Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas

Abstract

The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.

Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent

“…Q-M925 ( Figure 5 ) is most frequent in Mesoamerica and the Isthmo-Colombian area; it includes three branches (Q-CTS748, Q-Y12421, and Q-Y26547) with different geographic distributions: Q-CTS748 is mainly observed in Mexico and not reported south of El Salvador; Q-Y12421 reaches considerable frequencies in the Isthmo-Colombian area [ 19 ]; Q-Y26547 is only found in three Brazilians from Amazonia [ 41 ]. Although not represented by any sequence, Q-M925* was reported at a moderate frequency in Panama [ 19 ] and in a few samples from Costa Rica, Guatemala, and Peru [ 37 , 79 ]. Our phylogeographic results ( Figure 5 ) are in accordance with previous reports.…”

“…Salvador; Q-Y12421 reaches considerable frequencies in the Isthmo-Colombian area [19]; Q-Y26547 is only found in three Brazilians from Amazonia [41]. Although not represented by any sequence, Q-M925* was reported at a moderate frequency in Panama [19] and in a few samples from Costa Rica, Guatemala, and Peru [37,79].…”

“…One of the main obstacles in obtaining a detailed genetic picture of the Americas first peopling is the lack of clear and complete information about the autochthonous gene pool because of the European colonization, the subsequent slave trade, and numerous more recent events of gene flow. Due to the uneven male/female native population decline and the high historical rate of European male-mediated admixture into Native American communities, the Y chromosome gene pool was the most affected [ 16 , 17 , 18 , 19 ].…”