About

Dr. José M. Capriles is an anthropological archaeologist specializing in environmental archaeology, human ecology, and zooarchaeology. He earned his Licentiate Degree in Archaeology from Universidad Mayor de San Andrés in La Paz, Bolivia in 2004, followed by an M.A. in 2006 and a Ph.D. in Anthropology in 2011 from Washington University in St. Louis. Prior to joining Penn State University, Dr. Capriles was a Visiting Scholar at the University of Pittsburgh from 2012 to 2013, a Chilean FONDECYT Postdoctoral Researcher from 2013 to 2015, and an Assistant Professor at Universidad de Tarapacá from 2015 to 2016. His research employs cutting-edge scientific methods to address a broad range of questions related to past and present societal transformations, ecological dynamics, and human-environment interactions in South America. Specifically, his work investigates how humans adapted to changing environmental conditions in the Atacama desert, Andean highlands, and Amazonian tropical lowlands over time; the social and ecological dynamics involved in animal and plant domestication, early food production, and the development of increasingly unequal institutions; and the socio-environmental factors influencing the emergence and disintegration of complex polities such as the Tiwanaku and Inca states, as well as other population and cultural continuities and discontinuities. Dr. Capriles conducts research primarily in Bolivia and Chile in collaboration with international and interdisciplinary teams. He is also committed to cultural heritage preservation through public outreach and active participation of Indigenous and local communities in archaeological research. In addition to his primary appointment in the Department of Anthropology, Dr. Capriles is affiliated with the Latin American Studies Program and the Climate Science Dual-Title Degree Program at Penn State University.

Research topics

• Biology
• Geography
• Computer Science
• Archaeology
• Evolutionary biology
• Demography
• Horticulture
• Forestry
• Agroforestry
• Botany
• Geology
• Ecology
• Agronomy

Selected publications

• Leveraging Phytolith Research using Artificial Intelligence

  ArXiv.org · 2026-03-12

  articleOpen access

  Phytolith analysis is a crucial tool for reconstructing past vegetation and human activities, but traditional methods are severely limited by labour-intensive, time-consuming manual microscopy. To address this bottleneck, we present Sorometry: a comprehensive end-to-end artificial intelligence pipeline for the high-throughput digitisation, inference, and interpretation of phytoliths. Our workflow processes z-stacked optical microscope scans to automatically generate synchronised 2D orthoimages and 3D point clouds of individual microscopic particles. We developed a multimodal fusion model that combines ConvNeXt for 2D image analysis and PointNet++ for 3D point cloud analysis, supported by a graphical user interface for expert annotation and review. Tested on reference collections and archaeological samples from the Bolivian Amazon, our fusion model achieved a global classification accuracy of 77.9\% across 24 diagnostic morphotypes and 84.5% for segmentation quality. Crucially, the integration of 3D data proved essential for distinguishing complex morphotypes (such as grass silica short cell phytoliths) whose diagnostic features are often obscured by their orientation in 2D projections. Beyond individual object classification, Sorometry incorporates Bayesian finite mixture modelling to predict overall plant source contributions at the assemblage level, successfully identifying specific plants like maize and palms in complex mixed samples. This integrated platform transforms phytolith research into an "omics"-scale discipline, dramatically expanding analytical capacity, standardising expert judgements, and enabling reproducible, population-level characterisations of archaeological and paleoecological assemblages.

  PublisherOA PDF

• Archaeogenomic identification of ancient plant and feather remains from Túcume, Peru

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Pleistocene Settlement: First Settlers in South America

  Oxford University Press eBooks · 2026-05-21

  book-chapterSenior author

  Abstract The technological, stylistic, and ecological diversity evident among the earliest archaeological sites with evidence of humans in South America suggests this process likely began much earlier than assumed by most scholars and questions theories and models about the human colonization of the entire New World. Relying on examples from some of South America’s earliest archaeological sites, we review the state of the art of what we know about this process and about how this knowledge is produced. As a result, we argue not only that somewhat arbitrary biases have favored certain kinds of evidence and later cultural developments over others but also that epistemological and even ontological misunderstandings have shrouded our discussions regarding the complexity and variability featured in the formation of the archaeological record of the earliest human occupations of the continent. Nevertheless, understanding how the late Pleistocene peopling of South America unfolded is still a largely unresolved but immensely provocative question fueling creative and provocative research.

