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Decrypting the mitochondrial gene pool of modern Panamanians.

Perego UA, Lancioni H, Tribaldos M, Angerhofer N, Ekins JE, Olivieri A, Woodward SR, Pascale JM, Cooke R, Motta J, Achilli A - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America.

ABSTRACT
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.

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Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.Exact values are listed in Table S3A.
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pone-0038337-g005: Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.Exact values are listed in Table S3A.

Mentions: To increase the resolution of our analyses, we also evaluated entire mitochondrial genomes. A total of 18 novel A2af mitochondrial genomes were completely sequenced (Table 2): 16 were collected in Panama (listed in Table S1); two others, collected in El Salvador and Chile, were already available in the SMGF dataset [40]. Overall, when looking at the TMA of these 18 samples, 12 were from Panama, two from Costa Rica, two from Nicaragua, one from El Salvador, and one from Chile. The evolutionary history of their mtDNAs was inferred by a parsimony approach and compared to two other Mexican American mtDNAs (MA145 and MA148) reported by Kumar et al. [51]. The latter two samples were misclassified as A2s, but they actually carry a clear A2af mutational motif. Through the phylogeny of Figure 4, rooted with the (revised) Cambridge Reference Sequence rCRS [52], we found that the Nicaraguan sequence #07 did not cluster either with A2af, or any of the known Old World A2 branches [39]. Its presence allows us to better define the A2af basal motif (73@, 106–111d, 5460, 16360), while the reversion at np 64, previously thought to be ancestral to the A2af (Figure 3), characterizes a major sub-branch A2af1 together with two coding-region transitions at nps 6794 and 7960. On the other hand, the Nicaraguan sequence #07 most likely indicates an additional and very rare Native American A2af sub-clade, here named A2af2. Concerning the major cluster of the phylogeny, we were able to date the terminal maternal ancestor of haplogroup A2af1 at ∼17 ka ago. The complete sequence analysis confirms the main sub-branching (A2af1a) marked by the control-region mutation 89, already detected in the control-region network analysis, but reveals also an additional sister branch defined only by a coding region transition at np 11482, here named A2af1b. Surprisingly, a member of A2af1a is from Chile and was one of the two A2af mtDNAs from South America that were found in the SMGF control-region database, the other one was from Colombia. Considering the overlapping patterns of Native lineages (obtained in some recent papers [5], [49]) when comparing haplogroup frequency distributions from general-mixed populations to that of Native American tribes or communities, we proceeded to analyze the incidence of A2af among the 79,928 records (as of March 2nd, 2012) of the SMGF database (Table S3A). Figure 5 shows that this peculiar haplogroup is detected at low frequencies along the Pacific coast and the western side of the Andes, but with great incidences in lower Central America, having its highest peaks in Costa Rica (12.16%) and Panama (24.15%). Previously, A2's HVS-I haplotypes carrying the 6-bp deletion were observed almost exclusively in Central America (Table S3B), especially (frequency >10%) among the Huetars (56%) [36] and the Bribri (74%) [38] of Costa Rica, and in Panama among the Ngäbe (9–12%) [32][41] and the Kuna (53%) [41].


Decrypting the mitochondrial gene pool of modern Panamanians.

Perego UA, Lancioni H, Tribaldos M, Angerhofer N, Ekins JE, Olivieri A, Woodward SR, Pascale JM, Cooke R, Motta J, Achilli A - PLoS ONE (2012)

Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.Exact values are listed in Table S3A.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3366925&req=5

pone-0038337-g005: Spatial distribution of A2af and A2ad mtDNAs identified in general mixed populations.Exact values are listed in Table S3A.
Mentions: To increase the resolution of our analyses, we also evaluated entire mitochondrial genomes. A total of 18 novel A2af mitochondrial genomes were completely sequenced (Table 2): 16 were collected in Panama (listed in Table S1); two others, collected in El Salvador and Chile, were already available in the SMGF dataset [40]. Overall, when looking at the TMA of these 18 samples, 12 were from Panama, two from Costa Rica, two from Nicaragua, one from El Salvador, and one from Chile. The evolutionary history of their mtDNAs was inferred by a parsimony approach and compared to two other Mexican American mtDNAs (MA145 and MA148) reported by Kumar et al. [51]. The latter two samples were misclassified as A2s, but they actually carry a clear A2af mutational motif. Through the phylogeny of Figure 4, rooted with the (revised) Cambridge Reference Sequence rCRS [52], we found that the Nicaraguan sequence #07 did not cluster either with A2af, or any of the known Old World A2 branches [39]. Its presence allows us to better define the A2af basal motif (73@, 106–111d, 5460, 16360), while the reversion at np 64, previously thought to be ancestral to the A2af (Figure 3), characterizes a major sub-branch A2af1 together with two coding-region transitions at nps 6794 and 7960. On the other hand, the Nicaraguan sequence #07 most likely indicates an additional and very rare Native American A2af sub-clade, here named A2af2. Concerning the major cluster of the phylogeny, we were able to date the terminal maternal ancestor of haplogroup A2af1 at ∼17 ka ago. The complete sequence analysis confirms the main sub-branching (A2af1a) marked by the control-region mutation 89, already detected in the control-region network analysis, but reveals also an additional sister branch defined only by a coding region transition at np 11482, here named A2af1b. Surprisingly, a member of A2af1a is from Chile and was one of the two A2af mtDNAs from South America that were found in the SMGF control-region database, the other one was from Colombia. Considering the overlapping patterns of Native lineages (obtained in some recent papers [5], [49]) when comparing haplogroup frequency distributions from general-mixed populations to that of Native American tribes or communities, we proceeded to analyze the incidence of A2af among the 79,928 records (as of March 2nd, 2012) of the SMGF database (Table S3A). Figure 5 shows that this peculiar haplogroup is detected at low frequencies along the Pacific coast and the western side of the Andes, but with great incidences in lower Central America, having its highest peaks in Costa Rica (12.16%) and Panama (24.15%). Previously, A2's HVS-I haplotypes carrying the 6-bp deletion were observed almost exclusively in Central America (Table S3B), especially (frequency >10%) among the Huetars (56%) [36] and the Bribri (74%) [38] of Costa Rica, and in Panama among the Ngäbe (9–12%) [32][41] and the Kuna (53%) [41].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus