February 14, 2016

Patrilineages of Panama


Viola Grugni et al., Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0144223]


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.

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.


  1. The abstract makes mention of Panamanian mtDNA frequencies. Where can this been found?

    Also, I am curious how provinces like Bocas del Toro Colon (with such a high percentage of Anglophone/West Indian African descendants) have such low SSA Y-DNA frequencies. I was in Panama a few weeks ago and the aside from the shockingly low SSA Y-DNA frequency the statistics seem quite representative.

  2. The answer to the first question is probably as easy as following the referenced link (it's open access: it costs nothing to read online or download for home-printing). Reading the intro, we soon reach the relevant note #3 that sends us to Perego et al.: http://dx.doi.org/10.1371/journal.pone.0038337

    Regarding the second question, I initially read the bar you mention as belonging to the aboriginal nation Ngabe-Buglé but the same data is clearly labeled Bocas del Toro in table 3, so unsure. Perego 2012 did differentiate both samples more clearly, showing strong African matrilineal ancestry in Bocas, Colón and Darién, although in general the Native American one dominates through the country, with almost no European matrilineal ancestry at all.

  3. There's also a more detailed note on the African component:

    The sub-Saharan African component (5.9%) is characterized by the sub-Saharan African sub-clades of haplogroup E (in particular, E-M2) [78, 83, 84]. With the exception of the high frequency (44.4%) observed in Darién, its incidences range from 5% to 10% in Chiriquí, Herrera, Los Santos and Panamá provinces where during the Colonial period thousands of slaves were employed and where, before and after emancipation, they dispersed through the countryside. The sub-Saharan African component was not observed in Bocas del Toro, Veraguas, and Coclé, (Fig 1), three provinces which lay outside the trans-isthmian axis between Old Panama and the Caribbean ports of Colón that in different periods harboured important numbers of sub-Saharan African peoples. Although referred to a small size sample, the exceptionally high frequency of this component in Darién could represent the legacy of bands of escaped slaves, known as Cimarrones, who were established in Darién during the latter part of the 16th and early 17th centuries and whose descendants still live along the rivers and in the coastal zones of this province.

    So I read that the authors attribute the high frequency of African Y-DNA in Darién to rebel ex-slaves rather than to slaves proper, whose patrilineal legacy seems low, although (via Perego) the matrilineal one persists. There's a strong imbalance among these two lines because the Y-DNA is mostly European (or Native among the surviving original peoples), with a much lesser role for Native American one, while the matrilineages are instead mostly native, with a secondary role in some districts for African ones. It's possible that people actually look (and display autosomal DNA) more European that a simple 50-50 mixture if male immigration arrived in several waves, reinforcing its influence once and again but always from the patrilineal side, as has been documented at least in Caribbean Colombia using the X-chromosome as guide. This pattern is however not extrapolable to most other male-biased migrations through the World because in most cases the mtDNA is a much better approximation to autosomal ancestry than Y-DNA, when they conflict each other, suggesting single instance male-biased sweeps instead, rather than sustained, repeated immigration as we can see in some parts of America.

  4. Thanks for the clarification. An autosomal study would be interesting. Panama's autosomal SSA contribution is considerable, just based on the phenotypes of the majority of the people.

    Now these are simply my observations, but:

    - The majority of Panamanians are triracials, with a slight predominance of Afro and native elements overall
    - The percent of visibly of Euro-Native mestizos is MUCH lower than the census states. It's probably equal to the amount of mulatto-ish people
    - The provinces of western Coclé, Herrera, Los Santos, Veraguas and Chiriquí are probably the "whitest" parts of Panamá, but far from white
    - Panamá City has a little bit of everything, but less pred. native looking people
    - Colón is pred. Afro (both Antillean and colonial)
    - Mulatto-ish (but still pretty triracial) people can be found all along the Pacific coast of Panamá
    - Most of the area east of Tocumen Airport is pred. native or Afro-native
    - Most of the mountainous areas are pred. Native

    1. Sure, it'd be interesting but I must say that Panama or in general Latin America is better researched than Latin Europe, where there is institutional reluctance to study these matters (particularly bad is the case of France).

    2. BTW, while I'm not aware of any autosomal study of Panama specifically, there are several about other nearby areas, for example this one about Caribbean genetics, with data from Honduras, Colombia, Mexico, etc. which may well be extrapolable, even if not in the fine detail at least in the general idea.

  5. How many of the mtDNA U in the Perego et al study were U6a?

    1. No idea she only talks of generic U. Maybe in the supp. materials? But look them up yourself, OK?

      (PS- Sorry but the comment languished accidentally in pre-moderation queue).

    2. Well, "he". Perego is Ugo.

  6. Yes I have read through that study a few times. To be honest though, the ethnogenesis of the Belize, Costa Rica and Panamá are more complicated than El Salvador and the Pacific side of Central America.

    I have seen a couple Costa Rican autosomal studies. The Central Valley was more West Eurasian than the rest of the country, with Guanacaste (formerly part of Nicaragua) and Limon (the main concentration of Jamaican descendants) being more SSA and Native.


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