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1. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Author

Posth, C., Yu, H., Ghalichi, A., Rougier, H., Crevecoeur, I., Huang, Y., Ringbauer, H., Rohrlach, A., Nägele, K., Villalba-Mouco, V., Radzeviciute, R., Ferraz, T., Stoessel, A., Tukhbatova, R., Drucker, D., Lari, M., Modi, A., Vai, S., Saupe, T., Scheib, C., Catalano, G., Pagani, L., Talamo, S., Fewlass, H., Klaric, L., Morala, A., Rué, M., Madelaine, S., Crépin, L., Caverne, J., Bocaege, E., Ricci, S., Boschin, F., Bayle, P., Maureille, B., Le Brun-Ricalens, F., Bordes, J., Oxilia, G., Bortolini, E., Bignon-Lau, O., Debout, G., Orliac, M., Zazzo, A., Sparacello, V., Starnini, E., Sineo, L., van der Plicht, J., Pecqueur, L., Merceron, G., Garcia, G., Leuvrey, J., Garcia, C., Gómez-Olivencia, A., Połtowicz-Bobak, M., Bobak, D., Le Luyer, M., Storm, P., Hoffmann, C., Kabaciński, J., Filimonova, T., Shnaider, S., Berezina, N., González-Rabanal, B., Morales, G., R., M., Marín-Arroyo, A., López, B., Alonso-Llamazares, C., Ronchitelli, A., Polet, C., Jadin, I., Cauwe, N., Soler, J., Coromina, N., Rufí, I., Cottiaux, R., Clark, G., Straus, L., Julien, M., Renhart, S., Talaa, D., Benazzi, S., Romandini, M., Amkreutz, L., Bocherens, H., Wißing, C., Villotte, S., de Pablo, Fernández-López, J., Gómez-Puche, M., Esquembre-Bebia, M., Bodu, P., Smits, L., Souffi, B., Jankauskas, R., Kozakaitė, J., Cupillard, C., Benthien, H., Wehrberger, K., Schmitz, R., Feine, S., Schüler, T., Thevenet, C., Grigorescu, D., Lüth, F., Kotula, A., Piezonka, H., Schopper, F., Svoboda, J., Sázelová, S., Chizhevsky, A., Khokhlov, A., Conard, N., Valentin, F., Harvati, K., Semal, P., Jungklaus, B., Suvorov, A., Schulting, R., Moiseyev, V., Mannermaa, K., Buzhilova, A., Terberger, T., Caramelli, D., Altena, E., Haak, W., and Krause, J.

Abstract

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants. Ancient DNA data generation Before the LGM LGM in southwestern and western Europe Post-LGM in the Italian peninsula Post-LGM in western and central Europe Post-14 ka to Neolithic Phenotypically relevant variants Discussion and conclusions Methods

Published
2023

2. Ten millennia of hepatitis B virus evolution

Author

Salazar-García, Domingo C., Papac L., Barquera R., Key F.M., Spyrou M.A., Hübler R., Rohrlach A.B., Aron F., Stahl R., Wissgott A., van Bömmel F., Pfefferkorn M., Mittnik A., Villalba-Mouco V., Neumann G.U., Rivollat M., van de Loosdrecht M.S., Majander K., Tukhbatova R.I., Musralina L., Ghalichi A., Penske S., Sabin S., Michel M., Gretzinger J., Nelson E.A., Ferraz T., NÄgele K., Parker C., Keller M., Guevara E.K., Feldman M., Eisenmann S., Skourtanioti E., Giffin K., Gnecchi-Ruscone G.A., Friederich S., Schimmenti V., Khartanovich V., and Karapetian M.K.

Subjects
virus diseases, Arqueologia
Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

Published
2021

3. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Author

Department of Archeology and History of Art, Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B.; Papac, L.; Childebayeva, A.; Rivollat, M.; Villalba Mouco, V.; Neumann, G.U.; Penske, S.; Skourtanioti, E.; van de Loosdrecht, M.; Akar, M.; Boyadzhiev, K.; Boyadzhiev, Y.; Deguilloux, M.F.; Dobes, M.; Erdal, Y.S.; Ernée, M.; Frangipane, M.; Furmanek, M.; Friederich, S.; Ghesquière, E.; Ha?uszko, A.; Hansen, S.; Küßner, M.; Mannino, M.; Reinhold, S.; Rottier, S.; Salazar García, D.C.; Diaz, J.S.; Stockhammer, P.W.; de Togores Muñoz, C.R.; Yener, K.A.; Posth, C.; Krause, J.; Herbig, A.; Haak, W., Department of Archeology and History of Art, Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), and Rohrlach, A.B.; Papac, L.; Childebayeva, A.; Rivollat, M.; Villalba Mouco, V.; Neumann, G.U.; Penske, S.; Skourtanioti, E.; van de Loosdrecht, M.; Akar, M.; Boyadzhiev, K.; Boyadzhiev, Y.; Deguilloux, M.F.; Dobes, M.; Erdal, Y.S.; Ernée, M.; Frangipane, M.; Furmanek, M.; Friederich, S.; Ghesquière, E.; Ha?uszko, A.; Hansen, S.; Küßner, M.; Mannino, M.; Reinhold, S.; Rottier, S.; Salazar García, D.C.; Diaz, J.S.; Stockhammer, P.W.; de Togores Muñoz, C.R.; Yener, K.A.; Posth, C.; Krause, J.; Herbig, A.; Haak, W.

Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the ""mappable"" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

