig, Alexander, additional, Haak, Wolfgang, additional, and Bos, Kirsten I., additional

Published
2023
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3. 14th century Yersinia pestis genomes support emergence of pestis secunda within Europe.

Author

Parker, Cody E., Hiss, Alina N., Spyrou, Maria A., Neumann, Gunnar U., Slavin, Philip, Nelson, Elizabeth A., Nagel, Sarah, Dalidowski, Xandra, Friederich, Susanne, Krause, Johannes, Herbig, Alexander, Haak, Wolfgang, and Bos, Kirsten I.

Subjects
*YERSINIA pestis, *BLACK Death pandemic, 1348-1351, *ANTIQUITIES, *HISTORICAL source material, *GENOTYPES
Abstract

Pestis secunda (1356–1366 CE) is the first of a series of plague outbreaks in Europe that followed the Black Death (1346–1353 CE). Collectively this period is called the Second Pandemic. From a genomic perspective, the majority of post-Black Death strains of Yersinia pestis thus far identified in Europe display diversity accumulated over a period of centuries that form a terminal sub-branch of the Y. pestis phylogeny. It has been debated if these strains arose from local evolution of Y. pestis or if the disease was repeatedly reintroduced from an external source. Plague lineages descended from the pestis secunda, however, are thought to have persisted in non-human reservoirs outside Europe, where they eventually gave rise to the Third Pandemic (19th and 20th centuries). Resolution of competing hypotheses on the origins of the many post-Black Death outbreaks has been hindered in part by the low representation of Y. pestis genomes in archaeological specimens, especially for the pestis secunda. Here we report on five individuals from Germany that were infected with lineages of plague associated with the pestis secunda. For the two genomes of high coverage, one groups within the known diversity of genotypes associated with the pestis secunda, while the second carries an ancestral genotype that places it earlier. Through consideration of historical sources that explore first documentation of the pandemic in today's Central Germany, we argue that these data provide robust evidence to support a post-Black Death evolution of the pathogen within Europe rather than a re-introduction from outside. Additionally, we demonstrate retrievability of Y. pestis DNA in post-cranial remains and highlight the importance of hypothesis-free pathogen screening approaches in evaluations of archaeological samples. Author summary: We present two high-coverage and three low-coverage ancient Y. pestis genomes that represent previously described diversity within a narrow time interval that immediately post-dates the Black Death (the pestis secunda), and a newly identified precursor strain. Viewed in context with recent historical revelations that define the time-span between the end of the Black Death and the emergence of the pestis secunda to a three-year interval, our analysis strongly supports this outbreak, similar to other post-Black Death outbreaks, as having originated from a local source of Y. pestis diversification. [ABSTRACT FROM AUTHOR]

Published
2023
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4. The Evolution and Changing Ecology of the African Hominid Oral Microbiome

Author

Geografía, prehistoria y arqueología, Geografia,historiaurrea eta arkeologia, Fellows Yates, James A., Velsko, Irina M., Aron, Franziska, Posth, Cosimo, Hofman, Courtney A., Austin, Rita M., Parker, Cody E., Mann, Allison E., Nagele, Kathrin, Weedman Arthur, Kathryn, Arthur, John W., Bauer, Catherine C., Crevecoeur, Isabelle, Cupillard, Christophe, Curtis, Matthew C., Dalen, Love, Díaz-Zorita Bonilla, Marta, Díez Fernández-Lomana, Carlos, Drucker, Dorothee G., Escribano Escrivá, Elena, Francken, Michael, Gibbon, Victoria E., González Morales, Manuel Ramón, Grande Mateu, Ana, Harvati, Katerina, Henry, Amanda G., Humphrey, Louise, Menéndez, Mario, Mihailović, Dušan, Peresani, Marco, Rodríguez Moroder, Sofía, Roksandic, Mirjana, Rougier, Helene, Sázelová, Sandra, Stock, Jay T., Straus, Lawrence Guy, Svoboda, Jirí, Tessmann, Barbara, Walker, Michael J., Power, Robert C., Lewis, Cecil M., Sankaranarayanan, Krithivasan, Guschanski, Katerina, Wrangham, Richard W., Dewhirst, Floyd E., Salazar García, Domingo Carlos, Krause, Johannes, Herbig, Alexander, Warinner, Christina, Geografía, prehistoria y arqueología, Geografia,historiaurrea eta arkeologia, Fellows Yates, James A., Velsko, Irina M., Aron, Franziska, Posth, Cosimo, Hofman, Courtney A., Austin, Rita M., Parker, Cody E., Mann, Allison E., Nagele, Kathrin, Weedman Arthur, Kathryn, Arthur, John W., Bauer, Catherine C., Crevecoeur, Isabelle, Cupillard, Christophe, Curtis, Matthew C., Dalen, Love, Díaz-Zorita Bonilla, Marta, Díez Fernández-Lomana, Carlos, Drucker, Dorothee G., Escribano Escrivá, Elena, Francken, Michael, Gibbon, Victoria E., González Morales, Manuel Ramón, Grande Mateu, Ana, Harvati, Katerina, Henry, Amanda G., Humphrey, Louise, Menéndez, Mario, Mihailović, Dušan, Peresani, Marco, Rodríguez Moroder, Sofía, Roksandic, Mirjana, Rougier, Helene, Sázelová, Sandra, Stock, Jay T., Straus, Lawrence Guy, Svoboda, Jirí, Tessmann, Barbara, Walker, Michael J., Power, Robert C., Lewis, Cecil M., Sankaranarayanan, Krithivasan, Guschanski, Katerina, Wrangham, Richard W., Dewhirst, Floyd E., Salazar García, Domingo Carlos, Krause, Johannes, Herbig, Alexander, and Warinner, Christina

