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Clinical Trial
. 2015 Dec 4;10(12):e0144223.
doi: 10.1371/journal.pone.0144223. eCollection 2015.

Exploring the Y Chromosomal Ancestry of Modern Panamanians

Free PMC article
Clinical Trial

Exploring the Y Chromosomal Ancestry of Modern Panamanians

Viola Grugni et al. PLoS One. .
Free PMC article


Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama's population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.

Conflict of interest statement

Competing Interests: NM is employed by a commercial company: This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.


Fig 1
Fig 1. Spatial distributions of Y-chromosome components in Panama.
Bars show Native American (violet), West Eurasian/North African (green), sub-Saharan African (yellow) and South Asian (light blue) components in each province or comarca. In grey the Y-chromosome portion with discordant haplogroup predictions. The physical map of Panama is from NASA Earth Observatory (
Fig 2
Fig 2. Principal Components (PC) plot based on the predicted Y-chromosome haplogroup frequencies.
Numbers in parentheses indicate the proportion of the total genetic information retained by a given PC. The inset plot illustrates the contribution of each haplogroup. Red diamonds are for Panamanian groups; blue circles are for neighbouring countries.
Fig 3
Fig 3. Principal Coordinates (PCo) plots.
Analysis was performed on the 33 STR loci haplotypes (S1 Table) screened here together with those previously typed by Battaglia et al. [43]. On the whole, 46.13% of the total variance is represented: 25.62% by the first PCo and 20.51% by the second PCo. Plots are in relation to haplogroup affiliation (A), macrogeographic distribution (B), and Panamanian province distribution in the Central-South American context (C). In panel A, yellow squares are the Panamanian Y chromosomes predicted as belonging to haplogroup Q and not further sub-classified; dotted yellow squares indicate six samples (two of these are completely overlapping) characterized by the DYS391-6 allele. The tree on the right illustrates the phylogenetic relationships among haplogroups. Nomenclature is in agreement with Battaglia et al. [43]. In panel B, Panamanian samples are represented by yellow symbols: squares are for predicted haplotypes and circles for haplotypes that were instead classified by SNP analysis [43]. South East America includes Argentina, Brazil, Paraguay and Uruguay; Central America includes Costa Rica, El Salvador, Guatemala and Nicaragua [43].
Fig 4
Fig 4. Network of Panamanian Q STR haplotypes.
The analysis was performed on 15 loci (S1 Table). Samples were subdivided according to their PGF birthplaces, marked by different colours. The size of each circle is proportional to the haplotype frequency; the smallest circle is equal to one subject. The coalescence time estimates of the three branches were obtained by using the rho statistic and the 15 STRs loci considered in this analysis.
Fig 5
Fig 5. MultiDimensional Scaling (MDS) plot.
Analysis was based on the pairwise RST genetic distance matrix calculated on eight STR loci haplotypes of haplogroup Q samples from Panama and neighbouring countries (S3 Table). Panamanian provinces are indicated in bold. The neighbouring provinces of Herrera and Los Santos were pooled to reach the minimum number of four samples per considered area. The province of Darién was not considered, being represented by only one sample. Stress value: 0.251. In the inset, the physical map of Panama (from NASA Earth Observatory:
Fig 6
Fig 6. Combined analysis of Y-chromosome and mtDNA components.
Analysis was performed on the male individuals classified in the present paper for Y-chromosome haplogroups and by Perego et al.[3] for mtDNA haplogroups (S1 Table). (A): along the X-axis subjects are classified on the basis of the Y-chromosome component they belong to; on the Y-axis the coloured portions of the histogram indicate the percentage of each mtDNA component (e.g. almost the totality of males carrying a Native Y-chromosome haplogroup have also a Native mtDNA). (B): on the X-axis subjects are classified according to the mtDNA component they belong to; along the Y-axis coloured portions indicate the percentage of each Y-chromosome component. In the inset plot the Eurasian component has been split into North West Eurasian and South West Eurasian / North African components.

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    1. Hoopes JW, Fonseca Zamora O. Goldwork and Chibchan identity: endogenous change and diffuse unity in the Isthmo-Colombian Area In: Quilter J, Hoopes JM, editors. Gold and power in ancient Costa Rica, Panama and Colombia. Washington DC: Dumbarton Oaks; 2003. pp. 49–89.
    1. Cooke R, Ranere A, Pearson G, Dickau R. Radiocarbon chronology of early human settlement on the Isthmus of Panama (13,000–7000 BP) with comments on cultural affinities, environments, subsistence, and technological change. Quatern Int. 2013;301:3–22.
    1. Perego UA, Lancioni H, Tribaldos M, Angerhofer N, Ekins JE, Olivieri A, et al. Decrypting the mitochondrial gene pool of modern Panamanians. PLoS One. 2012;7:e38337 10.1371/journal.pone.0038337 - DOI - PMC - PubMed
    1. Aceituno FJ, Loaiza N, Delgado-Burbano ME, Barrientos G. The initial human settlement of Northwest South America during the Pleistocene/Holocene transition: synthesis and perspectives. Quatern Int. 2013;301:23–33.
    1. Ranere AJ, Lopez CE. Cultural diversity in Late Pleistocene/Early Holocene populations in Northwest South America and lower Central America. Int J of South Am Archaeol. 2007;1:25–31.

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Grant support

This research is part of the University of Pavia strategic theme "Towards a governance model for international migration: an interdisciplinary and diachronic perspective" (MIGRAT-IN-G) and received support from the Instituto Conmemorativo Gorgas de Estudios de la Salud (to JM, JMP), the Sorenson Molecular Genealogy Foundation (to UAP, NM, SRW), the Italian Ministry of the University: Progetti di Ricerca Interesse Nazionale 2012 (to AA, AT and OS) and Progetti Futuro in Ricerca 2012 (RBFR126B8I) (to AO, AA). provided support in the form of salaries for author [NM], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.