The Cayapas and their D4h3a mtDNA

The Cayapa people in Ecuador carry the very rare D4h3a mtDNA haplogroup in high rates in comparison to other Native Americans. See my previous post (D4h3a revisited).

When it was discovered in 1999, this variante was reported as the "Cayapa lineage", later it was found in other native groups, but at extremely low frequencies. This is the paper published back in 1999 that reported this unique Amerindian mtDNA founding lineage for the first time.

Cayapa territory. From O. Rickards, C. Martínez-Labarga, J.K. Lum, G.F. De Stefano, and R.L. Cann (1999)

A 2013 study reported that "The “Cayapa” lineage, D4h3a, was confirmed in the expected high proportion (22.5%)." Meaning that over 1 in 5 Cayapas carry this variant. It didn't find any European, Asian or African mtDNA among the natives.

A 2020 paper, citing Bravi, reported that "the highest frequencies of this lineage are found in Cayapa and Tehuelche populations, with a percentage of 25% of the total samples". Interesting link to the Patagonian people!

I found the extremely interesting thesis, by Bravi, 2005, (see it here - Spanish). In it, Bravi analyzed this new founding lineage. The frequency is high in certain groups, between 13% and 25% in the Fuegian Yamaná, the Patagonian Tehuelche, the Paraguayan Lengua, and the Cayapas. It is much Lower among the Araucanian people (Mapuche and Huilliche) of Chile and the Peruvian and Bolivian Quechuas (Image below is from the paper). This discontinuity in the distribution (Chile, Peru and Bolivia lie between the Ecuadorian Cayapas and the Amazonian Lenguas, and the Patagonian-Fuegian people) suggests that the original D4h3a migration was later overlaid by more recent arrivals with other mtDNA halpogroups diluting its presence.

Araucanization

The author of this thesis notes that the Patagonians probably had a higher ratio of this rare haplogroup before the Mapuche people crossed the Andes (pushed by Spanish conquest in the late 1500s), a process known as "Araucanization" (disliked by the Mapuche people, who feign they are original inhabitants of Argentina's Patagonia - they aren't, they are original people in Chile, not Argentina).

The paper states: "Since the beginning of the "Araucanization of the Pampas and Patagonia" in the 17th century, the cis-Andean Pampas-Patagonian populations interbred with "Araucanian" immigrants of trans-Andean origin. Given that some of the "Araucanian" fractions lack "Cayapa" lineages ... or possess them in low frequency... it is reasonable to interpret that their presence at such high frequency among the Tehuelches would not be a consequence of recent Araucanian female introgression (in the last 350 years) but rather a reflection of their ancestral condition. Although very high, the actual frequency of 26% for the “Cayapa” haplotypes among the Tehuelches, it must have been higher in the past, towards the end of the 16th century, before the massive influx of “Araucanians” from this side of the Andes."

The table above shows (left to right), the population, the sample size "N" the number of D4h3a found "Cayapa", the frequency "frecuencia" and the source.

The Cayapa people

Rickards et al, (1999), had noted that the Cayapas were "of distinct interest to geneticists, for at least three reasons. First, their oral traditions recount a migration from the western Amazon basin into the Andes (Barriga-Lopez 1987; Carrasco 1988) and then a flight from Ibarra into the lowland jungles to escape first Inca and finally Spanish enslavement (Barrett 1925). These movements suggest that historical events and forced acculturation have not significantly distorted their genetic identity. Second, although they have been exposed to disease epidemics brought by foreign contact, their population appears to have been stable during the past 250 years of colonial rule and has been slowly increasing to its current size of ∼3,600 individuals, without significant admixture from either European- or African-derived settlements adjacent to tribal communities."

The fact they migrated from the Amazon basin, suggests that this ancient lineage was present there, well inland, (not on the Pacific coast) and dispersed across the continent from that node.

The 1999 paper pointed out that even though the Cayapas spoke a Chibchan language, "the Cayapa appear closer to non-Chibchan speakers of South America than to representatives of the same language family in Central America, a classic case of discordance between genetic and linguistic data."

The Chibchans reached Colombia and NW South America around 2000 years BP, and are, relatively speaking, "newcomers". This is mentioned in a recent paper: "original “Chibchan homeland” in Central America is supported not only by mtDNA studies on present-day populations who speak Chibchan languages but also from linguistic observations, indicating that the isthmus region exhibits the highest diversity within this language family."

The Amazonian Cayapas probably adopted a Chibcha family language the same way that the Northern Tehuelche, Puelche and Pampa groups in Argentina adopted the Mapuche Araucanian language: trade and war, simplicity of the language helped spread the Mapdungun Mapuche language replacing the Chon of the Tehuelche groups. I agree, language and genes don't necessarily go together or imply a common origin and heritage.

According to a book published in 1919, the Cayapas lived an isolated lifestyle (it may have helped preserve their unique genetic marker), in 1641 the Spanish "Visitador", an official recorded that the tribe at Piñán consisted of 334 people. They were "antisocial like all savage tribes, and didn't live in villages. Instead the families built separate huts along the river banks, and seldom did so further inland. They moved frequently, and when cocoa cultivation replaces the jungle in which they live, they move away. They bury their dead in the middle of the dead person's former home, and move away.

