Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

Marco Rosario Capodiferro,Alessandro Achilli,Ornella Semino,Francesco Montinaro,Alessandra Modi,Jorge Motta,Viola Grugni,Nicola Rambaldi Migliore,Juan Miguel Pascale,David Caramelli,Anna Olivieri,Antonio Salas,Luca Pagani,Iosvany Hernández-Mora,Cristina Cereda,Garrett Hellenthal,Maribel Tribaldos,Linda Ongaro,Antonio Torroni,Martina Lari,Corina Knipper,Bethany Aram,Alessandro Raveane,Gianluca Lombardo,Mait Metspalu,Javier Rivera,Ripan S Malhi ,Ugo A Perego ,Richard G Cooke ,Christiana L Scheib ,Gaetano S Grieco ,Alberto Gómez-Carballa ,Giulia Colombo ,Juan Guillermo Martín ,Tomás Mendizábal

doi:10.2139/ssrn.3661949

Abstract

The genomic histories of Indigenous groups in the Americas have been recently enriched by modern and ancient data, but the dataset on continental Central America is still meagre. Here, we report ten ancient pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama, on the Isthmian land-bridge connecting North and South America. Our analysis reveals extensive sub-structure in the geographic area with pre-colonial Panamanians clustering separately. On a continental scale, the Isthmian populations are distinguished by a previously unknown Indigenous component in the Americas. This component derives from the admixture of different early Indigenous groups that originated from the same northern North American source in the late Pleistocene. The earlier population(s) moved further south, leaving differential footprints in South America, while another group remained restricted to the Isthmo-Colombian area, expanded locally during the early Holocene and left genomic traces up to now.

Highlights

Archaeological and genetic evidence suggests that the peopling of sub-Arctic America started from Beringia before, during, and immediately after late Glacial times (Achilli et al, 2018; Ardelean et al, 2020; Becerra-Valdivia and Higham, 2020; Braje et al, 2017; Skoglund and Reich, 2016; Waters, 2019; Yu et al, 2020)
The tropical environment and the proximity of the excavation sites to the ocean, with recurrent flooding, challenge the possibility of DNA preservation, we were able to obtain some of the first reliable ancient DNA (aDNA) data from the Isthmus
In order to characterize the genetics of Isthmian individuals with the greatest possible spatial range and temporal depth, the 12 ancient genomes were compared with genomewide data from 74 unrelated modern Panamanians and to available modern and ancient data by assembling different datasets (STAR Methods; Table S3)

Summary

Introduction

Archaeological and genetic evidence suggests that the peopling of sub-Arctic America started from Beringia before, during, and immediately after late Glacial times (Achilli et al, 2018; Ardelean et al, 2020; Becerra-Valdivia and Higham, 2020; Braje et al, 2017; Skoglund and Reich, 2016; Waters, 2019; Yu et al, 2020). Ancient individuals carrying SNA ancestries crossed the Panama land bridge and entered South America Their fast spread along the southern continent is evidenced by the earliest archaeological human presence in the Southern Cone at 14.6 kya and by ancient human genomes dating more than 9 kya on both sides of the continent: at Cuncaicha (Peru) and Los Rieles (Chile) on the Pacific and Lapa do Santo and Lagoa Santa (Brazil) on the Atlantic. Another UPop (UPopY) with Australasian ancestry may have contributed to the early peopling of South America as recognized in one sample from the Lagoa Santa site and in some Amazonian groups that experienced isolation events (e.g., Surui and Karitiana) (Moreno-Mayar et al, 2018; Skoglund et al, 2015)

Results

Discussion

Conclusion