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2. Fallen and Lost into the Abyss? A Mesolithic Human Skull from Sima Hedionda IV (Casares, Málaga, Iberian Peninsula)

Author

Martinez-Sanchez Rafael M., Bretones-García María Dolores, Valdiosera Cristina, Vera-Rodríguez Juan Carlos, López Flores Inmaculada, Simón-Vallejo María D., Ruiz Borrega Pilar, Martínez Fernández María J., Romo Villalba Jorge L., Bermúdez Jiménez Francisco, Martín de los Santos Rafael, Pardo-Gordó Salvador, and Cortés Sánchez Miguel

Subjects
human remains, mesolithic, southern iberia, sinkholes, radiocarbon, Archaeology, CC1-960
Abstract

The presence of scattered prehistoric human bones in caves and sinkholes is common in many regions of Iberia. These are usually interpreted as erratic elements coming from burial contexts, usually collective associations. These burial contexts are very frequent in karst areas of the Iberian Peninsula since the Early Neolithic, mostly in the Late Neolithic, and Copper Age, while findings from earlier chronologies are much more unusual. In this work, we present partial remains of a human skull from the Mesolithic period, recovered from a cave in the Strait of Gibraltar area. Although there is no conclusive evidence pointing to a dismantled burial context, this constitutes an isolated find, where its final location appears to be consistent with gravitational fall followed by water transportation.

Published
2022
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3. Uncialamycin-based antibody–drug conjugates : Unique enediyne ADCs exhibiting bystander killing effect

Author

Nicolaou, K. C., Rigol, Stephan, Pitsinos, Emmanuel N., Das, Dipendu, Lu, Yong, Rout, Subhrajit, Schammel, Alexander W., Holte, Dane, Lin, Baiwei, Gu, Christine, Sarvaiya, Hetal, Trinidad, Jose, Barbour, Nicole, Valdiosera, Amanda M., Sandoval, Joseph, Lee, Christina, Aujay, Monette, Fernando, Hanan, Dhar, Anukriti, Karsunky, Holger, Taylor, Nicole, Pysz, Marybeth, and Gavrilyuk, Julia

Published
2021

4. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant

Author

Megha Srigyan, Héctor Bolívar, Irene Ureña, Jonathan Santana, Andrew Petersen, Eneko Iriarte, Emrah Kırdök, Nora Bergfeldt, Alice Mora, Mattias Jakobsson, Khaled Abdo, Frank Braemer, Colin Smith, Juan José Ibañez, Anders Götherström, Torsten Günther, and Cristina Valdiosera

Subjects
Biology (General), QH301-705.5
Abstract

Ancient genomic and archaeological data combine to identify a surprisingly early Islamic burial in modern day Syria.

Published
2022
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6. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Bălăşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoğan, Aslı, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

7. Genetic turnovers and northern survival during the last glacial maximum in European brown bears

Author

Erik Ersmark, Gennady Baryshnikov, Thomas Higham, Alain Argant, Pedro Castaños, Doris Döppes, Mihaly Gasparik, Mietje Germonpré, Kerstin Lidén, Grzegorz Lipecki, Adrian Marciszak, Rebecca Miller, Marta Moreno‐García, Martina Pacher, Marius Robu, Ricardo Rodriguez‐Varela, Manuel Rojo Guerra, Martin Sabol, Nikolai Spassov, Jan Storå, Christina Valdiosera, Aritza Villaluenga, John R. Stewart, and Love Dalén

Subjects
LGM, mtDNA, phylogeography, refugia, Ursus arctos, Ecology, QH540-549.5
Abstract

Abstract The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid‐Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter‐specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

Published
2019
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8. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Author

Valdiosera, Cristina, Günther, Torsten, Vera-Rodríguez, Juan Carlos, Ureña, Irene, Iriarte, Eneko, Rodríguez-Varela, Ricardo, Simões, Luciana G., Martínez-Sánchez, Rafael M., Svensson, Emma M., Malmström, Helena, Rodríguez, Laura, de Castro, José-María Bermúdez, Carbonell, Eudald, Alday, Alfonso, Vera, José Antonio Hernández, Götherström, Anders, Carretero, José-Miguel, Arsuaga, Juan Luis, Smith, Colin I., and Jakobsson, Mattias

Published
2018

15. Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

Author

Günther, Torsten, Valdiosera, Cristina, Malmström, Helena, Ureña, Irene, Rodriguez-Varela, Ricardo, Sverrisdóttir, Óddny Osk, Daskalaki, Evangelia A., Skoglund, Pontus, Naidoo, Thijessen, Svensson, Emma M., de Castro, José María Bermúdez, Carbonell, Eudald, Dunn, Michael, Storå, Jan, Iriarte, Eneko, Arsuaga, Juan Luis, Carretero, José-Miguel, Götherström, Anders, and Jakobsson, Mattias

Published
2015

16. Northwest African Neolithic initiated by migrants from Iberia and Levant

Author

Simões, Luciana G., Günther, Torsten, Martinez-Sanchez, Rafael M., Vera-Rodriguez, Juan Carlos, Iriarte, Eneko, Rodriguez-Varela, Ricardo, Bokbot, Youssef, Valdiosera, Cristina, and Jakobsson, Mattias

Subjects
Archaeology, Arkeologi
Abstract

In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa(1-3) or (2) that local hunter-gatherers adopted technological innovations(4,5). The latter view is also supported by archaeogenetic data(6). Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

Published
2023

18. Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.

