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3. An Introduction to Simulating Transitions to Agriculture in Prehistory

Author

Bergin, Sean, Pardo-Gordó, Salvador, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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4. The Essential Geography of the Impresso-Cardial Neolithic Spread

Author

Bergin, Sean, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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6. Genome sequences of two isolates of the yeast Candida zeylanoides : UCD849 from soil in Ireland, and AWD from an African wild dog

Author

McLaughlin, Richard W., primary, Hession, Conor, additional, Bergin, Sean, additional, Cosgrove, Aoife, additional, Dowd, Andrew, additional, Garvey, Niall, additional, Litovskich, Gabrielle, additional, Osaigbovo, Evita, additional, Popa, Denis, additional, Thuku, Cynthia, additional, Butler, Geraldine, additional, Wolfe, Kenneth H., additional, and Byrne, Kevin P., additional

Published
2024
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7. Drivers of large mammal distribution: an overview and modelling approach for palaeoecological reconstructions of extinct ecosystems.

Author

Brooke, Christopher F, Marean, Curtis W, Wren, Colin D, Bergin, Sean, Fahey, B Patrick, and Venter, Jan A

Subjects
PALEOECOLOGY, ANIMAL ecology, HABITAT selection, SEA level, ATMOSPHERIC models
Abstract

One of the primary goals of the palaeosciences is to produce robust understandings of palaeoecologies of extinct ecosystems. The time has arrived where such palaeoecologies can be significantly improved—agent-based models (ABMs) that synthesize our modern understandings of animal ecology with past conditions provide a unique opportunity for this. The Palaeo-Agulhas Plain (PAP), a now submerged landscape off the south coast of South Africa, formed a novel ecosystem during the lower sea levels of the Pleistocene. Here we provide a review of the utility of ABMs for understanding herbivores in prehistoric environments using the Paleoscape Model. The Paleoscape Model is fortunate to have features models of climate, geology and vegetation upon which we can understand how herbivores used the PAP environment. To incorporate aspects of herbivore behaviour and habitat suitability into the model requires analogies from extant systems. In addition to reconstructions of the availability of resources and associated risks, data on herbivore behaviour and physiology are imperative to our understanding of these systems. Behaviour, driven by changes in the environment, is interpreted by species, leading to selection of suitable habitats ultimately driving the herbivore's decisions within ABMs. Finally, we discuss herbivore integration into these models that can be used in numerous other scenarios (past, present and future). [ABSTRACT FROM AUTHOR]

Published
2024
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13. ArchaeoSRP: An R Package for Extracting and Synthesizing Federal Cultural Resources Data for Research and Management.

Author

Bergin, Sean and Snitker, Grant

Subjects
*CULTURAL property, *FOREST reserves, *PROTECTION of cultural property, *FILES (Records), *LAND use
Abstract

For much of its history, archaeological research has relied on site-specific projects, regional comparisons, and theory building from case studies. However, recent research themes concerning the emergence of complex social-ecological systems and long-term land-use legacies require a new approach to archaeological data. Large-scale syntheses of archaeological data provide an effective way forward to address these new research themes. In more concise terms, "big questions" require "big data" to help answer them. The archaeological information collected by the USDA Forest Service is one such "big dataset" and represents an incalculable investment in time, resources, and expertise. This article explores this concept and presents an R package (ArchaeoSRP) designed to extract archaeological information from USDA Forest Service site record files. We demonstrate the functionality of this R package through a case study examining the archaeological data for the Cle Elum Ranger District, within Central Washington's Okanogan-Wenatchee National Forest. Our results reveal the efficiency of using automated methods to extract, organize, and synthesize district-level archaeological data, which, in turn, reveal patterns of precontact and historic land use that were otherwise not distinguishable. [ABSTRACT FROM AUTHOR]

Published
2023
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15. Draft Genome Sequence of the Yeast Blastobotrys aristata Strain UCD613, Isolated from Soil in Ireland

Author

Don, Aida, primary, Byrne, Kevin P., additional, Alqaderi, Fouz, additional, Mazhova, Alexandra, additional, O’Leary Chaney, Ben, additional, Redmond, Sarah, additional, Allen, Stephen, additional, Gao, Jiaran, additional, Ó Cinnéide, Eoin, additional, Bergin, Sean A., additional, Hession, Conor, additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2022
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16. Draft Genome Sequence of the Yeast Torulaspora quercuum Strain UCD657, Isolated from Soil in Ireland