Abstract

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

Published
2021

5. The evolution and changing ecology of the African hominid oral microbiome

Author

Fellows Yates, James A., primary, Velsko, Irina M., additional, Aron, Franziska, additional, Posth, Cosimo, additional, Hofman, Courtney A., additional, Austin, Rita M., additional, Parker, Cody E., additional, Mann, Allison E., additional, Nägele, Kathrin, additional, Arthur, Kathryn Weedman, additional, Arthur, John W., additional, Bauer, Catherine C., additional, Crevecoeur, Isabelle, additional, Cupillard, Christophe, additional, Curtis, Matthew C., additional, Dalén, Love, additional, Díaz-Zorita Bonilla, Marta, additional, Díez Fernández-Lomana, J. Carlos, additional, Drucker, Dorothée G., additional, Escribano Escrivá, Elena, additional, Francken, Michael, additional, Gibbon, Victoria E., additional, González Morales, Manuel R., additional, Grande Mateu, Ana, additional, Harvati, Katerina, additional, Henry, Amanda G., additional, Humphrey, Louise, additional, Menéndez, Mario, additional, Mihailović, Dušan, additional, Peresani, Marco, additional, Rodríguez Moroder, Sofía, additional, Roksandic, Mirjana, additional, Rougier, Hélène, additional, Sázelová, Sandra, additional, Stock, Jay T., additional, Straus, Lawrence Guy, additional, Svoboda, Jiří, additional, Teßmann, Barbara, additional, Walker, Michael J., additional, Power, Robert C., additional, Lewis, Cecil M., additional, Sankaranarayanan, Krithivasan, additional, Guschanski, Katerina, additional, Wrangham, Richard W., additional, Dewhirst, Floyd E., additional, Salazar-García, Domingo C., additional, Krause, Johannes, additional, Herbig, Alexander, additional, and Warinner, Christina, additional

Published
2021
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7. Observations of Multiple Nuclear Reaction Histories and Fuel-Ion Species Dynamics in Shock-Driven Inertial Confinement Fusion Implosions

Author

Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Plasma Science and Fusion Center, Sio, Hong Weng, Frenje, Johan A, Gatu Johnson, Maria, Li, Changhao, Parker, Cody E, Kabadi, Neel Vinayak, Bose, Anoushka R., Seguin, Fredrick Hampton, Petrasso, Richard D, Le, A., Atzeni, S., Kwan, T. J. T., Kagan, G., Stoeckl, C., Forrest, C. J., Glebov, V., Rinderknecht, H. G., Amendt, P., Casey, D. T., Mancini, R., Taitano, W. T., Keenan, B., Simakov, A. N., Chacón, L., Regan, S. P., Sangster, T. C., Campbell, E. M., Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Plasma Science and Fusion Center, Sio, Hong Weng, Frenje, Johan A, Gatu Johnson, Maria, Li, Changhao, Parker, Cody E, Kabadi, Neel Vinayak, Bose, Anoushka R., Seguin, Fredrick Hampton, Petrasso, Richard D, Le, A., Atzeni, S., Kwan, T. J. T., Kagan, G., Stoeckl, C., Forrest, C. J., Glebov, V., Rinderknecht, H. G., Amendt, P., Casey, D. T., Mancini, R., Taitano, W. T., Keenan, B., Simakov, A. N., Chacón, L., Regan, S. P., Sangster, T. C., and Campbell, E. M.

Abstract

Fuel-ion species dynamics in hydrodynamiclike shock-driven DT³He-filled inertial confinement fusion implosion is quantitatively assessed for the first time using simultaneously measured D³He and DT reaction histories. These reaction histories are measured with the particle x-ray temporal diagnostic, which captures the relative timing between different nuclear burns with unprecedented precision (∼10 ps). The observed 50±10 ps earlier D³He reaction history timing (relative to DT) cannot be explained by average-ion hydrodynamic simulations and is attributed to fuel-ion species separation between the D, T, and ³He ions during shock convergence and rebound. At the onset of the shock burn, inferred ³He/T fuel ratio in the burn region using the measured reaction histories is much higher as compared to the initial gas-filled ratio. As T and ³He have the same mass but different charge, these results indicate that the charge-to-mass ratio plays an important role in driving fuel-ion species separation during strong shock propagation even for these hydrodynamiclike plasmas., United States. Department of Energy (Grant DE-FC52-08NA28752)

Published
2019

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