Author

Torsten Günther, Helena Malmström, Emma M Svensson, Ayça Omrak, Federico Sánchez-Quinto, Gülşah M Kılınç, Maja Krzewińska, Gunilla Eriksson, Magdalena Fraser, Hanna Edlund, Arielle R Munters, Alexandra Coutinho, Luciana G Simões, Mário Vicente, Anders Sjölander, Berit Jansen Sellevold, Roger Jørgensen, Peter Claes, Mark D Shriver, Cristina Valdiosera, Mihai G Netea, Jan Apel, Kerstin Lidén, Birgitte Skar, Jan Storå, Anders Götherström, and Mattias Jakobsson

Subjects
Biology (General), QH301-705.5
Abstract

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

Published
2018
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19. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Author

Carpenter, Meredith L., Buenrostro, Jason D., Valdiosera, Cristina, Schroeder, Hannes, Allentoft, Morten E., Sikora, Martin, Rasmussen, Morten, Gravel, Simon, Guillén, Sonia, Nekhrizov, Georgi, Leshtakov, Krasimir, Dimitrova, Diana, Theodossiev, Nikola, Pettener, Davide, Luiselli, Donata, Sandoval, Karla, Moreno-Estrada, Andrés, Li, Yingrui, Wang, Jun, Gilbert, M. Thomas P., Willerslev, Eske, Greenleaf, William J., and Bustamante, Carlos D.

Published
2013
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20. From Red to Mexican Pink

Author

De Orellana, Margarita, Smithies, Padraic, Vargas, Rafael, Suderman, Michelle, Olivier, Guilhem, Magaloni, Diana, Marín, Clara, Neurath, Johannes, Pope, Quentin, Barrientos, Leopoldo Trejo, Durango, Laura, Turok, Marta, Pereda, Juan Carlos, Valdiosera, Ramón, and Zurita, Ricardo Muñoz

Published
2013

23. The ancestry and affiliations of Kennewick Man

Author

Rasmussen, Morten, Sikora, Martin, Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moreno-Mayar, J. Victor, Poznik, G. David, Zollikofer, Christoph P.E., de Leon, Marcia S. Ponce, Allentoft, Morten E., Moltke, Ida, Jonsson, Hakon, Valdiosera, Cristina, Malhi, Ripan S., Orlando, Ludovic, Bustamante, Carlos D., Stafford, Jr., Thomas W., Meltzer, David J., Nielsen, Rasmus, and Willerslev, Eske

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP) (1). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted (2). Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans (2). In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ~1X coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia., The skeleton of Kennewick Man was inadvertently discovered in July of 1996 in shallow water along the Columbia River shoreline outside Kennewick, Washington state, USA. On several visits to the [...]

Published
2015
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24. Osteological identification criteria for Capra pyrenaica and Capra hircus validated with DNA

Author

Cristina Valdiosera, Juan Luis Arsuaga, Mª Ángeles Galindo-Pellicena, and Irene Ureña

Subjects
capra pyrenaica, capra hircus, dna, neolithic, palaeolithic, chaves site, Osteology, Evolutionary biology, Capra hircus, Paleontology, Identification (biology), Biology, Osteometry, biology.organism_classification, Capra pyrenaica, QE701-760, Identification criteria
Abstract

The taxonomic identification of Capra hircus and Capra pyrenaica from bone remains is essential in order to be able to infer a prehistoric society’s subsistence strategy. Although osteometry is the criterion that is typically used to distinguish both of these species, Sarrion (1988) also defined morphological characteristics for distinguishing them. The objective of this work is to validate these morphological criteria with the genetic identification of ovicaprine bone remains from Palaeolithic and Neolithic levels of the Chaves site (Sierra de Guara, Huesca). The preliminary results indicate that the astragalus and calcaneus are more adequate for identifying Capra pyrenaica and Capra hircus and the discrimination criteria of mandibles and metacarpals are called into question

Published
2020

25. El ADN antiguo aplicado a contextos arqueopaleontológicos: el caso de la cueva de Arlanpe (Lemoa, Bizkaia)

Author

Iriarte, E., Arsuaga, J.L., Rodríguez, R., Arceredillo, D., Ureña, I., Garate, D., Svensson, E.M., Ríos-Garaizar, J., Gómez-Olivencia, A., and Valdiosera, C.

