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. 2012;7(6):e38337.
doi: 10.1371/journal.pone.0038337. Epub 2012 Jun 4.

Decrypting the Mitochondrial Gene Pool of Modern Panamanians

Free PMC article

Decrypting the Mitochondrial Gene Pool of Modern Panamanians

Ugo A Perego et al. PLoS One. .
Free PMC article


The Isthmus of Panama--the narrow neck of land connecting the northern and southern American landmasses--was an obligatory corridor for the Paleo-Indians as they moved into South America. Archaeological evidence suggests an unbroken link between modern natives and their Paleo-Indian ancestors in some areas of Panama, even if the surviving indigenous groups account for only 12.3% of the total population. To evaluate if modern Panamanians have retained a larger fraction of the native pre-Columbian gene pool in their maternally-inherited mitochondrial genome, DNA samples and historical records were collected from more than 1500 volunteer participants living in the nine provinces and four indigenous territories of the Republic. Due to recent gene-flow, we detected ~14% African mitochondrial lineages, confirming the demographic impact of the Atlantic slave trade and subsequent African immigration into Panama from Caribbean islands, and a small European (~2%) component, indicating only a minor influence of colonialism on the maternal side. The majority (~83%) of Panamanian mtDNAs clustered into native pan-American lineages, mostly represented by haplogroup A2 (51%). These findings reveal an overwhelming native maternal legacy in today's Panama, which is in contrast with the overall concept of personal identity shared by many Panamanians. Moreover, the A2 sub-clades A2ad and A2af (with the previously named 6 bp Huetar deletion), when analyzed at the maximum level of resolution (26 entire mitochondrial genomes), confirm the major role of the Pacific coastal path in the peopling of North, Central and South America, and testify to the antiquity of native mitochondrial genomes in Panama.

Conflict of interest statement

Competing Interests: NA and SRW are employed by a commercial company: This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials.


Figure 1
Figure 1. Distributions in Panama of the 1565 samples analyzed in this paper.
Bars show both place of collection and terminal maternal ancestor (TMA) origin. This means the origin of the last known ancestor on the maternal side of the recorded pedigree.
Figure 2
Figure 2. Spatial frequency (%) distributions of mtDNA haplogroups among the analyzed samples.
Figure 3
Figure 3. Network of A2af control-region haplotypes from Panama subdivided according to their geographic origin.
The mutations on the connecting branches refer to the (revised) Cambridge reference sequence (rCRS) . Markers of different clusters are in colors. Mutations are transitions unless the base change is explicitly indicated. Insertions, deletions and heteroplasmic mutations were excluded, with the notable exception of the 106–111 6 bp deletion. The size of each circle is proportional to the haplotype frequency and geographical origins are indicated by different colors. Coalescence ages of A2af and A2af1 are also reported using the control-region mutation rate reported by Soares et al. .
Figure 4
Figure 4. Phylogeny of complete mtDNA sequences belonging to haplogroups A2ad and A2af.
The tree was rooted by using the reference sequence rCRS that is indicated for reading off sequence motifs. All sequences are new except for #04, #25 and #26 (Table 2). Mutations are shown on the branches; they are transitions unless a base is explicitly indicated. Suffixes indicate: reversions (@), transversions (to A, G, C, or T), indels (ins, del), gene locus, synonymous or non-synonymous changes. Recurrent mutations within the A2 branch are underlined. Any length variations in the C-stretch between nucleotides 303–315 and 16184–16193 were disregarded. Additional information regarding each mtDNA is available on Table 2. Coalescence times were calculated by converting into years the averaged distance (rho, in blue) and the maximum likelihood (ML, in green) estimate, calculated by considering all the substitutions on the entire mitochondrial genome.
Figure 5
Figure 5. Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.
Exact values are listed in Table S3A.

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