Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes

Abstract

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en-masse. In this study we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 - 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.

Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

“…If the distribution shares the peak of LTR-RT abundances aged 1–4 mya observed in V. pacos , then it would suggest the V. pacos lineage diverged from the extant wild guanaco lineage more than 4 mya. If the distribution does not share the peak, it would suggest V. pacos is derived from an extinct wild guanaco lineage, in agreement with the model of llama domestication proposed by [ 26 ]. It would also be interesting to investigate whether genes in C. ferus and V. pacos have LTR-RT insertions near promoters of transcription factors or other genes which might be implicated in phenotypic differences between these species [ 7 ].…”

The immunogenetic impact of European colonization in the Americas

“…Archaeological evidence suggests that the transition to farming practices evolved regionally and fluidly, with some populations alternating between hunting-gathering and farming through time (Dillehay, 2011). Camelids and guinea pigs were domesticated around 6-8 ka ago and 11-13 ka ago, respectively, though there were no known major diseasecausing zoonotic pathogens that may have been transmitted humans from any of these species (Lord et al, 2020;Diaz-Maroto et al, 2021). Furthermore, in many population-dense regions across the Americas, urban structures of Indigenous people were highly organized and included well-developed water storage and distribution systems, possibly aiding in better sanitation and reducing microbial spread (Patterson and Runge, 2002).…”

El manejo territorial de los camélidos en la circumpuna de Atacama desde el Arcaico al Formativo (10.000-2400 aP): Una aproximación isotópica y taxonómica

“…En trabajos anteriores se planteó como hipótesis que la movilidad asociada a la crianza de camélidos habría sido más limitada durante el Arcaico tardío en comparación al Formativo temprano (López et al 2017), y los resultados de los análisis isotópicos sugerían movimientos más restringidos para el Arcaico, mientras que para el Formativo temprano los valores de δ 13 C y δ 15 N se mostraban más heterogéneos. Estos antecedentes ya planteaban la dificultad de distinguir camélidos domésticos y silvestres a partir de los análisis osteométricos, aspecto que aquí será tratado mediante la combinación de análisis de isótopos estables, osteométricos y estudios genéticos realizados sobre muestras provenientes de Tulán (Díaz-Maroto et al 2021).

Figura 1.(a) Ubicación del área de estudio; (b) ubicación de las quebradas Puripica y Tulán y Salar de Punta Negra; (c) vista general del sitio TU-109; (d) sitio TU-122; (e) sitio TU-52; y (f) vista general del templete TU-54.

…”

“…En el Desierto de Atacama (18°-29°S) el proceso de domesticación derivó en nuevas formas de articular el espacio y modificó notablemente la relación entre los grupos humanos y la naturaleza. Las investigaciones arqueológicas realizadas en esta área —específicamente en el Salar de Atacama— han enfatizado la identificación taxonómica de restos de camélidos mediante análisis morfológicos, osteométricos, de identificación de fibras y, en años recientes, a través de estudios genéticos y de isótopos estables (Cartajena et al 2007, 2009; Díaz-Maroto et al 2021; Hesse 1982a; López et al 2017). Estos análisis se llevaron a cabo en dos áreas con trayectorias culturales similares: las quebradas de Puripica y Tulán.…”