Published
2021

4. Ten millennia of hepatitis B virus evolution

Author

Kocher, A, Papac, L, Barquera, R, Key, FM, Spyrou, MA, Hubler, R, Rohrlach, AB, Aron, F, Stahl, R, Wissgott, A, van Bommel, F, Pfefferkorn, M, Mittnik, A, Villalba-Mouco, V, Neumann, GU, Rivollat, M, van de Loosdrecht, MS, Majander, K, Tukhbatova, R, Musralina, L, Ghalichi, A, Penske, S, Sabin, S, Michel, M, Gretzinger, J, Nelson, EA, Ferraz, T, Nagele, K, Parker, C, Keller, M, Guevara, EK, Feldman, M, Eisenmann, S, Skourtanioti, E, Giffin, K, Gnecchi-Ruscone, GA, Friederich, S, Schimmenti, V, Khartanovich, V, Karapetian, MK, Chaplygin, MS, Kufterin, VV, Khokhlov, AA, Chizhevsky, AA, Stashenkov, DA, Kochkina, AF, Tejedor-Rodriguez, C, Garcia-Martinez de Lagran, I, Arcusa-Magallon, H, Garrido-Pena, R, Ignacio Royo-Guillen, J, Novacek, J, Rottier, S, Kacki, S, Saintot, S, Kaverzneva, E, Belinskiy, AB, Veleminsky, P, Limbursky, P, Kostka, M, Loe, L, Popescu, E, Clarke, R, Lyons, A, Mortimer, R, Sajantila, A, Chinique de Armas, Y, Hernandez Godoy, ST, Hernandez-Zaragoza, D, Pearson, J, Binder, D, Lefranc, P, Kantorovich, AR, Maslov, VE, Lai, L, Zoledziewska, M, Beckett, JF, Langova, M, Ingman, T, Garcia Atienzar, G, de Miguel Ibanez, MP, Romero, A, Sperduti, A, Beckett, S, Salter, SJ, Zilivinskaya, ED, Vasil, DV, von Heyking, K, Burger, RL, Salazar, LC, Amkreutz, L, Navruzbekov, M, Rosenstock, E, Alonso-Fernandez, C, Slavchev, V, Kalmykov, AA, Atabiev, BC, Batieva, E, Alvarez Calmet, M, Llamas, B, Schultz, M, Krauss, R, Jimenez-Echevarria, J, Francken, M, Shnaider, S, de Knijff, P, Altena, E, Van de Vijver, K, Fehren-Schmitz, L, Tung, TA, Losch, S, Dobrovolskaya, M, Makarov, N, Read, C, Van Twest, M, Sagona, C, Ramsl, PC, Akar, M, Yener, KA, Carmona Ballestero, E, Cucca, F, Mazzarello, V, Utrilla, P, Rademaker, K, Fernandez-Dominguez, E, Baird, D, Semal, P, Marquez-Morfin, L, Roksandic, M, Steiner, H, Carlos Salazar-Garcia, D, Shishlina, N, Erdal, YS, Hallgren, F, Boyadzhiev, Y, Boyadzhiev, K, Kuessner, M, Sayer, D, Onkamo, P, Skeates, R, Rojo-Guerra, M, Buzhilova, A, Khussainova, E, Djansugurova, LB, Beisenov, AZ, Samashev, Z, Massy, K, Mannino, M, Moiseyev, V, Mannermaa, K, Balanovsky, O, Deguilloux, M-F, Reinhold, S, Hansen, S, Kitov, EP, Dobes, M, Ernee, M, Meller, H, Alt, KW, Prufer, K, Warinner, C, Schiffels, S, Stockhammer, PW, Bos, K, Posth, C, Herbig, A, Haak, W, Krause, J, Kuehnert, D, Kocher, A, Papac, L, Barquera, R, Key, FM, Spyrou, MA, Hubler, R, Rohrlach, AB, Aron, F, Stahl, R, Wissgott, A, van Bommel, F, Pfefferkorn, M, Mittnik, A, Villalba-Mouco, V, Neumann, GU, Rivollat, M, van de Loosdrecht, MS, Majander, K, Tukhbatova, R, Musralina, L, Ghalichi, A, Penske, S, Sabin, S, Michel, M, Gretzinger, J, Nelson, EA, Ferraz, T, Nagele, K, Parker, C, Keller, M, Guevara, EK, Feldman, M, Eisenmann, S, Skourtanioti, E, Giffin, K, Gnecchi-Ruscone, GA, Friederich, S, Schimmenti, V, Khartanovich, V, Karapetian, MK, Chaplygin, MS, Kufterin, VV, Khokhlov, AA, Chizhevsky, AA, Stashenkov, DA, Kochkina, AF, Tejedor-Rodriguez, C, Garcia-Martinez de Lagran, I, Arcusa-Magallon, H, Garrido-Pena, R, Ignacio Royo-Guillen, J, Novacek, J, Rottier, S, Kacki, S, Saintot, S, Kaverzneva, E, Belinskiy, AB, Veleminsky, P, Limbursky, P, Kostka, M, Loe, L, Popescu, E, Clarke, R, Lyons, A, Mortimer, R, Sajantila, A, Chinique de Armas, Y, Hernandez Godoy, ST, Hernandez-Zaragoza, D, Pearson, J, Binder, D, Lefranc, P, Kantorovich, AR, Maslov, VE, Lai, L, Zoledziewska, M, Beckett, JF, Langova, M, Ingman, T, Garcia Atienzar, G, de Miguel Ibanez, MP, Romero, A, Sperduti, A, Beckett, S, Salter, SJ, Zilivinskaya, ED, Vasil, DV, von Heyking, K, Burger, RL, Salazar, LC, Amkreutz, L, Navruzbekov, M, Rosenstock, E, Alonso-Fernandez, C, Slavchev, V, Kalmykov, AA, Atabiev, BC, Batieva, E, Alvarez Calmet, M, Llamas, B, Schultz, M, Krauss, R, Jimenez-Echevarria, J, Francken, M, Shnaider, S, de Knijff, P, Altena, E, Van de Vijver, K, Fehren-Schmitz, L, Tung, TA, Losch, S, Dobrovolskaya, M, Makarov, N, Read, C, Van Twest, M, Sagona, C, Ramsl, PC, Akar, M, Yener, KA, Carmona Ballestero, E, Cucca, F, Mazzarello, V, Utrilla, P, Rademaker, K, Fernandez-Dominguez, E, Baird, D, Semal, P, Marquez-Morfin, L, Roksandic, M, Steiner, H, Carlos Salazar-Garcia, D, Shishlina, N, Erdal, YS, Hallgren, F, Boyadzhiev, Y, Boyadzhiev, K, Kuessner, M, Sayer, D, Onkamo, P, Skeates, R, Rojo-Guerra, M, Buzhilova, A, Khussainova, E, Djansugurova, LB, Beisenov, AZ, Samashev, Z, Massy, K, Mannino, M, Moiseyev, V, Mannermaa, K, Balanovsky, O, Deguilloux, M-F, Reinhold, S, Hansen, S, Kitov, EP, Dobes, M, Ernee, M, Meller, H, Alt, KW, Prufer, K, Warinner, C, Schiffels, S, Stockhammer, PW, Bos, K, Posth, C, Herbig, A, Haak, W, Krause, J, and Kuehnert, D

Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

Published
2021

5. Ten millennia of hepatitis B virus evolution

Author

Ingman, Tara, Kocher, A.; Papac, L.; Barquera, R.; Key, FM.; Spyrou, MA.; Hubler, R.; Rohrlach, AB.; Aron, F.; Stahl, R.; Wissgott, A.; van Bommel, F.; Pfefferkorn, M.; Mittnik, A.; Villalba-Mouco, V.; Neumann, GU.; Rivollat, M.; van de Loosdrecht, MS.; Majander, K.; Tukhbatova, RI.; Musralina, L.; Ghalichi, A.; Penske, S.; Sabin, S.; Michel, M.; Gretzinger, J.; Nelson, EA.; Ferraz, T.; Nagele, K.; Parker, C.; Keller, M.; Guevara, EK.; Feldman, M.; Eisenmann, S.; Skourtanioti, E.; Giffin, K.; Gnecchi-Ruscone, GA.; Friederich, S.; Schimmenti, V.; Khartanovich, V.; Karapetian, MK.; Chaplygin, MS.; Kufterin, VV.; Khokhlov, AA.; Chizhevsky, AA.; Stashenkov, DA.; Kochkina, AF.; Tejedor-Rodriguez, C.; de Lagran, IGM.; Arcusa-Magallon, H.; Garrido-Pena, R.; Royo-Guillen, JI.; Novacek, J.; Rottier, S.; Kacki, S.; Saintot, S.; Kaverzneva, E.; Belinskiy, AB.; Veleminsky, P.; Limbursky, P.; Kostka, M.; Loe, L.; Popescu, E.; Clarke, R.; Lyons, A.; Mortimer, R.; Sajantila, A.; de Armas, YC.; Godoy, STH.; Hernandez-Zaragoza, DI.; Pearson, J.; Binder, D.; Lefranc, P.; Kantorovich, AR.; Maslov, VE.; Lai, L.; Zoledziewska, M.; Beckett, JF.; Langova, M.; Atienzar, GG.; Ibanez, MPD; Romero, A.; Sperduti, A.; Beckett, S.; Salter, SJ.; Zilivinskaya, ED.; Vasil, DV.; von Heyking, K.; Burger, RL.; Salazar, LC.; Amkreutz, L.; Navruzbekov, M.; Rosenstock, E.; Alonso-Fernandez, C.; Slavchev, V.; Kalmykov, AA.; Atabiev, BC.; Batieva, E; Calmet, MA.; Llamas, B.; Schultz, M.; Krauss, R.; Jimenez-Echevarria, J.; Francken, M.; Shnaider, S.; de Knijff, P.; Altena, E.; Van de Vijver, K.; Fehren-Schmitz, L.; Tung, TA.; Losch, S.; Dobrovolskaya, M.; Makarov, N.; Read, C.; Van Twest, M.; Sagona, C.; Ramsl, PC.; Akar, M.; Yener, KA.; Ballestero, EC.; Cucca, F.; Mazzarello, V.; Utrilla, P.; Rademaker, K.; Fernandez-Dominguez, E.; Baird, D.; Semal, P.; Marquez-Morfin, L; Roksandic, M.; Steiner, H.; Salazar-Garcia, DC.; Shishlina, N. Erdal, YS.; Hallgren, F.; Boyadzhiev, Y.; Boyadzhiev, K.; Kussner, M.; Sayer, D.; Onka, Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED), Ingman, Tara, Kocher, A.; Papac, L.; Barquera, R.; Key, FM.; Spyrou, MA.; Hubler, R.; Rohrlach, AB.; Aron, F.; Stahl, R.; Wissgott, A.; van Bommel, F.; Pfefferkorn, M.; Mittnik, A.; Villalba-Mouco, V.; Neumann, GU.; Rivollat, M.; van de Loosdrecht, MS.; Majander, K.; Tukhbatova, RI.; Musralina, L.; Ghalichi, A.; Penske, S.; Sabin, S.; Michel, M.; Gretzinger, J.; Nelson, EA.; Ferraz, T.; Nagele, K.; Parker, C.; Keller, M.; Guevara, EK.; Feldman, M.; Eisenmann, S.; Skourtanioti, E.; Giffin, K.; Gnecchi-Ruscone, GA.; Friederich, S.; Schimmenti, V.; Khartanovich, V.; Karapetian, MK.; Chaplygin, MS.; Kufterin, VV.; Khokhlov, AA.; Chizhevsky, AA.; Stashenkov, DA.; Kochkina, AF.; Tejedor-Rodriguez, C.; de Lagran, IGM.; Arcusa-Magallon, H.; Garrido-Pena, R.; Royo-Guillen, JI.; Novacek, J.; Rottier, S.; Kacki, S.; Saintot, S.; Kaverzneva, E.; Belinskiy, AB.; Veleminsky, P.; Limbursky, P.; Kostka, M.; Loe, L.; Popescu, E.; Clarke, R.; Lyons, A.; Mortimer, R.; Sajantila, A.; de Armas, YC.; Godoy, STH.; Hernandez-Zaragoza, DI.; Pearson, J.; Binder, D.; Lefranc, P.; Kantorovich, AR.; Maslov, VE.; Lai, L.; Zoledziewska, M.; Beckett, JF.; Langova, M.; Atienzar, GG.; Ibanez, MPD; Romero, A.; Sperduti, A.; Beckett, S.; Salter, SJ.; Zilivinskaya, ED.; Vasil, DV.; von Heyking, K.; Burger, RL.; Salazar, LC.; Amkreutz, L.; Navruzbekov, M.; Rosenstock, E.; Alonso-Fernandez, C.; Slavchev, V.; Kalmykov, AA.; Atabiev, BC.; Batieva, E; Calmet, MA.; Llamas, B.; Schultz, M.; Krauss, R.; Jimenez-Echevarria, J.; Francken, M.; Shnaider, S.; de Knijff, P.; Altena, E.; Van de Vijver, K.; Fehren-Schmitz, L.; Tung, TA.; Losch, S.; Dobrovolskaya, M.; Makarov, N.; Read, C.; Van Twest, M.; Sagona, C.; Ramsl, PC.; Akar, M.; Yener, KA.; Ballestero, EC.; Cucca, F.; Mazzarello, V.; Utrilla, P.; Rademaker, K.; Fernandez-Dominguez, E.; Baird, D.; Semal, P.; Marquez-Morfin, L; Roksandic, M.; Steiner, H.; Salazar-Garcia, DC.; Shishlina, N. Erdal, YS.; Hallgren, F.; Boyadzhiev, Y.; Boyadzhiev, K.; Kussner, M.; Sayer, D.; Onka, and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)

Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., European Union (EU); Horizon 2020; European Research Council (ERC); Research and Innovation Program; PALEoRIDER; CoDisEASe; ARCHCAUCASUS; Seventh Framework Programme; Marie Curie Actions; Programme SASPRO; ERA.NET RUS Plus-S&T Programme; Institute of Archaeology of the Czech Academy of Sciences; Russian Foundation for Basic Research; German Research Foundation; French National Research Agency; Wenner-Gren Dissertation Fieldwork Grant; Ministry of Education and Science of the Republic of Kazakhstan; Max Planck Society; Slovak Academy of Sciences; Werner Siemens Stiftung; Paleobiochemistry; Award Praemium Academiae of the Czech Academy of Sciences

