Advances in genetics shed light on the human history of the Isthmo-Colombian area from the last ten thousand years

The research conducted by an interdisciplinary research team, led by the Universities of Pavia and Pablo de Olavide, has revealed a previously undescribed ancestry among ancient Indigenous people of the Americas

Corina Knipper (CEZA) y Alesssandro Achilli (Pavía) trabajan con restos de individuos de los periodos pre-hispánicos y colonial temprano conservados en el Patronato Panamá Viejo
Corina Knipper (CEZA) and Alesssandro Achilli (Pavia) while sampling the remains of pre-Hispanic and early colonial individuals preserved in the Patronato Panamá Viejo

Based on the analysis of DNA from present-day and ancient individuals on the Isthmus of Panama, an interdisciplinary research team, led from the Universities of Pavia and Pablo de Olavide (Seville), explains complex pre-Hispanic burials excavated in Panama City and highlights the genomic distinctiveness of the Isthmo-Colombian area. The research has also revealed a previously undescribed ancestry among ancient Indigenous peoples of the Americas, unique to the region and detectable in the ancient pre-Hispanic individuals as well among the self-identified descendants of current Indigenous, African and Hispano-Indigenous groups.

The study, entitled “Archaeogenomic distinctiveness of the Isthmo-Colombian area”, has been published on-line in Cell, one of the leading journals for life science research, on March 23. Based on an international collaborative effort involving anthropologists, archaeologists, historians, and geneticists from Panama, Colombia, the USA, the UK, Germany, Estonia, Spain and Italy, headed by geneticists Alessandro Achilli and Marco Rosario Capodiferro at the University of Pavia and in collaboration with historian Bethany Aram at the Universidad Pablo de Olavide of Seville, the work entails an unprecedented effort to reconstruct the Isthmian region’s demographic history over the last ten thousand years using DNA as the principal tool.

Although the tropical environment and the proximity of the excavation sites to the ocean challenged the possibility of DNA preservation, Capodiferro et al. have successfully applied to the most up to date techniques to extract and analyze the first reliable ancient genomes from the Isthmus together with modern Panamanians’ genome-wide data. Their findings draw upon the DNA extracted from the ancient bone samples of ten pre-Hispanic and two early colonial individuals buried in Panama City (specifically, Coco del Mar and Panamá Viejo) and the DNA that 84 individuals living in various regions of Panama donated to this research in 2016.

A graph summarizing the main findings of the paper on a continental scale. Ancestries and admixture events that shaped the archaeogenomic distinctiveness of the Isthmo Colombian area are shown.

Dr. Marco Capodiferro describes the genetic variation on the Isthmus: “The research identified a strong genomic structure (differentiation) within Panama, mostly matching the Indigenous groups analyzed in this study, as well as the pre-Hispanic individuals sampled. This implies that each group has its own genetic history. However, these groups also show relatedness, especially in the Caribbean region on the border between western Panama and southeastern Costa Rica (the Bribri, Cabécar, Naso Djërdi and Ngäbe) over thousands of years. Fewer genetic similarities were identified between the Indigenous groups located in eastern Panama (the Guna and Emberá), and between the Emberá and the pre-Hispanic Panamanians who lived in the area around Old Panama before European contact. «Regarding the connection with local pre-Hispanic cultures,” Capodiferro continues: “These macro-groups in part reflect the pre-colonial cultural areas, already identified, especially the western area of the Isthmus, which mirrors the cultural region of Greater Chiriquí, while the link to the eastern region often known as the ‘Greater Darien’ is less evident”.

The present research has an impact that expands far beyond the Isthmian area. It confirms that the ancient and modern Indigenous groups on the Isthmus of Panama share a common genetic history with other Indigenous peoples in North, Central and South America, but along a specific variability axis of the Americas’ genetic landscape. “On a continental scale”, Prof. Alessandro Achilli explains, “the comparison with more than 1800 available ancient and modern genomic data revealed a distinctive Isthmo-Colombian Indigenous genetic component. To explain this genomic uniqueness”, according to Prof. Achilli, “at least three ancestries linked to different Pleistocene Indigenous groups of northern North American origin(s) should be considered, including a still Unsampled Population of the Isthmus, which we called UPopI. This ancestry reached the Panama land bridge over 10 thousand years ago, expanded locally during the early Holocene, and left genomic traces up to the present day, especially among the Guna”.

Prof. Bethany Aram, an historian, adds that the study also addresses long-standing questions on pre-contact burials. The ancient genomes facilitate new interpretations of two pre-Hispanic burials in Panamá Viejo and Coco del Mar, “highlighting the roles of female individuals interred with the skulls of nine and three male individuals, respectively, 600-1450 CE.” Prof. Aram considers further research with high-resolution genomes essential to test evidence of a population contraction in the region that began before 1500 and intensified during the sixteenth century, also reported in this study, as well as to estimate the size of the region’s pre-Hispanic population.

“This research provides a suggestive baseline for future interdisciplinary studies of the Isthmo-Colombian crossroads”, Prof. Achilli concludes. “In the next step we will include whole genomes from present-day individuals and high-coverage ancient data from other archeological sites and covering a wider timeframe, from early Holocene through colonial times, to further refine the region’s genetic history.”

The research for this paper has received financial support from the European Research Council (Horizon 2020) grant ERC CoG 648535, “ArtEmpire,” directed by Prof. Aram, the University of Pavia – INROAd program, the Fondazione Cariplo project no. 2018–2045 and the Italian Ministry of Education, University and Research (MIUR) PRIN2017 20174BTC4R project. It has been undertaken with collaboration from the Patronato Panamá Viejo, the Gorgas Memorial Institute for Health Studies of Panama, and the ancient DNA and modern population genetics labs at the University of Illinois and the University of Tartu, and with the permission of Panama’s Authorities (Dirección Nacional de Patrimonio Histórico, Instituto Nacional de Cultura).

Marco Rosario Capodiferro (Pavía), Javier Aceituno (Antioquía), Tomás Mendizábal (Patronato Panamá Viejo), Juan Guillermo Martín (Uninorte), Iosvany Hernández Mora (Uninorte), Alejandro García Montón (UPO), Bethany Aram (UPO), Alessandro Achilli (Pavía), Corina Knipper (CEZA), Rainer Schreg (Bamberg) y Javier Rivera Sandoval (Uninorte)

Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco G, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. March 23, 2021. Cell [IF2019: 38.637]. https://doi.org/10.1016/j.cell.2021.02.040