Subjects
Determinación taxonómica, domesticación, ADN mitocondrial., Auxiliary sciences of history, Archaeology, CC1-960
Abstract

Los estudios de ADN antiguo están permitiendo conocer nuevos datos sobre la biología de especies actuales y extintas. Las técnicas de ADN antiguo pueden ser una herramienta adicional y complementaria dentro de los estudios multidisciplinares que son necesarios para abordar distintas problemáticas arqueopaleontológicas. En este artículo repasamos algunas de las aplicaciones en estos contextos: la determinación taxonómica y sexual, los estudios para conocer el proceso de domesticación, o la estructura filogeográfica durante ciclos glaciares subrayando la existencia o no de refugios glaciares. También proporcionamos información preliminar referente a la aplicación de estas técnicas en el yacimiento de Arlanpe (Lemoa, Bizkaia). En este yacimiento hemos obtenido ADN mitocondrial de muestras de oso pardo, gran bóvido y cabra montés. Una de las muestras de oso pardo de Arlanpe está dentro del clado 3c compuesto de osos pardos extintos de Alaska. Dos de las muestras de gran bóvido de Arlanpe han sido clasificadas como uro (Bos primigenius) mediante métodos genéticos.

Published
2011

30. Evaluation of PNU-159682 antibody drug conjugates (ADCs)

Author

Holte, Dane, Lyssikatos, Joseph P., Valdiosera, Amanda M., Swinney, Zachary, Sisodiya, Vikram, Sandoval, Joseph, Lee, Christina, Aujay, Monette A., Tchelepi, Robert B., Hamdy, Omar M., Gu, Christine, Lin, Baiwei, Sarvaiya, Hetal, Pysz, Marybeth A., Laysang, Amy, Williams, Samuel, Jun Lee, Dong, Holda, Magda K., Purcell, James W., and Gavrilyuk, Julia

Published
2020
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32. Correction for Frantz et al., Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Ceiridwen J. Edwards, Anders Götherström, Benjamin S. Arbuckle, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Michael J Richards, Katerina Trantalidou, Cristina Valdiosera, M. Thomas P. Gilbert, Joris Peters, Louis du Plessis, Jean-Denis Vigne, Joachim Burger, Dian Boric, Richard P. M. A. Crooijmans, Melinda A. Zeder, Erik Meijaard, Wolfram Schier, Panoraia Alexandri, Jörg Schibler, John Chapman, Adrian Balasescu, Greger Larson, Jörg Orschiedt, Anne Tresset, Simon Stoddart, Keith Dobney, Antonio Tagliacozzo, Thomas H. McGovern, Canan Çakirlar, Bea De Cupere, Caroline Malone, Laurent A. F. Frantz, Vesna Dimitrijević, Sepideh Maziar, Andrea Zeeb-Lanz, Cevdet Merih Erek, Adina Boroneant, Ash Erim-Ozdogan, Hendrik-Jan Megens, Azadeh Fatemeh Mohaseb, Hitomi Hongo, Marjan Mashkour, Amelie Scheu, Evan K. Irving-Pease, Michelle Alexander, David Orton, Richard Sabin, László Bartosiewicz, Nenad Tasić, François-Xavier Ricaut, Anastasia Papathanasiou, Darko Radmanovic, Liora Kolska Horwitz, Christina Geoerg, Clive Bonsall, Anna Linderholm, Peter Rowley-Conwy, Audrey T. Lin, Daniel Helmer, Daniel G. Bradley, Roger Matthews, Ron Pinhasi, Ninna Manaseryan, Shiva Sheikhi, Sophie Van Poucke, Lionel Gourichon, Mike J. Church, Kevin G. Daly, Valentin Dumitraşcu, Joséphine Lesur, Mihai Gligor, Martien A. M. Groenen, Alexander Yanevich, Vincent M. Battista, Cleia Detry, Max Price, Rose-Marie Arbogast, Holley Martlew, Allowen Evin, Elisabeth Stephan, Norbert Benecke, John R. Stewart, Ophélie Lebrasseur, Giedre Motuzaite Matuzeviciute, Gennady F. Baryshnikov, Lucia Sarti, Youri van den Hurk, James Haile, Mike Parker Pearson, Arkadiusz Marciniak, Victoria E. Mullin, Jose-Miguel Carreterow, Kurt J. Gron, Alexandros Triantafyllidis, Thomas Cucchi, Rebecca Miller, Jelena Bulatović, and Anton Ervynck