Published
2021

6. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Author

Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B.; Papac, L.; Childebayeva, A.; Rivollat, M.; Villalba Mouco, V.; Neumann, G.U.; Penske, S.; Skourtanioti, E.; van de Loosdrecht, M.; Akar, M.; Boyadzhiev, K.; Boyadzhiev, Y.; Deguilloux, M.F.; Dobes, M.; Erdal, Y.S.; Ernée, M.; Frangipane, M.; Furmanek, M.; Friederich, S.; Ghesquière, E.; Ha?uszko, A.; Hansen, S.; Küßner, M.; Mannino, M.; Reinhold, S.; Rottier, S.; Salazar García, D.C.; Diaz, J.S.; Stockhammer, P.W.; de Togores Muñoz, C.R.; Yener, K.A.; Posth, C.; Krause, J.; Herbig, A.; Haak, W., College of Social Sciences and Humanities, Department of Archeology and History of Art, Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B.; Papac, L.; Childebayeva, A.; Rivollat, M.; Villalba Mouco, V.; Neumann, G.U.; Penske, S.; Skourtanioti, E.; van de Loosdrecht, M.; Akar, M.; Boyadzhiev, K.; Boyadzhiev, Y.; Deguilloux, M.F.; Dobes, M.; Erdal, Y.S.; Ernée, M.; Frangipane, M.; Furmanek, M.; Friederich, S.; Ghesquière, E.; Ha?uszko, A.; Hansen, S.; Küßner, M.; Mannino, M.; Reinhold, S.; Rottier, S.; Salazar García, D.C.; Diaz, J.S.; Stockhammer, P.W.; de Togores Muñoz, C.R.; Yener, K.A.; Posth, C.; Krause, J.; Herbig, A.; Haak, W., College of Social Sciences and Humanities, and Department of Archeology and History of Art

Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the ""mappable"" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe., INTERACT Project; French (ANR) Research Foundation; German (DFG) Research Foundation; European Union (EU); Horizon 2020; European Research Council (ERC); Research and Innovation Program; Institute of Archaeology of the Czech Academy of Sciences; Projekt DEAL; Max Planck Society; Praemium Academiae of the Czech Academy of Sciences

Published
2021

7. Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily

Author

He Yu, Marieke S. van de Loosdrecht, Marcello A. Mannino, Sahra Talamo, Adam B. Rohrlach, Ainash Childebayeva, Vanessa Villalba-Mouco, Franziska Aron, Guido Brandt, Marta Burri, Cäcilia Freund, Rita Radzeviciute, Raphaela Stahl, Antje Wissgott, Helen Fewlass, Antonio Tagliacozzo, Marcello Piperno, Sebastiano Tusa, Carmine Collina, Vittoria Schimmenti, Rosaria Di Salvo, Kay Prüfer, Cosimo Posth, Jean-Jacques Hublin, Detlef Gronenborn, Didier Binder, Choongwon Jeong, Wolfgang Haak, Johannes Krause, Max Planck Society, European Research Council, Yu H., van de Loosdrecht M.S., Mannino M.A., Talamo S., Rohrlach A.B., Childebayeva A., Villalba-Mouco V., Aron F., Brandt G., Burri M., Freund C., Radzeviciute R., Stahl R., Wissgott A., Fewlass H., Tagliacozzo A., Piperno M., Tusa S., Collina C., Schimmenti V., Di Salvo R., Prufer K., Posth C., Hublin J.-J., Gronenborn D., Binder D., Jeong C., Haak W., and Krause J.

Subjects
Biological science, Biological sciences, Multidisciplinary, Evolutionary biology, Paleobiology, Paleogenetics
Abstract

Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell'Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition., Funding. The Max Planck Society financed the genetic, isotopic, and radiocarbon analyses. S. Talamo has received funding from the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program (grant agreement No. 803147 RESOLUTION, https://site.unibo.it/resolution-erc/en).

Published
2022

8. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Author

Marie-France Deguilloux, Agata Hałuszko, Maïté Rivollat, Sandra Penske, J. S. Díaz, Michal Ernée, Eirini Skourtanioti, Miroslav Dobeš, Cosimo Posth, Mario Küßner, Stéphane Rottier, Gunnar U. Neumann, Emmanuel Ghesquière, Susanne Friederich, Yılmaz Selim Erdal, Adam Ben Rohrlach, Rana Özbal, Svend Hansen, Marcella Frangipane, Marcello A. Mannino, Ainash Childebayeva, Consuelo Roca de Togores Muñoz, Sabine Reinhold, Murat Akar, Wolfgang Haak, Alexander Herbig, Luka Papac, Yavor Boyadzhiev, Domingo C. Salazar-García, Vanessa Villalba-Mouco, Kamen Boyadzhiev, Johannes Krause, K. Aslıhan Yener, Mirosław Furmanek, Marieke Sophia van de Loosdrecht, Philipp W. Stockhammer, European Commission, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, University of Adelaide, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Spanish National Research Council (CSIC), Mustafa Kemal University, Bulgarian Academy of Sciences (BAS), Czech Academy of Sciences [Prague] (CAS), Hacettepe University = Hacettepe Üniversitesi, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], University of Wrocław [Poland] (UWr), State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Institut national de recherches archéologiques préventives (Inrap), Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)-Nantes Université (NU), German Archaeological Institute (DAI), Aarhus University [Aarhus], Koç University, Basque Foundation for Science (Ikerbasque), University of Cape Town, Departamento de Inteligencia Artificial [UPM, Spain] (DIA), Universidad Politécnica de Madrid (UPM), Universitat de València (UV), Medizinische Klinik und Poliklinik III [Bonn, Germany], Universitätsklinikum Bonn (UKB), MARQ - Museo Arqueológico Provincial de Alicante (MARQ), Ludwig Maximilian University [Munich] (LMU), New York University [New York] (NYU), NYU System (NYU), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, University of South Australia [Adelaide], Max Planck Society Foundation CELLEX, French (ANR) French National Research Agency (ANR), German (DFG) Research Foundations under the INTERACT project German Research Foundation (DFG) [ANR17-FRAL-0010, DFG-HA-5407/4-1], European Research Council (ERC) under the European Union European Research Council (ERC) [771234-PALEoRIDER], Czech Academy of Sciences Czech Academy of Sciences, Institute of Archaeology of the Czech Academy of Sciences, Prague Czech Academy of Sciences [RVO 67985912], Projekt DEAL, ANR-17-FRAL-0010,INTERACT,Interactions entre groupes humains en Europe de l'Ouest durant la transition Mésolithique-Néolithique: la double perspective des échanges biologiques et culturels(2017), Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B., Papac, L., Childebayeva, A., Rivollat, M., Villalba Mouco, V., Neumann, G.U., Penske, S., Skourtanioti, E., van de Loosdrecht, M., Akar, M., Boyadzhiev, K., Boyadzhiev, Y., Deguilloux, M.F., Dobes, M., Erdal, Y.S., Ernée, M., Frangipane, M., Furmanek, M., Friederich, S., Ghesquière, E., Ha?uszko, A., Hansen, S., Küßner, M., Mannino, M., Reinhold, S., Rottier, S., Salazar García, D.C., Diaz, J.S., Stockhammer, P.W., de Togores Muñoz, C.R., Yener, K.A., Posth, C., Krause, J., Herbig, A., Haak, W., College of Social Sciences and Humanities, Department of Archeology and History of Art, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Université de Nantes (UN)-Le Mans Université (UM)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Nantes (UN)-Université de Nantes (UN)-Ministère de la Culture (MC), Max Planck Society, Agence Nationale de la Recherche (France), German Research Foundation, European Research Council, Academy of Sciences of the Czech Republic, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), and Ikerbasque - Basque Foundation for Science