  PublisherDOI

• <i>Llamas beyond the Andes: Untold Histories of Camelids in the Modern World</i> . Marcia Stephenson. 2023. University of Texas Press, Austin. x + 380 pp. $45.00 (hardcover), ISBN 978-1-4773-2840-8.

  American Antiquity · 2026-04-08

  article1st authorCorresponding
  PublisherDOI

• PASTOREO DE CAMÉLIDOS Y USO TERRITORIAL DURANTE EL PERIODO FORMATIVO TARDÍO: ANÁLISIS ZOOARQUEOLÓGICO DEL SITIO SUMERGIDO DE OJJELAYA, BOLIVIA

  Chungara · 2026-01-01 · 1 citations

  articleOpen access

  Las sociedades prehispnicas que se asentaron a orillas del Lago Titicaca desarrollaron procesos de crecimiento econmico gracias a estrategias de intensificacin agrcola y pastoreo de camlidos.Sin embargo, existen pocos estudios que hayan abordado cmo estos procesos acompaaron la formacin de organizaciones complejas como el Estado de Tiwanaku (550-1100 DC), particularmente porque los territorios lacustres dedicados al pastoralismo antes de Tiwanaku han sido sumergidos debido a las variaciones del nivel del agua del Lago Titicaca.Excavaciones arqueolgicas en Ojjelaya, un sitio arqueolgico actualmente subacutico ubicado cerca de la orilla norte del lago menor o Wiaymarka del Lago Titicaca, han revelado la existencia de una antigua pennsula, hoy sumergida, que conserva vestigios arqueolgicos de actividades pastorales durante el periodo Formativo Tardo (200 AC -550 DC).Este artculo pretende establecer cules fueron las estrategias de gestin local de los recursos camlidos antes de la expansin de Tiwanaku, a travs del estudio de los restos de fauna recuperados de Ojjelaya.Identificamos una serie de patrones de consumo vinculados a intensificacin pastoril, pero tambin evidencia concreta de que el sitio y sus restos arqueofaunsticos fueron afectados por procesos tafonmicos vinculados con el aumento del nivel del agua y la inundacin del sitio.Finalmente, concluimos que el pastoreo lacustre fue una estrategia econmica crucial para las sociedades asentadas en las orillas del Lago Titicaca antes y durante la emergencia de Tiwanaku.Palabras claves:

  PublisherOA PDFDOI

• Leveraging Phytolith Research using Artificial Intelligence

  arXiv (Cornell University) · 2026-03-12

  preprintOpen access

  Phytolith analysis is a crucial tool for reconstructing past vegetation and human activities, but traditional methods are severely limited by labour-intensive, time-consuming manual microscopy. To address this bottleneck, we present Sorometry: a comprehensive end-to-end artificial intelligence pipeline for the high-throughput digitisation, inference, and interpretation of phytoliths. Our workflow processes z-stacked optical microscope scans to automatically generate synchronised 2D orthoimages and 3D point clouds of individual microscopic particles. We developed a multimodal fusion model that combines ConvNeXt for 2D image analysis and PointNet++ for 3D point cloud analysis, supported by a graphical user interface for expert annotation and review. Tested on reference collections and archaeological samples from the Bolivian Amazon, our fusion model achieved a global classification accuracy of 77.9\% across 24 diagnostic morphotypes and 84.5% for segmentation quality. Crucially, the integration of 3D data proved essential for distinguishing complex morphotypes (such as grass silica short cell phytoliths) whose diagnostic features are often obscured by their orientation in 2D projections. Beyond individual object classification, Sorometry incorporates Bayesian finite mixture modelling to predict overall plant source contributions at the assemblage level, successfully identifying specific plants like maize and palms in complex mixed samples. This integrated platform transforms phytolith research into an "omics"-scale discipline, dramatically expanding analytical capacity, standardising expert judgements, and enabling reproducible, population-level characterisations of archaeological and paleoecological assemblages.