Subjects
Gene Flow, Multidisciplinary, Swine, Library science, Skin Pigmentation, Biological Sciences, Corrections, DNA, Mitochondrial, Domestication, Europe, Middle East, Anthropology, evolution, Animals, Neolithic, DNA, Ancient, History, Ancient, Phylogeny
Abstract

Significance Archaeological evidence indicates that domestic pigs arrived in Europe, alongside farmers from the Near East ∼8,500 y ago, yet mitochondrial genomes of modern European pigs are derived from European wild boars. To address this conundrum, we obtained mitochondrial and nuclear data from modern and ancient Near Eastern and European pigs. Our analyses indicate that, aside from a coat color gene, most Near Eastern ancestry in the genomes of European domestic pigs disappeared over 3,000 y as a result of interbreeding with local wild boars. This implies that pigs were not domesticated independently in Europe, yet the first 2,500 y of human-mediated selection applied by Near Eastern Neolithic farmers played little role in the development of modern European pigs., Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Published
2020

33. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Marjan Mashkour, Anastasia Papathanasiou, Joris Peters, John Chapman, Anne Tresset, Simon Stoddart, Antonio Tagliacozzo, Canan Çakirlar, Jörg Schibler, Daniel Helmer, Ceiridwen J. Edwards, Caroline Malone, Vesna Dimitrijević, Andrea Zeeb-Lanz, Christina Geörg, Alexandros Triantafyllidis, Panoraia Alexandri, Ophélie Lebrasseur, Thomas Cucchi, Victoria E. Mullin, Michael P. Richards, James Haile, Laurent A. F. Frantz, Cevdet Merih Erek, John R. Stewart, Joachim Burger, Mihai Gligor, Jörg Orschiedt, Gennady F. Baryshnikov, Lucia Sarti, Rebecca Miller, Youri van den Hurk, Evan K. Irving-Pease, Allowen Evin, Hitomi Hongo, Richard P. M. A. Crooijmans, Jelena Bulatović, Max Price, Keith Dobney, Adina Boroneanţ, Anton Ervynck, Mike Parker Pearson, Joséphine Lesur, Elisabeth Stephan, Holley Martlew, Sepideh Maziar, Kurt J. Gron, Bea De Cupere, Kevin G. Daly, Valentin Dumitraşcu, Anders Götherström, Arkadiusz Marciniak, Azadeh Fatemeh Mohaseb, Richard Sabin, David Orton, Greger Larson, Lionel Gourichon, Cleia Detry, Clive Bonsall, François-Xavier Ricaut, Louis du Plessis, Jean-Denis Vigne, José Miguel Carretero, Benjamin S. Arbuckle, Mike J. Church, Hendrik-Jan Megens, Giedre Motuzaite Matuzeviciute, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Ron Pinhasi, Ninna Manaseryan, Liora Kolska Horwitz, Melinda A. Zeder, Peter Rowley-Conwy, Alexander Yanevich, Daniel G. Bradley, Amelie Scheu, László Bartosiewicz, Darko Radmanovic, Shiva Sheikhi, Michelle Alexander, Katerina Trantalidou, Cristina Valdiosera, Adrian Bӑlӑşescu, M. Thomas P. Gilbert, Vincent M. Battista, Anna Linderholm, Norbert Benecke, Aslı Erim-Özdoğan, Rose-Marie Arbogast, Thomas H. McGovern, Audrey T. Lin, Sophie Van Poucke, Roger Matthews, Martien A. M. Groenen, Erik Meijaard, Wolfram Schier, Nenad Tasić, Dusan Boric, Frantz, Laurent A. F., Haile, Jame, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balaşescu, Adrian, Barnett, Ro, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, ̧, Dušan Boric Adina Boroneant, Bulatovic, Jelena, Çakirlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitras ̧cu, Valentin, du Plessis, Loui, Edwards, Ceiridwen J., Merih Erek, Cevdet, ̆an, AslıErim-Özdog, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Ander, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Motuzaite Matuzeviciute, Giedre, Maziar, Sepideh, Meijaard, Erik, Mcgovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Parker Pearson, Mike, Pinhasi, Ron, Radmanovic, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Deni, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandro, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Jori, Cucchi, Thoma, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linu, Larson, Greger, Archaeology of Northwestern Europe, Groningen Institute of Archaeology, Piperno, Dolores R., Repositório da Universidade de Lisboa, Department of Natural Sciences, German Archaeological Institute (DAI), Texas A&M University [College Station], Transplant Research Program [Boston, MA, USA], Boston Children's Hospital, Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anthropology, Baylor University, Baylor University, University of York [York, UK], Stockholm University, Cardiff School of History, Ancient History, Archaeology and Religion, Cardiff University, Romanian Academy of Sciences, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), UNIARQ, Universidade de Lisboa = University of Lisbon (ULISBOA), Department of Structural and Functional Biology, University of Naples Federico II = Università degli studi di Napoli Federico II, Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden, Gestion des ressources naturelles , environnements et sociétés (GReNES), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Goethe-Universität Frankfurt am Main, University of Liverpool, HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), School of Archaeology, University College Dublin [Dublin] (UCD), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Human Evolution [Leipzig], Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Connaissance Organisation et Systèmes TECHniques (COSTECH), Université de Technologie de Compiègne (UTC), Department of Archaeology, University of Cambridge [UK] (CAM), Laboratorio di Paleontologia e Archeozoologia, Soprintendenza Speciale al Museo Nazionale Preistorico ed Etnografico 'L. Pigorini', Roma, Museo Nazionale Preistorico Etnografico 'L. Pigorini, Institute of archaeology (UCL), University College of London [London] (UCL), University of Copenhagen = Københavns Universitet (UCPH), University of Basel (Unibas), Institut für Paläoanatomie und Geschichte der Tiermedizin, Ludwig-Maximilians-Universität München (LMU), Department of Archaeology, University of Aberdeen, University of Aberdeen, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Universidade de Lisboa (ULISBOA), Università degli studi di Napoli Federico II, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), University of Oxford [Oxford], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0301 basic medicine, Swine, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Skin Pigmentation, [SHS]Humanities and Social Sciences, Gene flow, Domestication, ddc:590, BREEDS, DOMESTIC PIGS, HISTORY, 0601 history and archaeology, Neolithic, History, Ancient, Phylogeny, Multidisciplinary, 060102 archaeology, INTROGRESSION, Europe, pigs, domestication, genomes, WILD, 06 humanities and the arts, Archaeological evidence, SPREAD, Coat, Mitochondrial DNA, Evolution, Zoology, Locus (genetics), Biology, Animal Breeding and Genomics, DNA, Mitochondrial, Middle East, 03 medical and health sciences, Animals, Fokkerij en Genomica, DNA, Ancient, General, ddc:930, Haplotype, DNA, 900 Geschichte und Geografie::930 Geschichte des Altertums (bis ca. 499), Archäologie::930 Geschichte des Altertums bis ca. 499, Archäologie, LONG, SIZE, 030104 developmental biology, domestication evolution gene flow Neolithic, WIAS
Abstract