Author

Igharo, Blessing, primary, Byrne, Kevin P., additional, Ghnewa, Heytham, additional, Davey, Ryan P., additional, Fubara, Athaliah, additional, Welc, Julia, additional, Oubihi, Shafik, additional, Moore, Luke, additional, Smith, Cian, additional, Ó Cinnéide, Eoin, additional, Bergin, Sean A., additional, Hession, Conor, additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2022
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17. Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in RTA3 That is Associated with Drug Resistance

Author

Bergin, Sean A., primary, Zhao, Fang, additional, Ryan, Adam P., additional, Müller, Carolin A., additional, Nieduszynski, Conrad A., additional, Zhai, Bing, additional, Rolling, Thierry, additional, Hohl, Tobias M., additional, Morio, Florent, additional, Scully, Jillian, additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2022
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21. Echinocandin heteroresistance causes prophylaxis failure and facilitates breakthrough Candida parapsilosis infection

Author

Zhai, Bing, primary, Liao, Chen, additional, Jaggavarapu, Siddharth, additional, Rolling, Thierry, additional, Bergin, Sean A., additional, Gjonbalaj, Mergim, additional, Miranda, Edwin, additional, Babady, N. Esther, additional, Butler, Geraldine, additional, Taur, Ying, additional, Xavier, Joao B., additional, Weiss, David S., additional, and Hohl, Tobias M., additional

Published
2022
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24. Resistance to miltefosine results from amplification of the RTA3 floppase or inactivation of flippases in Candida parapsilosis

Author

Bergin, Sean A., primary, Zhao, Fang, additional, Ryan, Adam P., additional, Müller, Carolin A., additional, Nieduszynski, Conrad A., additional, Zhai, Bing, additional, Rolling, Thierry, additional, Hohl, Tobias M., additional, Morio, Florent, additional, Scully, Jillian, additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2021
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26. Draft Genome Sequence of the Yeast Ogataea degrootiae Strain UCD465, Isolated from Soil in Ireland

Author

Ó Cinnéide, Eoin, primary, Jones, Max, additional, Bahate, Elijah, additional, Boyd, Elizabeth, additional, Clavero, Rebeca, additional, Doherty, Harry, additional, Drozdz, Izabela, additional, Dumana, Maja, additional, Gonzales, Cristina, additional, Kennedy, Jane, additional, Khan, Maria, additional, Maher, Shane, additional, McGurk, Clare, additional, Moreau, Katherine, additional, Neville, Ruby, additional, Norton, Jade, additional, Ó Cróinín, Tadhg, additional, O’Gorman, Elizabeth, additional, Olliff, Juliana C., additional, Orimaco, Rhys, additional, Quinn, Ellen, additional, Webb Kennedy, Sarah, additional, Bergin, Sean A., additional, Byrne, Kevin P., additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2021
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27. Draft Genome Sequence of a Diploid and Hybrid Candida Strain, Candida sanyaensis UCD423, Isolated from Compost in Ireland

Author

Ryan, Adam, primary, Ó Cinnéide, Eoin, additional, Bergin, Sean A., additional, Alhajeri, Ghozlan, additional, Almotawaa, Hawraa, additional, Daly, Isabelle, additional, Heneghan, Sophia, additional, Horan, Kellie, additional, Kavanagh, Roslyn, additional, Keane, Christopher, additional, Martin, Aaron, additional, McDonagh, Ada, additional, O’Leary, Julia, additional, Osborne, Matthieu, additional, Watson, Emma, additional, Byrne, Kevin P., additional, Wolfe, Kenneth H., additional, and Butler, Geraldine, additional

Published
2021
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29. Resiliencia y cambio durante el Holoceno en La Canal de Navarrés (Valencia): recientes trabajos de prospección

Author

Diez Castillo, Agustín, García Puchol, Oreto, Bernabeu, Joan, 1954, Barton, C. Michael, Pardo Gordó, Salvador, Snitker, Grant, Cegielski, Wendy, and Bergin, Sean