Subjects
Czech, SELECTION, Population genetics, MITOCHONDRIAL-DNA, early farmers, DIVERSITY, mitochondrial DNA, shotgun sequencing, Prehistòria, Haplogroup, German, 0302 clinical medicine, Medicine and Health Sciences, DNA sequencing, Science and technology, media_common, 0303 health sciences, Multidisciplinary, Horizon (archaeology), Critical event, Shotgun sequencing, chromosomal haplogroups, European research, STEPPE, Western europe, language, Medicine, Genetic Markers, Mitochondrial DNA, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, uniparentally-inherited markers, Science, Library science, Biology, Y chromosome, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Target enrichment, Article, 03 medical and health sciences, Political science, Humans, media_common.cataloged_instance, ANCIENT DNA, Genetic Testing, European union, Alleles, 030304 developmental biology, MUTATION-RATE, Chromosomes, Human, Y, Saturation (genetic), History and Archaeology, Y-mappable capture assay, Ancient DNA, Neanderthals, Anatomically modern humans, language.human_language, Neolithic transition, Genetics, Population, Haplotypes, Evolutionary biology, GENOMIC HISTORY, 030217 neurology & neurosurgery
Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe., Open Access funding enabled and organized by Projekt DEAL. This study was funded by the Max Planck Society, the French (ANR) and German (DFG) Research Foundations under the INTERACT project (ANR-17-FRAL-0010, DFG-HA-5407/4-1, 2018-2021) to M.R. and W.H., the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 771234-PALEoRIDER to W.H., the award Praemium Academiae of the Czech Academy of Sciences to M.E. and the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague to M.S.

Published
2021

9. Ten millennia of hepatitis B virus evolution

Author

Oleg Balanovsky, Lourdes Marquez-Morfin, Magdalena Zoledziewska, Susannah J. Salter, Cody E. Parker, Kirsten I. Bos, Kathrin Nägele, Domingo C. Salazar-García, Kerttu Majander, Vittorio Mazzarello, Cosimo Posth, Kurt W. Alt, Elmira Khussainova, Silvia Teresita Hernández Godoy, Richard Mortimer, Ayshin Ghalichi, Alexander Herbig, Lars Fehren-Schmitz, Leyla B. Djansugurova, Dmitry A. Stashenkov, Raiko Krauß, Mikhail S. Chaplygin, Tiago Ferraz, Patrick Semal, Eva Rosenstock, Michal Kostka, Yavor Boyadzhiev, Harald Meller, Petr Limburský, Mario Küßner, Tara Ingman, Maïté Rivollat, Eva Fernández-Domínguez, Rodrigo Barquera, Robin Skeates, Kamen Boyadzhiev, Denise Kühnert, Mirjana Roksandic, Adam Ben Rohrlach, Alexandra P. Buzhilova, Alissa Mittnik, Yadira Chinique de Armas, Johannes Krause, Marie-France Deguilloux, Aleksandr Khokhlov, Rezeda I. Tukhbatova, Elizabeth Popescu, Lucy C. Salazar, Andrey A. Chizhevsky, Christopher Read, Hubert Steiner, Melanie Van Twest, Eveline Altena, Diana Iraíz Hernández-Zaragoza, Lyazzat Musralina, Megan Michel, Íñigo García-Martínez de Lagrán, Anatoly R. Kantorovich, Katrien Van de Vijver, Alžbeta Danielisová, Rachel Clarke, Duncan Sayer, Bastien Llamas, Nikolaj Makarov, Alejandro Romero, Luka Papac, Alessandra Sperduti, Vladimir E. Maslov, Rafael Garrido-Pena, Gunnar U. Neumann, Arman Z. Beisenov, Zainolla Samashev, Guido Alberto Gnecchi-Ruscone, Päivi Onkamo, Eduardo Carmona Ballestero, Javier Jimenez-Echevarria, Valery Khartanovich, Manuel Rojo-Guerra, Fredrik Hallgren, Eirini Skourtanioti, Natalia Shishlina, Luca Lai, Petr Velemínský, Antti Sajantila, Peter C. Ramsl, Claudia Sagona, Susanne Friederich, Miroslav Dobeš, Marcel Keller, Francesco Cucca, Sabine Reinhold, Florian van Bömmel, Luc Amkreutz, Vittoria Schimmenti, Raphaela Stahl, Douglas Baird, Marina K. Karapetian, Kurt Rademaker, Stephan Schiffels, Sacha Kacki, Evelyn K. Guevara, Michael Francken, Christina Warinner, Kay Prüfer, Karen Giffin, Felix M. Key, Joscha Gretzinger, Alexey Kalmykov, Svetlana Shnaider, Sandra Penske, Antje Wissgott, Tiffiny A. Tung, Biaslan Ch. Atabiev, Philippe Lefranc, Elizabeth A. Nelson, Peter de Knijff, Vladimir Slavchev, Jessica Pearson, Yılmaz Selim Erdal, Louise Loe, Jan Nováček, Micaela Alvarez Calmet, José I. Royo-Guillén, Richard L. Burger, Kristiina Mannermaa, K. Aslıhan Yener, Maria Pfefferkorn, Vyacheslav Moiseyev, Svend Hansen, Didier Binder, Michal Ernée, Maria A. Spyrou, Michal Feldman, Vladimir V. Kufterin, Murat Akar, Héctor Arcusa-Magallón, Andrej B. Belinskiy, Egor Kitov, Franziska Aron, Ron Hübler, Vanessa Villalba-Mouco, Sophie Beckett, Jessica Beckett, Arthur Kocher, Michael Schultz, Elena Batieva, Pilar Utrilla, Cristina Tejedor-Rodríguez, Kristin von Heyking, Masnav Navruzbekov, Michaela Langová, Maria Paz Miguel de Ibáñez, Stéphane Rottier, Maria V. Dobrovolskaya, Sandra Lösch, Emma D. Zilivinskaya, Dmitry V. Vasilev, Gabriel García Atiénzar, Marcello A. Mannino, Wolfgang Haak, Philipp W. Stockhammer, Sylvie Saintot, Alice Lyons, Ken Massy, Elena Kaverzneva, Susanna Sabin, Carmen Alonso-Fernández, Anna F. Kochkina, Marieke Sophia van de Loosdrecht, Stefanie Eisenmann, Max Planck Society, European Commission, Slovak Academy of Sciences, Academy of Sciences of the Czech Republic, Russian Foundation for Basic Research, German Research Foundation, Agence Nationale de la Recherche (France), Wenner-Gren Foundation, Ministry of Education and Science (Kazakhstan), Universidad de Alicante. Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante. Departamento de Biotecnología, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Prehistoria y Protohistoria, Grupo de Inmunología, Biología Celular y del Desarrollo, Ingman, Tara, Kocher, A., Papac, L., Barquera, R., Key, FM., Spyrou, MA., Hubler, R., Rohrlach, AB., Aron, F., Stahl, R., Wissgott, A., van Bommel, F., Pfefferkorn, M., Mittnik, A., Villalba-Mouco, V., Neumann, GU., Rivollat, M., van de Loosdrecht, MS., Majander, K., Tukhbatova, RI., Musralina, L., Ghalichi, A., Penske, S., Sabin, S., Michel, M., Gretzinger, J., Nelson, EA., Ferraz, T., Nagele, K., Parker, C., Keller, M., Guevara, EK., Feldman, M., Eisenmann, S., Skourtanioti, E., Giffin, K., Gnecchi-Ruscone, GA., Friederich, S., Schimmenti, V., Khartanovich, V., Karapetian, MK., Chaplygin, MS., Kufterin, VV., Khokhlov, AA., Chizhevsky, AA., Stashenkov, DA., Kochkina, AF., Tejedor-Rodriguez, C., de Lagran, IGM., Arcusa-Magallon, H., Garrido-Pena, R., Royo-Guillen, JI., Novacek, J., Rottier, S., Kacki, S., Saintot, S., Kaverzneva, E., Belinskiy, AB., Veleminsky, P., Limbursky, P., Kostka, M., Loe, L., Popescu, E., Clarke, R., Lyons, A., Mortimer, R., Sajantila, A., de Armas, YC., Godoy, STH., Hernandez-Zaragoza, DI., Pearson, J., Binder, D., Lefranc, P., Kantorovich, AR., Maslov, VE., Lai, L., Zoledziewska, M., Beckett, JF., Langova, M., Atienzar, GG., Ibanez, MPD, Romero, A., Sperduti, A., Beckett, S., Salter, SJ., Zilivinskaya, ED., Vasil, DV., von Heyking, K., Burger, RL., Salazar, LC., Amkreutz, L., Navruzbekov, M., Rosenstock, E., Alonso-Fernandez, C., Slavchev, V., Kalmykov, AA., Atabiev, BC., Batieva, E, Calmet, MA., Llamas, B., Schultz, M., Krauss, R., Jimenez-Echevarria, J., Francken, M., Shnaider, S., de Knijff, P., Altena, E., Van de Vijver, K., Fehren-Schmitz, L., Tung, TA., Losch, S., Dobrovolskaya, M., Makarov, N., Read, C., Van Twest, M., Sagona, C., Ramsl, PC., Akar, M., Yener, KA., Ballestero, EC., Cucca, F., Mazzarello, V., Utrilla, P., Rademaker, K., Fernandez-Dominguez, E., Baird, D., Semal, P., Marquez-Morfin, L, Roksandic, M., Steiner, H., Salazar-Garcia, DC., Shishlina, N. Erdal, YS., Hallgren, F., Boyadzhiev, Y., Boyadzhiev, K., Kussner, M., Sayer, D., Onkamo, P., Skeates, R., Rojo-Guerra, M., Buzhilova, A., Khussainova, E., Djansugurova, LB., Beisenov, AZ., Samashev, Z., Massy, K., Mannino, M., Moiseyev, V., Mannermaa, K., Balanovsky, O., Deguilloux, MF., Reinhold, S., Hansen, S., Kitov, EP., Dobes, M., Ernee, M., Meller, H., Prufer, Kay., Warinner, C., Schiffels, S., Stockhammer, PW., Bos, K., Posth, C., Herbig, A., Haak, W., Krause, J., Kuhnert, D., and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)