International audience; Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic

Published
2019
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35. Erratum: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose Marie, Arbuckle, Benjamin, Bǎlǎşescu, Adrian, Barnettl, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, Jose Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoǧan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jorg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, Francois Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Van Den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Subjects
Aquaculture and Fisheries, Aquacultuur en Visserij, WIAS, Life Science, Fokkerij en Genomica, Animal Breeding and Genomics
Abstract

The authors note that the affiliation for Alexandros Triantafyllidis and Panoraia Alexandri should be listed as Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; and that the affiliation for Rose-Marie Arbogast should be listed as CNRS UMR 7044, Maison interuniversitaire des sciences de l'Homme, F-67083 Strasbourg Cedex, France. The corrected author and affiliation lines appear below. The online version has been corrected.

Published
2020

37. Efficient and Specific Multi-Locus Editing of Allogeneic CAR T Cells for Hypoimmunity during Large Scale Manufacture Using Cas12b

Author

Chaivorapol, Christina, Beauchesne, Pascal, De Jesus, Rowena, Dowdle, William E, Chen, Xiaoyu, Bayley, Alison, Qiu, Yunjiang, Birnberg, Andrew, Zheng, Yu, Montalbano, Antonino, Liu, Angela, Zafar, Misbah, Manner, Karl, Ankala, Ramya, Tham, Eleonore, Shah, Heer, Lam, Ben, Lock, Jaclyn, Weng, Lindong, Watts, Kate, Valdiosera, Amanda, Davis, Kimberly, Wang, Lei, Kangeyan, PhD, Divy, Devos, Nicolas, Wong, Athena, Lih, Jason, and Rebar, Edward J

Published
2022
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39. Genetic turnovers and northern survival during the last glacial maximum in European brown bears

Author

Ersmark, Erik, Baryshnikov, Gennady F., Higham, Thomas, Argant, Alain, Castaños, Pedro, Döppes, Doris, Gasparik, Mihaly, Germonpré, M., Lidén, Kerstin, Lipecki, Grzegorz, Marciszak, Adrian, Miller, Rebecca, Moreno García, Marta, Pacher, Martina, Robu, Marius, Rodriguez Varela, Ricardo, Rojo-Guerra, Manuel, Sabol, Martin, Spassov, N., Storå, Jan, Valdiosera, Cristina E., Villaluenga, Aritza, Stewart, J.R., Dalén, Love, Oxford Radiocarbon Accelerator Unit, RLAHA, Aix Marseille Université (AMU), Laboratoire méditerranéen de préhistoire Europe-Afrique (LAMPEA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Department of Palaeontology, Royal Belgian Institue of Natural Sciences, University of Wrocław [Poland] (UWr), Universidad de Valladolid [Valladolid] (UVa), Department of Geology and Paleontology, Comenius University in Bratislava, National Museum of Natural History, Bulgarian Academy of Sciences (BAS), Connaissance Organisation et Systèmes TECHniques (COSTECH), Université de Technologie de Compiègne (UTC), National Science Centre (Poland), Rojo-Guerra, Manuel [0000-0002-9317-8654], Moreno García, Marta [0000-0002-6735-9355], Rojo-Guerra, Manuel, and Moreno García, Marta

