Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

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.