Subjects
Phylogeographic history, Hepatitis B/history, 01 natural sciences, The Republic, Communicable Diseases, Emerging, German, Communicable Diseases, Emerging/history, Agency (sociology), Science and technology, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, media_common, 0303 health sciences, Multidisciplinary, Ancient DNA, European research, virus diseases, Genomics, Hepatitis B, 3. Good health, Europe, language, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Christian ministry, Paleogenomic analyses, Asian Continental Ancestry Group, 010506 paleontology, Hepatitis B virus, Asia, Hepatitis B virus/classification, European Continental Ancestry Group, Library science, Biología Celular, White People, Marie curie, Evolution, Molecular, 03 medical and health sciences, American Natives, Asian People, Political science, Genomic data, media_common.cataloged_instance, Humans, Slovak, European union, American Indian or Alaska Native, 030304 developmental biology, 0105 earth and related environmental sciences, Genetic Variation, Paleontology, Prehistoria, A300, language.human_language, digestive system diseases, American natives, Americas, Asian continental ancestry group, Communicable diseases, Emerging, European continental ancestry group, Evolution, molecular, Genetic variation
Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., The research was funded by the Max Planck Society, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (771234–PALEoRIDER, to W.H.; 805268–CoDisEASe to K. Bos; 834616–ARCHCAUCASUS to S.H.), the Slovak Academy of Sciences and the European Union’s Seventh Framework Programme and Marie Curie Actions under the Programme SASPRO (1340/03/03 to P.C.R.), the ERA.NET RUS Plus–S&T programm of the European Union’s Seventh Framework Programme (277–BIOARCCAUCASUS to S.Re. and S.H.), the Werner Siemens Stiftung (“Paleobiochemistry”, to CW), the Award Praemium Academiae of the Czech Academy of Sciences (to M.E.), the Institute of Archaeology of the Czech Academy of Sciences (RVO 67985912, to M.Dobe.), the Russian Foundation for Basic Research (19-09-00354a, to M.K.K. and V.V.K.; 19-78-10053 to SSh), the German Research Foundation (DFG-HA-5407/4-1–INTERACT to W.H. and RE2688/2 to S.Re.), the French National Research Agency (ANR-17-FRAL-0010–INTERACT, to M.F.D., M.Ri., S.Ro., S.Sai., D.Bi., and P.Le.), the Wenner-Gren Dissertation Fieldwork Grant (9558 to S.Sab.), and the Ministry of Education and Science of the Republic of Kazakhstan (AP08856654 to L.B.D., L.M., and E.Kh. and AP08857177 to A.Z.B.).