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, mtDNA, MtDNA, Refugia, phylogeography, LGM, Ursus arctos, Phylogeography, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, refugia, lcsh:QH540-549.5, Naturvetenskap, lcsh:Ecology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Natural Sciences, ComputingMilieux_MISCELLANEOUS, Original Research
Abstract

[EN] The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid‐Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter‐specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought, We are very thankful to all institutions and individuals that provided samples for this study: the Natural History Museums of Mainz (Germany), Rotterdam (The Netherlands), Brussels (Belgium), Barcelona (Spain), Verona (Italy), Vienna (Austria), Sofia (Bulgaria), Budapest (Hungary), Zagreb (Croatia), the Emil Racoviță Institute of Speleology (Romania), the Aranzadi Society of Sciences (Basque Country, Spain), the Institute of Systematics and Evolution of Animals PAS (Poland), and the Zoological Institute of Saint‐Petersburg (Russia). For providing samples from within Sweden, we wish to acknowledge Friedrike Johansson at the Natural History Museum in Gothenburg, Linda Wickström at SGU in Uppsala, Maria Mostadius at the Zoological Museum in Lund, and finally Gunilla Eriksson and Markus Fjellström at the Department of Archaeology, Stockholm University. For access to samples from the North Sea, we are in gratitude to Charles Schouwenburg and Albert Hoekman/NorthSeaFossils. For valuable assistance in the DNA Lab at the Swedish Museum of Natural History, we would like to thank Martin Irestedt, Bodil Cronholm, and Rodrigo Esparza‐Salas. Dr. Rebecka Miller sadly passed away during work on this manuscript. Her contribution was very much appreciated and her work at Trou Al'Wesse was funded by the Region Wallonne. Financial support for this study was obtained from the Swedish Research Council (VR), Tullbergs stiftelse, and FORMAS through the FP6 BiodivERsA ERA‐NET program. The samples from Polish sites were partially financed by the National Science Centre, grant nr 2015/17/D/ST10/01907, “The history of the brown bear (Ursus arctos Linnaeus, 1758) evolution in Central Europe as a key to modern species conservation,” awarded to Adrian Marciszak

Published
2019
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41. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Author

Valdiosera, C., Günther, T., Vera-Rodríguez, J.C., Ureña, I., Iriarte, E., Rodríguez-Varela, R., Simões, L.G., Martínez-Sánchez, R.M., Svensson, E.M., Malmström, H., Rodríguez, L., De Castro, J.-M.B., Carbonell, E., Alday, A., Hernández Vera, J.A., Götherström, A., Carretero, J.-M., Arsuaga, J.L., Smith, C.I., and Jakobsson, M.

Abstract

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7, 500–3, 500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

Published
2018

43. Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

Author

John Lindo, Jerome S. Cybulski, Brian M. Kemp, Eske Willerslev, Ugo A. Perego, Morten Rasmussen, Cristina Valdiosera, Michael DeGiorgio, Ripan S. Malhi, Terence E. Fifield, David Archer, Alessandro Achilli, Joycelynn Mitchell, E. James Dixon, Barbara Petzelt, and Rosita Worl

Subjects
0301 basic medicine, Male, Lineage (genetic), Pleistocene, peopling, Social Sciences, DNA, Mitochondrial, Indigenous, Evolution, Molecular, Sequence (geology), 03 medical and health sciences, Cave, Genetic variation, Humans, 0601 history and archaeology, indigenous, ancient DNA, Holocene, Phylogeny, 030304 developmental biology, 0303 health sciences, Multidisciplinary, geography.geographical_feature_category, 060102 archaeology, Native American, Genetic Variation, 06 humanities and the arts, Genomics, Before Present, 15. Life on land, Emigration and Immigration, Archaeology, 030104 developmental biology, Geography, Ancient DNA, Genetics, Population, paleogenomics, Genome, Mitochondrial, Indians, North American, Female, Human mitochondrial DNA haplogroup
Abstract