Subjects
Arqueologia
Abstract

Presentamos en este trabajo una evaluación inicial de los trabajos de prospección sistemática llevados a cabo en la comarca de La Canal de Navarrés (Valencia) desde el año 2014 en el marco del proyecto NSF "The Emergence of Coupled Natural and Human Landscapes in the Western Mediterranean". El programa desarrollado ha seguido un protocolo previamente establecido por nuestro equipo de trabajo con la novedad de la incorporación de nuevas tecnologías en el trabajo de campo (dispositivos electrónicos) cuyo objetivo ha sido agilizar el procesado de la información posterior en el laboratorio mediante el uso de un entorno GIS. Los resultados obtenidos confirman la presencia de materiales en diferentes puntos del valle indicativos de una amplia cronología (entre el Pleistoceno final y el desarrollo del Holoceno) que se suman a los registros prehistóricos conocidos en el área desde el Paleolítico medio a la Edad del Bronce. In this paper we present a preliminary approach to the survey work carried out in La Canal de Navarrés (Valencia) since 2014 in the framework of the NSF Project 'The Emergence of Coupled Natural and Human Landscapes in the Western Mediterranean'. The programme developed follows previous protocols established by us with the novelty of the use of new technologies (electronic devices) with the goal to make more dynamic the analysis of data in a GIS environment. The results confirm the existence, in several open-air locations, of prehistoric artefacts along the valley regarding to a wide chronology (from the final Pleistocene and covering the Holocene) that can be added to the sequence known at the area including Middle Palaeolithic to Bronze Age evidences.

Published
2016

31. Paperless survey? New methodological approaches to archaeological fieldwork, the case of Navarrés (València)

Author

Diez Castillo, Agustín, García Puchol, Oreto, Barton, C. Michael, Pardo Gordó, Salvador, Snitker, Grant, Cegielski, Wendy, and Bergin, Sean

Subjects
UNESCO::HISTORIA, archaeolgical survey, holocene, geographical Information Systems (gis), HISTORIA [UNESCO], new methodologies
Abstract

El trabajo que presentamos se ha desarrollado en el marco del proyecto NSF “The Emergence of Coupled Natural and Human Landscapes in the Western Mediterranean” en el área comprendida por la actual comarca de La Canal de Navarres, situada al suroeste de la provincia de Valencia. Este espacio se convierte en una de las áreas elegidas para un programa de recogida de datos centrado en la prospección sistemática “off site “. En las jornadas “Dando sentido a la prospección arqueológica” nos centraremos en los aspectos metodológicos que hemos desarrollado para llevar a cabo el trabajo de campo. Esta ha sido la primera vez que hemos realizado una prospección arqueológica, en una zona completamente nueva, sin ningún apoyo en documentos de papel ya fueran esto mapas, fichas, acetatos, fotos aéreas o cualquier otro tipo de documento. Toda la documentación de apoyo se ha llevado al campo en tabletas electrónicas (dos tabletas iPad mini y una tableta android) o smart-phones (iPhone o Samsung Galaxy). En el entorno operativo iOS, después de valorar otras alternativas (iGis, Autocad, …) nos decidimos por la utilización de la app CartoMobile©. The work we present has been developed within the framework of the NSF project “The Emergence of Coupled Natural and Human Landscapes in the Western Mediterranean” in the area covered by the current region of La Canal de Navarres, located southwest of the province of Valencia. This space becomes one of the areas chosen for a data collection program focused on systematic off-site prospecting. In the conference "Making sense of archaeological prospecting" we will focus on the methodological aspects that we have developed to carry out the field work. This has been the first time that we have carried out an archaeological survey, in a completely new area, without any support in paper documents, be it maps, files, acetates, aerial photos or any other type of document. All supporting documentation has been taken to the field on electronic tablets (two iPad mini tablets and an android tablet) or smart-phones (iPhone or Samsung Galaxy). In the iOS operating environment, after evaluating other alternatives (iGis, Autocad, ...) we decided to use the CartoMobile © app.