Published
2021

10. Ancient Plasmodium genomes shed light on the history of human malaria.

Author

Michel M, Skourtanioti E, Pierini F, Guevara EK, Mötsch A, Kocher A, Barquera R, Bianco RA, Carlhoff S, Coppola Bove L, Freilich S, Giffin K, Hermes T, Hiß A, Knolle F, Nelson EA, Neumann GU, Papac L, Penske S, Rohrlach AB, Salem N, Semerau L, Villalba-Mouco V, Abadie I, Aldenderfer M, Beckett JF, Brown M, Campus FGR, Chenghwa T, Cruz Berrocal M, Damašek L, Duffett Carlson KS, Durand R, Ernée M, Fântăneanu C, Frenzel H, García Atiénzar G, Guillén S, Hsieh E, Karwowski M, Kelvin D, Kelvin N, Khokhlov A, Kinaston RL, Korolev A, Krettek KL, Küßner M, Lai L, Look C, Majander K, Mandl K, Mazzarello V, McCormick M, de Miguel Ibáñez P, Murphy R, Németh RE, Nordqvist K, Novotny F, Obenaus M, Olmo-Enciso L, Onkamo P, Orschiedt J, Patrushev V, Peltola S, Romero A, Rubino S, Sajantila A, Salazar-García DC, Serrano E, Shaydullaev S, Sias E, Šlaus M, Stančo L, Swanston T, Teschler-Nicola M, Valentin F, Van de Vijver K, Varney TL, Vigil-Escalera Guirado A, Waters CK, Weiss-Krejci E, Winter E, Lamnidis TC, Prüfer K, Nägele K, Spyrou M, Schiffels S, Stockhammer PW, Haak W, Posth C, Warinner C, Bos KI, Herbig A, and Krause J

Subjects
Female, Humans, Male, Altitude, Americas epidemiology, Asia epidemiology, Biological Evolution, Disease Resistance genetics, Europe epidemiology, History, Ancient, Malaria, Falciparum epidemiology, Malaria, Falciparum history, Malaria, Falciparum parasitology, Malaria, Falciparum transmission, Malaria, Vivax epidemiology, Malaria, Vivax history, Malaria, Vivax parasitology, Malaria, Vivax transmission, Plasmodium falciparum genetics, Plasmodium falciparum isolation & purification, Plasmodium malariae genetics, Plasmodium malariae isolation & purification, Plasmodium vivax genetics, Plasmodium vivax isolation & purification, DNA, Ancient analysis, Genome, Mitochondrial genetics, Genome, Protozoan genetics, Malaria parasitology, Malaria history, Malaria transmission, Malaria epidemiology, Plasmodium genetics, Plasmodium classification
Abstract

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species 1 . Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe 1,2 . To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia 3 . Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago., (© 2024. The Author(s).)

Published
2024
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11. Author Correction: Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers.

Author

Posth C, Yu H, Ghalichi A, Rougier H, Crevecoeur I, Huang Y, Ringbauer H, Rohrlach AB, Nägele K, Villalba-Mouco V, Radzeviciute R, Ferraz T, Stoessel A, Tukhbatova R, Drucker DG, Lari M, Modi A, Vai S, Saupe T, Scheib CL, Catalano G, Pagani L, Talamo S, Fewlass H, Klaric L, Morala A, Rué M, Madelaine S, Crépin L, Caverne JB, Bocaege E, Ricci S, Boschin F, Bayle P, Maureille B, Le Brun-Ricalens F, Bordes JG, Oxilia G, Bortolini E, Bignon-Lau O, Debout G, Orliac M, Zazzo A, Sparacello V, Starnini E, Sineo L, van der Plicht J, Pecqueur L, Merceron G, Garcia G, Leuvrey JM, Garcia CB, Gómez-Olivencia A, Połtowicz-Bobak M, Bobak D, Le Luyer M, Storm P, Hoffmann C, Kabaciński J, Filimonova T, Shnaider S, Berezina N, González-Rabanal B, González Morales MR, Marín-Arroyo AB, López B, Alonso-Llamazares C, Ronchitelli A, Polet C, Jadin I, Cauwe N, Soler J, Coromina N, Rufí I, Cottiaux R, Clark G, Straus LG, Julien MA, Renhart S, Talaa D, Benazzi S, Romandini M, Amkreutz L, Bocherens H, Wißing C, Villotte S, de Pablo JF, Gómez-Puche M, Esquembre-Bebia MA, Bodu P, Smits L, Souffi B, Jankauskas R, Kozakaitė J, Cupillard C, Benthien H, Wehrberger K, Schmitz RW, Feine SC, Schüler T, Thevenet C, Grigorescu D, Lüth F, Kotula A, Piezonka H, Schopper F, Svoboda J, Sázelová S, Chizhevsky A, Khokhlov A, Conard NJ, Valentin F, Harvati K, Semal P, Jungklaus B, Suvorov A, Schulting R, Moiseyev V, Mannermaa K, Buzhilova A, Terberger T, Caramelli D, Altena E, Haak W, and Krause J

Published
2023
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12. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers.

Author

Posth C, Yu H, Ghalichi A, Rougier H, Crevecoeur I, Huang Y, Ringbauer H, Rohrlach AB, Nägele K, Villalba-Mouco V, Radzeviciute R, Ferraz T, Stoessel A, Tukhbatova R, Drucker DG, Lari M, Modi A, Vai S, Saupe T, Scheib CL, Catalano G, Pagani L, Talamo S, Fewlass H, Klaric L, Morala A, Rué M, Madelaine S, Crépin L, Caverne JB, Bocaege E, Ricci S, Boschin F, Bayle P, Maureille B, Le Brun-Ricalens F, Bordes JG, Oxilia G, Bortolini E, Bignon-Lau O, Debout G, Orliac M, Zazzo A, Sparacello V, Starnini E, Sineo L, van der Plicht J, Pecqueur L, Merceron G, Garcia G, Leuvrey JM, Garcia CB, Gómez-Olivencia A, Połtowicz-Bobak M, Bobak D, Le Luyer M, Storm P, Hoffmann C, Kabaciński J, Filimonova T, Shnaider S, Berezina N, González-Rabanal B, González Morales MR, Marín-Arroyo AB, López B, Alonso-Llamazares C, Ronchitelli A, Polet C, Jadin I, Cauwe N, Soler J, Coromina N, Rufí I, Cottiaux R, Clark G, Straus LG, Julien MA, Renhart S, Talaa D, Benazzi S, Romandini M, Amkreutz L, Bocherens H, Wißing C, Villotte S, de Pablo JF, Gómez-Puche M, Esquembre-Bebia MA, Bodu P, Smits L, Souffi B, Jankauskas R, Kozakaitė J, Cupillard C, Benthien H, Wehrberger K, Schmitz RW, Feine SC, Schüler T, Thevenet C, Grigorescu D, Lüth F, Kotula A, Piezonka H, Schopper F, Svoboda J, Sázelová S, Chizhevsky A, Khokhlov A, Conard NJ, Valentin F, Harvati K, Semal P, Jungklaus B, Suvorov A, Schulting R, Moiseyev V, Mannermaa K, Buzhilova A, Terberger T, Caramelli D, Altena E, Haak W, and Krause J

Subjects
Humans, Europe ethnology, Gene Pool, History, Ancient, Archaeology, Genomics, Hunting, Paleontology, Human Genetics, Genome, Human genetics
Abstract

Modern humans have populated Europe for more than 45,000 years 1,2 . Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period 3 . Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe 4 , but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants., (© 2023. The Author(s).)