Recent genome-wide studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific northwest coast proves an intriguing focus for these studies due to its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here we report the genome-wide sequence of an ancient individual known as “Shuká Káa” (“Man Ahead of Us”) recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to approximately 10,300 cal years before present (BP). We also analyze low coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from approximately 6075 to 1750 cal years BP. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal BP. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared to other North American individuals (i.e., Anzick-1 and Kennewick Man) from the late Pleistocene or early Holocene. Despite regional shifts in mitochondrial DNA haplogroups we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.Significance StatementThe peopling of the Americas has been examined on the continental level with the aid of single-nucleotide polymorphism arrays, next generation sequencing, and advancements in ancient DNA, all of which have helped elucidate major population movements. Regional paleogenomic studies, however, have received less attention and may reveal a more nuanced demographic history. Here we present genomewide sequences of individuals from the northern Northwest Coast covering a time span of ~10,000 years and show that continental patterns of demography do not necessarily apply on the regional level. In comparison with existing paleogenomic data, we demonstrate that geographically linked population samples from the Northwest Coast exhibit an early ancestral lineage and find that population structure existed among Native North American groups as early as the late Pleistocene.

Published
2017
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47. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Maanasa, Raghavan, Matthias, Steinrücken, Kelley, Harris, Stephan, Schiffels, Simon, Rasmussen, Michael, DeGiorgio, Anders, Albrechtsen, Cristina, Valdiosera, María C, Ávila-Arcos, Anna-Sapfo, Malaspinas, Anders, Eriksson, Ida, Moltke, Mait, Metspalu, Julian R, Homburger, Jeff, Wall, Omar E, Cornejo, J Víctor, Moreno-Mayar, Thorfinn S, Korneliussen, Tracey, Pierre, Morten, Rasmussen, Paula F, Campos, Peter, de Barros Damgaard, Morten E, Allentoft, John, Lindo, Ene, Metspalu, Ricardo, Rodríguez-Varela, Josefina, Mansilla, Celeste, Henrickson, Andaine, Seguin-Orlando, Helena, Malmström, Thomas, Stafford, Suyash S, Shringarpure, Andrés, Moreno-Estrada, Monika, Karmin, Kristiina, Tambets, Anders, Bergström, Yali, Xue, Vera, Warmuth, Andrew D, Friend, Joy, Singarayer, Paul, Valdes, Francois, Balloux, Ilán, Leboreiro, Jose Luis, Vera, Hector, Rangel-Villalobos, Davide, Pettener, Donata, Luiselli, Loren G, Davis, Evelyne, Heyer, Christoph P E, Zollikofer, Marcia S, Ponce de León, Colin I, Smith, Vaughan, Grimes, Kelly-Anne, Pike, Michael, Deal, Benjamin T, Fuller, Bernardo, Arriaza, Vivien, Standen, Maria F, Luz, Francois, Ricaut, Niede, Guidon, Ludmila, Osipova, Mikhail I, Voevoda, Olga L, Posukh, Oleg, Balanovsky, Maria, Lavryashina, Yuri, Bogunov, Elza, Khusnutdinova, Marina, Gubina, Elena, Balanovska, Sardana, Fedorova, Sergey, Litvinov, Boris, Malyarchuk, Miroslava, Derenko, M J, Mosher, David, Archer, Jerome, Cybulski, Barbara, Petzelt, Joycelynn, Mitchell, Rosita, Worl, Paul J, Norman, Peter, Parham, Brian M, Kemp, Toomas, Kivisild, Chris, Tyler-Smith, Manjinder S, Sandhu, Michael, Crawford, Richard, Villems, David Glenn, Smith, Michael R, Waters, Ted, Goebel, John R, Johnson, Ripan S, Malhi, Mattias, Jakobsson, David J, Meltzer, Andrea, Manica, Richard, Durbin, Carlos D, Bustamante, Yun S, Song, Rasmus, Nielsen, Eske, Willerslev, Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, and Willerslev E

Subjects
Gene Flow, Siberia, Models, Genetic, Athabascans and Amerindians, Human Migration, Genetic history of Native American, Indians, North American, Humans, Genomics, Americas, Population genetic, History, Ancient, Article
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

48. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Author

Luciana G. Simões, José Miguel Carretero, Cristina Valdiosera, Eudald Carbonell, Colin Smith, Helena Malmström, Juan Luis Arsuaga, Laura Rodríguez, José Antonio Hernández Vera, Mattias Jakobsson, Irene Ureña, Eneko Iriarte, Torsten Günther, Juan Carlos Vera Rodríguez, JoséMaría Bermúdez de Castro, Anders Götherström, Alfonso Alday, Emma M. Svensson, Ricardo Rodríguez-Varela, and Rafael M. Martinez-Sanchez