  PublisherDOI

• Nuevas dataciones sobre restos humanos del centro de Argentina y su aporte a la discusión del poblamiento de la región

  Arqueología · 2025-07-07

  articleOpen accessSenior author

  En el centro de Argentina, las primeras evidencias de presencia humana, ubicadas entre ca. 13.000 y 10.600 años cal AP, son escasas, mientras que con posterioridad a 9600 años cal AP la señal arqueológica es más intensa. En este último período se ubican los restos humanos recuperados en las localidades de Jesús María y Ascochinga (pcia. de Córdoba, Argentina), motivo de este trabajo. En Jesús María, J. Delprato excavó tres entierros espacialmente cercanos en 1951, en tanto que en Ascochinga, excavó un enterratorio en 1959, los primeros fueron analizados por Alfredo Castellanos y todos los restos humanos se conservaron en la colección Castellanos, alojada en el Museo Florentino y Carlos Ameghino de la Universidad Nacional de Rosario. En este trabajo se presenta nueva información a partir de las dataciones de dos de estos individuos, recientemente fechados por AMS en ca. 8500 y 7809 años cal. AP, ubicándolos temporalmente en el Holoceno medio. Se obtuvo, además, información isotópica que proporciona una primera aproximación a la dieta de estos individuos. Se analizan las implicancias de estas dataciones para la discusión del proceso de poblamiento del centro de Argentina considerando todos los fechados disponibles para la región. Se concluye que la datación de estos restos humanos en el Holoceno medio refuerza las evidencias arqueológicas correspondientes a este período, después de dos milenios con baja señal arqueológica en la región tras la Transición Pleistoceno-Holoceno, apoyando las propuestas sobre un nuevo proceso de colonización del centro de Argentina.

  PublisherOA PDFDOI

• Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation

  Science · 2025-03-06 · 11 citations

  article

  Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.

  PublisherDOI

• Short communication: Estimating radiocarbon reservoir effects in Bolivian Amazon freshwater lakes

  2025-05-14

  preprintOpen access

  Abstract. The Llanos de Moxos, in the Bolivian Amazon, preserves a remarkable archaeological record, featuring thousands of forest islands. These anthropogenic sites emerged as a result of activities of the earliest inhabitants of Amazonia during the Early and Middle Holocene. Excavations conducted to date on the forest islands have revealed that many assemblages contain a high number of ancient freshwater snail remains. In these shell middens, the most represented mollusc taxon, and in most cases the sole one, is Pomacea spp., a genus that inhabits inland shallow lakes and wetlands. Although human burials and faunal remains are typically recovered from these sites, their collagen is often not preserved or is of poor quality, and shell carbonates from Pomacea shells, along with carbonised plant remains, are often used for 14C measurements. However, it remains undetermined if these measurements are subject to radiocarbon reservoir effect (RRE). To determine if a freshwater RRE could affect the age estimations of Amazonian archaeological and other paleoecological deposits, we collected modern coeval Pomacea shells and tree leaves from four locations across the Llanos de Moxos area for AMS radiocarbon dating. The radiocarbon results combined with the environmental history of Llanos de Moxos during the Holocene, confirm an absence of significant RREs, and support the continued use of freshwater molluscs as viable material for radiocarbon dating in the region.

  PublisherOA PDFDOI

• Diversified human dietary strategies and settlement patterns in the core of the Atacama Desert during the late Pleistocene-Holocene transition (∼12.8 – 11.2 ka)

  Journal of Anthropological Archaeology · 2025-12-04

  article
  PublisherDOI

Frequent coauthors

• María Clara Álvarez

  Universidad Nacional del Centro de la Provincia de Buenos Aires

  43 shared

• Geoffrey E. Braswell

  University of California, San Diego

  43 shared

• Oswaldo Chinchilla

  Yale University

  43 shared

• Liz Haberkorn

  University of California, San Diego

  41 shared

• Calógero M. Santoro

  31 shared

• Claudio Latorre

  Pontificia Universidad Católica de Chile

  30 shared

• Jeffrey Quilter

  Harvard University Press

  27 shared

• Scott Macrae

  University of Central Florida

  26 shared

Labs

• Capriles Environmental Archaeology LabPI

Education

• Ph.D. in Anthropology, Department of Anthropology

  Washington University in St Louis

  2011

• M.A. in Anthropology, Department of Anthropology

  Washington University in St Louis

  2006

• Licenciate in Archaeology, Carreras de Antropología y Arqueología

  Universidad Mayor de San Andrés

  2004