Another book from 1876, states that "about 2,000 Cayapas, who still keep to the forests on the banks of the Rio Cayapas, holding carefully aloof both from the whites and the negroes... their language, which has also remained unaffected by Quichua and Spanish influences."

They built dugout canoes, from balsa wood tree trunks (pictured below - source).

An account published in 1894 says that the Cayapas river was 100 to 120 m wide (roughly 300 to 360 ft) and that "we met Cayapa boats all the time. They are light canoes, of elegant construction. On the sides they had whimsical mosaic-like designs painted with tars. They are maneouvered by an Indian using an oar 3 m long (10 ft), and by an Indian woman, who navigates from the stern with an other oar, very wide and short"

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025by Austin Whittall © 

D4h3a mtDNA revisited

Yu-Chun, lI et al. published a paper in 2023, that looked into the link between Native Americans (NAs) mitochondrial DNA (mtDNA) lineage D4h3a and the variant D4h3b which until now has been found only in East China and Thailand.

The authors noted that "D4h3 and its ancestor type D4h are relatively rare in contemporary populations (∼0.5%)" and estimated the age of the NA variant at 19,400 years (15.11 - 24.05 ky).

The interesting part is that they suggest that this haplogroup took a coastal route by sea from China to America, going through Japan's Islands. It didn't cross from Siberia and Beringia into America, walking.

"The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs."

The authors highlight that this is a genetic source that is outside of Siberia, which provided mtDNA (a matrilineal lineage) to Native Americans. They stress that it is an "additional ancestral source for the ancestors of NAs beyond Siberia", and that "although only contributed to a small proportion of the mtDNA gene pool of NAs (D4h3a) [it] would be important in complementing the whole picture of origination histories of early NAs."

Below is an image from this paper:

Given the location of the original D4h variant, on the coast of Northern China, the authors suggest that it could have dispersed along the Pacific coastal rim: "we speculate that D4h would have documented LGM and post-LGM dispersals along the eastern Pacific coast. This echoes well with the dispersal D4h3a along the Pacific coastal path when the ice-free corridor was closed. Similarly, Y chromosome C-L1373, which probably radiated in parallel with mtDNA D4h, has also been reported in South Koreans (http://koreangenome.org/) and the Nivkh, thus lending support to a coastal population expansion scenario initiated from northern coastal China. This, together with the Paleolithic cultural affinities along the Pacific, e.g., stemmed points, and the palaeoecological feasibility of maritime dispersals (e.g., kelp highway hypothesis) lends further support to the coastal route hypothesis of early NAs."

It is also found along the coastal people in South America. Stuart J. Fiedel (source) in 2017 wrote that "D4h3a is a relatively rare clade of haplogroup D... it was reported mainly from coastal peoples, including the Fuegians of southernmost Chile, the Chumash of southern California, and the Cayapa of Ecuador The 10,300-year–old skeletal remains from On Your Knees Cave in coastal Alaska belonged to a derived clade of D4h3a."

However, Fiedel says that "the recent distribution of this clade is “deceptive” and has nothing to do with a hypothetical coastal migration".

He bases this argument on the fact that the Anzick baby had D4h3a mt DNA, and is roughly 12,900 years old, but it was found in south-central Montana, far from the Pacific coast, and that other remains are also from the interior of the continent like the Hopewell remains found in the Klunk Mounds in Illinois, and that this variant has been found in extant people of Native American origin in Peru, Bolivia, Brazil, and Mexico.

I had posted about D4h3a back in 2014 and pointed out the same idea:

"We see that the D4h3a tends to have a coastal distribution along the Pacific Ocean from Canada to Tierra del Fuego: Canada, California, Ecuador, Southern Chile and Argentina.
The Yaghan, Alakaluf, Chono, Cayapa, Chumash and the man from On Your Knees Cave, all had this haplogroup.
They all built sea-going craft: rafts, dugout canoes, bark canoes and "sewn plank" canoes.
Other groups also built canoes or rafts; the Changos in Northern Chile, the Pericú, and the Aleuts, though we cannot tell if they also carried this rare haplogroup.
But, as we will see in our next post, it is also found quite far from the Western Coast: as it was detected in ancient remains from the Klunk Mound (Illinois) and in Shandong, China.
Furthermore, the Ainu people of Japan also built "lashed-canoes" -like the Chono and the Chumash (as well as dugouts), and they may have a link with the Amerindians."

It pointed out the Chinese connection, the coastal route, and the original Japanese people, the Ainus. The second post in that 2014 series reported the Klunk Mound remains with this haplogroup variant and proposed that "This haplogroup was widespread across America (Pacific coast and well across the Rockies) and became extinct among all native groups being replaced by the other more common haplogroups now found in those groups (A, B, C, D). These surely migrated later into America." It also suggested a back-migration from America to Asia.

Let's see what future investigations find.

My nest post will be about the Cayapa people of Ecuador.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall ©