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“There is a great difference of opinion among ethnologists who have seen these Negritos, as to the race to which they belong”, S. Kneeland writing in 1883 for Science [1]. He further adds that “they are not far above such an ape as might have been the ancestors of man, with the cerebral convolutions of the orang, the skull of a chimpanzee, the limbs of a gorilla, and the chest of a giboon – except that he can make a fire and cook his food.”

S. Kneeland didn’t have the necessary tools yet during his time to make any distinction other than looking at bones. Now, Delfin and his co-authors writing in the European Journal of Human Genetics visit the Filipino Negritos (and the Filipinos’ ancestry) using the nonrecombining region of the human Y chromosome (NRY).  This is also the same group which studied the Filipino mtDNA (see previous blog post).

Courtesy: NPG, 1883

The team observed 16 Filipino ethnic groups.   They classified Aetas from Zamboanga and Bataan, Agta, Iraya, Ati, and Mamanwa as the Negrito groups while the non-Negrito groups are composed of  Ivatan, natives of the Cordillera Autonomous Region (CAR), Bugkalot, Kalangoya, Tadyawan, Tawbuid, Hanunuo, Surigaonon, Manobo, and Maranao. Why they use these groups from over 170 ethno-linguistic group in the Islands is not clear from the paper but I am assuming that these groups are particularly intact with respect to the characteristics of the population.

What are the findings reported in this paper?

1.  There is NO SIMPLE dichotomy between Negrito and non-Negrito Filipinos based on NYR.  Although the paper says, “the Negritos show an old substrate (haplogroups C-RPS4Yand K-M9) suggesting ancient shared ancestry.” But these are also present in some non-Negritos.

2. The authors saw 3 clusters based on correspondence analysis  –  one associated with haplogroup K-M9 (Aeta of Zambales and Bataan, and Hanunuo), one associated with haplogroups O-M7, O-M110, and O-M134 (Ati,Kalangoya, Tawbuid, and Tadyawan), and one with the rest of the haplogroups. The authors add, “There was also no tendency for the three clusters of FE groups to reflect geographic relationships, with the exception of the three southern groups (Surigaonon, Manobo, and Mamanwa), all from northern Mindanao, that cluster together.”

3.  14 Ethnic Filipino groups in the sample share major haplogroups O-M119,O-M110, and O-M122 regardless of geographic proximity while 9 of these groups that are geographically close, share haplogroups C-RPS4Y and KM9.  The authors said, “These patterns seem to reflect different histories for these haplogroups and suggest that C-RPS4Y and K-M9 are likely to be older, while O-M119, O-M110, and O-M122 would have spread more recently.”

4. “The major O haplogroups appear to influence the association of the majority of FE groups with East Asian and Southeast Asian groups and, to a lesser extent, with Melanesian and Polynesian groups.”

Networks for Y-SNP haplogroups C-RPS4Y and K-M9. Courtesy: NPG, 2010

5. The haplogroup C-RPS4Y tell quite a story: The Ivatan, Manobo, and Surigaonon and  the Ati and Mamanwa haplotypes were associated with Southeast Asian haplotypes on one branch and on another branch,  one Ati and all Agta haplotypes were associated with indigenous Australians from Arnhem Land, one Fijian, and several Southeast Asians. There seems to be an association between the Australians aboriginals and the Agta.

6. And some more complicated story with the haplogroup K-M9: Iraya, Mamanwa, Maranao and Manobo haplotypes clustered with Southeast Asian and Melanesian haplotypes; Surigaonon and Manobo haplotypes clustered with Southeast Asian, Melanesian, and Fijian haplotypes; All Ati haplotypes were clustered with one Hanunuo haplotype; two Aeta groups and the Agta haplotypes were associated with Hanunuo and Southeast Asian haplotypes; two Aeta groups haplotypes were associated with one Polynesian, one Fijian, one Melanesian, and six Australian haplotypes; and two Aeta groups and the Agta haplotypes were clustered together.

What’s the take home? It’s complicated!

1. The haplogroups C-RPS4Y (~13 245 Y) and K-M9 (~13 608 Y) are founding lineages in the Asia-Pacific region, while O-M119, O-M110,and O-M122 are associated with the Austronesian expansion (5-6 kY).

2. There seemed to be a link between C-RPS4Y and K-M9 haplotypes of some Negrito groups and indigenous Australians.  But the authors could only infere how.

Maybe Kneeland is suprisingly somewhat correct.  He says,

“It seems to me that this people, the Negrillo of Dr. Charles Pickering (1848), and by him, and, after him, by Semper and Müller, classed as Papuans, – or, as Wallace maintains, of Asiatic origin, like the Andaman-islanders, – must be regarded as essentially Papuans, – Asiatic Papuans.”

Which leads me to ask: Is there a link between the archaic hominin from Denisova and these Filipinos? In a recent Nature article, this hominin contributed genes to the ancestors of present day Papuans and Melanesians [3].

Yes, it’s complicated.


[1] KNEELAND, S. (1883). THE NEGRITOS OF LUZON Science, ns-1 (15), 415-417 DOI: 10.1126/science.ns-1.15.415

[2]  Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, Halos SC, Gunnarsdóttir E, Myles S, Hughes DA, Xu S, Jin L, Lao O, Kayser M, Hurles ME, Stoneking M, & De Ungria MC (2010). The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European journal of human genetics : EJHG PMID: 20877414

[3] Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161


(a) Samuel Kneeland, a naturalist, is born in Boston, Massachusetts and was in the Philippines in the 1870’s.