Subjects
0301 basic medicine, Mediterranean climate, Steppe, Human Migration, Population, Social Sciences, Paleontología, Prehistory, Palaeodiet, 03 medical and health sciences, Migrations, Bronze Age, Genetics, Archaeogenomics, Humans, 0601 history and archaeology, Transect, education, History, Ancient, 2. Zero hunger, geography, Genetic diversity, education.field_of_study, Diversity, Farmers, Multidisciplinary, geography.geographical_feature_category, 060102 archaeology, Genome, Human, Human migration, business.industry, Ecology, Genetic Variation, High-Throughput Nucleotide Sequencing, DNA, Genomics, 06 humanities and the arts, Biological Sciences, 15. Life on land, Genética, Europe, Evolución, Genetics, Population, 030104 developmental biology, Archaeology, 13. Climate action, Anthropology, Iberia, business
Abstract

Significance The gene pool of modern Europeans was shaped through prehistoric migrations that reached the Western Mediterranean last. Obtaining biomolecular data has been challenging due to poor preservation related to adverse climatic conditions in this region. Here, we study the impact of prehistoric (Neolithic–Bronze Age) migrations in Iberia by analyzing genomic and dietary data, demonstrating that farming practices were introduced by a population genetically distinct from the first farmers in central and northern Europe. After recovering from a founder bottleneck, these first farmers mixed with local hunter-gatherers. Finally, post-Neolithic migrations had a much smaller impact on the Iberian gene pool than they had in other parts of Europe. Stable isotope analysis reveals a homogenous terrestrial diet throughout this period., Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

Published
2017

49. Ancient DNA reveals past existence of Eurasian lynx in Spain

Author

Ricardo Rodríguez-Varela, Diego J. Álvarez-Lao, Ross Barnett, Juan Luis Arsuaga, Nuria García, Carlos Nores, and Cristina Valdiosera

Subjects
0106 biological sciences, 010506 paleontology, geography, geography.geographical_feature_category, Pleistocene, biology, Cytochrome b, Eurasian lynx, Ecology, Population Replacement, 010603 evolutionary biology, 01 natural sciences, Paleontología, Phylogeography, Paleontology, Ancient DNA, Peninsula, biology.animal, Animal Science and Zoology, Ecology, Evolution, Behavior and Systematics, Holocene, 0105 earth and related environmental sciences
Abstract

The known distribution of the Iberian lynx Lynx pardinus within the Iberian Peninsula since the Middle Pleistocene and the lack of reliable records of Eurasian lynx Lynx lynx in this region have led to the assumption that the Iberian lynx was the sole inhabitant of Iberia. In this study, we identified ancient mitochondrial DNA (a total of 337 base pairs from the control region and cytochrome b) from eight northern Iberian lynx remains as Eurasian lynx. These results confirm the presence of Eurasian lynx in northern Iberia from the Pleistocene/Holocene boundary until just a few centuries ago. The paleontological record and our data indicate a population replacement of the Iberian lynx by the Eurasian lynx during the Pleistocene/Holocene transition in the Cantabrian cornice of Spain. Phylogeographic patterns of Late Pleistocene and Holocene Eurasian lynx from Iberia, France, Italy and Denmark show that this felid had a more complex phylogeographic history in the past than modern day populations suggest.

Published
2016

50. Pulling out the 1%:whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries

Author

Nikola Theodossiev, Cristina Valdiosera, Simon Gravel, Diana Dimitrova, Yingrui Li, Krasimir Leshtakov, M. Thomas P. Gilbert, William J. Greenleaf, Martin Sikora, Andrés Moreno-Estrada, Meredith L. Carpenter, Morten E. Allentoft, Sonia Guillén, Hannes Schroeder, Eske Willerslev, Georgi Nekhrizov, Karla Sandoval, Jason D. Buenrostro, Morten Rasmussen, Jun Wang, Davide Pettener, Carlos Bustamante, Donata Luiselli, Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, Sandoval K, Moreno-Estrada A, Li Y, Wang J, Gilbert MT, Willerslev E, Greenleaf WJ, and Bustamante CD.

Subjects
Male, 0106 biological sciences, Adolescent, Genomics, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Bone and Bones, Article, Deep sequencing, 03 medical and health sciences, Principal Component Analysi, Neanderthal genome, MTDNA, Genetics, Humans, ANCIENT DNA, Genetics(clinical), Genomic library, Environmental DNA, Child, History, Ancient, Genetics (clinical), Gene Library, 030304 developmental biology, Principal Component Analysis, 0303 health sciences, Fossils, Shotgun sequencing, whole genome sequence, High-Throughput Nucleotide Sequencing, Nucleic Acid Hybridization, DNA, Mummies, Sequence Analysis, DNA, aDNA sequencing librarie, Ancient DNA, RNA, Human genome, Tooth, Hair
Abstract

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain

Published
2013
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