Published
2023
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14. Kinship practices in the early state El Argar society from Bronze Age Iberia.

Author

Villalba-Mouco V, Oliart C, Rihuete-Herrada C, Rohrlach AB, Fregeiro MI, Childebayeva A, Ringbauer H, Olalde I, Celdrán Beltrán E, Puello-Mora C, Valério M, Krause J, Lull V, Micó R, Risch R, and Haak W

Subjects
Humans, Adult, Male, Female, History, Ancient, Europe, Europe, Eastern, Family, Archaeology, Burial
Abstract

The Early Bronze Age in Europe is characterized by social and genetic transformations, starting in the early 3rd millennium BCE. New settlement and funerary structures, artifacts and techniques indicate times of change with increasing economic asymmetries and political hierarchization. Technological advances in metallurgy also played an important role, facilitating trade and exchange networks, which became tangible in higher levels of mobility and connectedness. Archeogenetic studies have revealed a substantial transformation of the genetic ancestry around this time, ultimately linked to the expansion of steppe- and forest steppe pastoralists from Eastern Europe. Evidence for emerging infectious diseases such as Yersinia pestis adds further complexity to these tumultuous and transformative times. The El Argar complex in southern Iberia marks the genetic turnover in southwestern Europe ~ 2200 BCE that accompanies profound changes in the socio-economic structure of the region. To answer the question of who was buried in the emblematic double burials of the El Argar site La Almoloya, we integrated results from biological relatedness analyses and archaeological funerary contexts and refined radiocarbon-based chronologies from 68 individuals. We find that the El Argar society was virilocally and patrilineally organized and practiced reciprocal female exogamy, supported by pedigrees that extend up to five generations along the paternal line. Synchronously dated adult males and females from double tombs were found to be unrelated mating partners, whereby the incoming females reflect socio-political alliances among El Argar groups. In three cases these unions had common offspring, while paternal half-siblings also indicate serial monogamy or polygyny., (© 2022. The Author(s).)

Published
2022
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15. A Neandertal dietary conundrum: Insights provided by tooth enamel Zn isotopes from Gabasa, Spain.

Author

Jaouen K, Villalba-Mouco V, Smith GM, Trost M, Leichliter J, Lüdecke T, Méjean P, Mandrou S, Chmeleff J, Guiserix D, Bourgon N, Blasco F, Mendes Cardoso J, Duquenoy C, Moubtahij Z, Salazar Garcia DC, Richards M, Tütken T, Hublin JJ, Utrilla P, and Montes L

Subjects
Animals, Carbon analysis, Carbon Isotopes analysis, Collagen, Dental Enamel chemistry, Diet, Nitrogen Isotopes analysis, Oxygen analysis, Spain, Strontium analysis, Zinc analysis, Zinc Isotopes analysis, Carnivora, Neanderthals, Tooth chemistry, Trace Elements analysis
Abstract

The characterization of Neandertals' diets has mostly relied on nitrogen isotope analyses of bone and tooth collagen. However, few nitrogen isotope data have been recovered from bones or teeth from Iberia due to poor collagen preservation at Paleolithic sites in the region. Zinc isotopes have been shown to be a reliable method for reconstructing trophic levels in the absence of organic matter preservation. Here, we present the results of zinc (Zn), strontium (Sr), carbon (C), and oxygen (O) isotope and trace element ratio analysis measured in dental enamel on a Pleistocene food web in Gabasa, Spain, to characterize the diet and ecology of a Middle Paleolithic Neandertal individual. Based on the extremely low δ 66 Zn value observed in the Neandertal's tooth enamel, our results support the interpretation of Neandertals as carnivores as already suggested by δ 15 N isotope values of specimens from other regions. Further work could help identify if such isotopic peculiarities (lowest δ 66 Zn and highest δ 15 N of the food web) are due to a metabolic and/or dietary specificity of the Neandertals.

Published
2022
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16. Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily.

Author

Yu H, van de Loosdrecht MS, Mannino MA, Talamo S, Rohrlach AB, Childebayeva A, Villalba-Mouco V, Aron F, Brandt G, Burri M, Freund C, Radzeviciute R, Stahl R, Wissgott A, Fewlass H, Tagliacozzo A, Piperno M, Tusa S, Collina C, Schimmenti V, Di Salvo R, Prüfer K, Posth C, Hublin JJ, Gronenborn D, Binder D, Jeong C, Haak W, and Krause J

Abstract

Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell'Uzzo , resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

Published
2022
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17. Genomic transformation and social organization during the Copper Age-Bronze Age transition in southern Iberia.

Author

Villalba-Mouco V, Oliart C, Rihuete-Herrada C, Childebayeva A, Rohrlach AB, Fregeiro MI, Celdrán Beltrán E, Velasco-Felipe C, Aron F, Himmel M, Freund C, Alt KW, Salazar-García DC, García Atiénzar G, de Miguel Ibáñez MP, Hernández Pérez MS, Barciela V, Romero A, Ponce J, Martínez A, Lomba J, Soler J, Martínez AP, Avilés Fernández A, Haber-Uriarte M, Roca de Togores Muñoz C, Olalde I, Lalueza-Fox C, Reich D, Krause J, García Sanjuán L, Lull V, Micó R, Risch R, and Haak W

Abstract

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.

Published
2021
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18. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe.

Author

Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, and Haak W

Subjects
DNA, Mitochondrial, Genetic Markers, Genetic Testing, Humans, Polymorphism, Single Nucleotide, Alleles, Chromosomes, Human, Y, Genetics, Population methods, Haplotypes
Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe., (© 2021. The Author(s).)

Published
2021
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19. Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.

Author

Villalba-Mouco V, van de Loosdrecht MS, Posth C, Mora R, Martínez-Moreno J, Rojo-Guerra M, Salazar-García DC, Royo-Guillén JI, Kunst M, Rougier H, Crevecoeur I, Arcusa-Magallón H, Tejedor-Rodríguez C, García-Martínez de Lagrán I, Garrido-Pena R, Alt KW, Jeong C, Schiffels S, Utrilla P, Krause J, and Haak W

Subjects
Humans, Spain, DNA, Ancient analysis, Genome, Human, Human Migration
Abstract

The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3-9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000-15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. VIDEO ABSTRACT., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Published
2019
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