Published
2014

37. Resiliencia y cambio durante el Holoceno en La Canal de Navarrés (Valencia): recientes trabajos de prospección.

Author

DIEZ-CASTILLO, Agustín, GARCÍA-PUCHOL, Oreto, BERNABEU, Joan, BARTON, Michael, PARDO-GORDÓ, Salvador, SNITKER, Grant, CEGIELSKI, Wendy, and BERGIN, Sean

Subjects
HOLOCENE Epoch, ARCHAEOLOGICAL surveying, SOCIAL ecology
Abstract

Copyright of Archivo de Prehistoria Levantina is the property of Museu de Prehistoria de Valencia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2016

39. Book Reviews

Author

Root, Matthew J., primary, Whalen, Michael E., additional, Wilke, Philip J., additional, Bergin, Sean, additional, Senn, Matt, additional, Godino, Ivan Briz i, additional, McLaren, Andrew P., additional, Odell, George H., additional, Bement, Leland C., additional, and Carballo, Dave, additional

Published
2006
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41. Towards a Community Framework for Agent-Based Modelling.

Author

Janssen, Marco A., Alessa, Lilian Na'ia, Barton, Michael, Bergin, Sean, and Lee, Allen

Subjects
COMMUNICATION models, SOCIAL dynamics, EDUCATION, ECOLOGY, SCHOLARS, DATA analysis, MATHEMATICAL models, BUSINESS communication, SELECTIVE dissemination of information
Abstract

Agent-based modelling has become an increasingly important tool for scholars studying social and social-ecological systems, but there are no community standards on describing, implementing, testing and teaching these tools. This paper reports on the establishment of the Open Agent-Based Modelling Consortium, www.openabm.org, a community effort to foster the agent-based modelling development, communication, and dissemination for research, practice and education. [ABSTRACT FROM AUTHOR]

Published
2008

42. Evaluating the Influence of Neolithic Agropastoral Land Use on Holocene Fire Regimes Through Simulated Sedimentary Charcoal Records

Author

Snitker, Grant, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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43. Early Neolithic Farming Activities in High Mountain Landscapes of the Pyrenees: Simulating Changes in Settlement Patterns

Author

Gassiot-Ballbè, Ermengol, Salvador-Baiges, Guillem, Clemente-Conte, Ignacio, Díaz-Bonilla, Sara, Garcia-Casas, David, Mazzucco, Niccolò, Obea-Gómez, Laura, Rey-Lanaspa, Javier, Rodríguez-Antón, David, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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44. A Bayesian Chronomodel for an Economic Approach to the Onset of Farming in Northwestern Mediterranean and the Western Alpine Foreland

Author

Martínez-Grau, Héctor, Antolín, Ferran, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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45. 'Digital Proxies' for Validating Models of Past Socio-ecological Systems in the Mediterranean Landscape Dynamics Project

Author

Barton, C. Michael, Ullah, Isaac I. T., Gauthier, Nicolas, Miller, Nari, Snitker, Grant, Esteban-Alamá, Irene, Bernabeu Aubán, Joan, Heimsath, Arjun, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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46. The Transition to Early Farming in Europe

Author

Ammerman, Albert J., Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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47. The Dynamics of Risk Perception in a Mediterranean Agroecosystem

Author

Gauthier, Nicolas, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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48. The Spread of Agriculture: Quantitative Laws in Prehistory?

Author

Fort, Joaquim, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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49. Assessing Population Dynamics in the Spread of Agriculture in the Mediterranean Iberia Through Early Warning Signals Metrics

Author

García Puchol, Oreto, Diez Castillo, Agustín, Pardo-Gordó, Salvador, Bernabeu Aubán, Joan, Cortell Nicolau, Alfredo, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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50. Cultural Hitchhiking in the Context of the First Agricultural Groups of South-Western Europe: A Simulation Study

Author

Pardo-Gordó, Salvador, Bertino, Elisa, Series Editor, Cioffi-Revilla, Claudio, Series Editor, Foster, Jacob, Series Editor, Gilbert, Nigel, Series Editor, Golbeck, Jennifer, Series Editor, Gonçalves, Bruno, Series Editor, Kitts, James A., Series Editor, Liebovitch, Larry S., Series Editor, Matei, Sorin A., Series Editor, Nijholt, Anton, Series Editor, Nowak, Andrzej, Series Editor, Savit, Robert, Series Editor, Squazzoni, Flaminio, Series Editor, Vinciarelli, Alessandro, Series Editor, Pardo-Gordó, Salvador, editor, and Bergin, Sean, editor

Published
2021
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