Today there was a short article in Discover on a paper published last spring on the models for the settling of Madagascar. I didn’t pay too much attention when the paper came out for two reasons. First, it focused on Y and mtDNA, and I’ve been playing with Malagasy autosomes. Second, it seemed a ridiculously brutal computational attack on a question which seems to have a straightforward intuitive explanation: yes, Madagascar was settled by a small founding group. With hindsight I may have spoken too soon, or passed judgement too hastily. Looking at the paper the explicit model building of demography does still seem like overkill, but they obtain some important precision here. The phylogenetics and the archaeology align nicely.
Though the authors of the article talk about future directions, I think we will find that the Malagasy originate from a small group of Malayo-Polynesians who did find themselves stranded on Madagascar (later to absorb African admixture). This is not controversial. Rather, when I came to this position with enough solidity I began to look at the cultural anthropology of Madagascar. In particular, what do the Malagasy remember of about their own past in Southeast Asia? From what I could tell (the literature on Madagascar is not too rich in English) the Malagasy don’t recall much. This is important, because it tells us just how fragile oral memory can be when you have a major geographical and demographic rupture. The influence of Sanskrit is apparently evident within Malagasy, attesting to the early period if Indic influence in Southeast Asia. But the Malagasy are not part of Dharmic or Islamic civilization. They are the people forgotten by time. I think what little we know about the Malagasy can shed on light memories and legends preserved by peoples who we suspect were migrants into the only homelands they knew (e.g., how could the Aryans be exogenous if they didn’t record any memory of lands before India?).
A month ago I posted the genetic results of a Malagasy individual of Merina identity. Today I post those for someone of Betsileo heritage. All the technical details are the same. You can find all the ADMIXTURE and PCA files here.
This genotyping was paid for by readers. I’ll update the post with the names of those who contributed below the fold later. If you contributed but don’t want to be named, email me at contactgnxp -at- gmail -dot- com, and I’ll leave you off the list.
I’m going to address two points in this post. The next possible target for getting an undersampled population, and the Malagasy results.
First, lots of great submissions in regards to populations which are undersampled. Some of them are actually already in the data sets. For example, the Burusho and Kalash are in the HGDP. There has been a major dump of data from the Americans recently as well. Zack Ajmal at HAP has the most systematic description online about where to find these that I know of. Additionally, I’m looking for stuff which is interesting where N = 1 would make a difference. I think that was the case for the Tutsi sample, as well as the Malagasy. When you have no prior information, adding one data point is notable. Obviously I can’t afford the money, time, and energy, required to get a good representative sample from a given region. Though I hope researchers who have a gusher of grant money might look at the above thread for ideas.
I think the next population to look for is someone with Ainu ancestry. This is easier said that done, so I need to think about it (both because of dilution and the language barrier). But then again, the Tutsi and Malagasy requests had a much more positive and faster turnaround than I had expected. So I’m not going to get all down about the likelihood.
Last week I begged for a Malagasy genotype. I didn’t quite get that, but I got the second best thing: a part Malagasy-genotype. I decided to take it for a spin.
But first some preliminaries. Here’s what we know about this individual (or what this individual knows):
– 25% French (paternal grandfather)
– 18.75% West African? 6.25% French? (paternal grandmother French Antilles)
– 19% Indian Muslim Bohras from Bombay + 6.25% Malagas, Sakalava tribe, royal family of Mahajanga (maternal grand -father)
– 25% Malagasy (Sakalava, maternal grandmother mtDNA haplogroup M23)
This is a very mixed individual in terms of ancestry. As for the Malagasy people, we know both a lot and a little about them. They’re a hybrid population, more or less, of Austronesians with a very close connection to the to the Dayaks of southern Borneo. I have hypothesized that these Austronesians were part of a circum-Indian ocean trading network which was marginalized by the rise of Islam in the second half of the first millennium. Such an early date would explain why the Malagasy seem to have been only lightly touched by Indic cultural influences, let alone Islamic ones. There is also the African component to their ancestry, which is more prominent in the lowland populations to the west of the island of Madagascar. The Sakalava are a somewhat more African group (as opposed to the Merina of the eastern highlands, who are more Austronesian).
Below are some results from ADMIXTURE and PCA generated with EIGENSOFT. Most of the PCA plots were not too useful, because I didn’t fine-tune the populations ahead of time too much (this is a first pass), so I didn’t post them. The ADMIXTURE runs are those which seem highly informative to me. There were three data sets into which I merged the part-Malagasy individual:
– #1, A Southeast Asian focused one, using mostly the Pan-Asian Consortium populations
– #2, An Asian focused data set which used the HGDP
– #3, An African focused data set which used the Henn et al. populations as well as some HGDP ones
I would like to throw out the word that I am looking for a person with Malagasy ancestry for the African Ancestry Project. To my knowledge there are no thick marker autosomal analyses of the Malagasy people. After my recent exploration of Southeast Asian genetics I think even one individual would be highly informative.
As usual I would guarantee that these data are entirely private, and I do not share it with anyone. But in this case I would like to make an exception and stipulate that Joseph K. Pickrell, a graduate student at the University of Chicago, would also be very interested in access to a Malagasy genotype for the purposes of research. Since this is an undersampled population the marginal returns to a Malagasy genotype would be enormous for science, a public good rather than just a private gain.
Also, I am still looking for a Tutsi genotype so that I can ascertain the origin of this population.
Please contact me at africanancestryproject -at- gmail -dot- com.
In my post on Empires of the Word I observed that quite often the written record is silent on many matters which only language or genes tell us must have occurred. The Indo-Aryan character of the dominant language on the island of Sri Lanka seems to be a geographical anomaly in the least, but perhaps most strange of all is the existence of a language and ethnic group of clear Southeast Asian provenance on the island of Madagascar. To my knowledge Arab, Persian and South Asian sources do not record the existence of a prominent Southeast Asian maritime diaspora which spanned the Indian ocean in the years before 1000 A.D., but we know that it did exist. A new paper on the genetics of the island of Comoros fleshes out another piece of the puzzle, Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean:
Yesterday I pointed to a new paper, Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. P. vivax is the least virulent of the malaria inducing pathogens, and it is presumably responsible for the fact that the Duffy antigen locus is one of the more ancestrally informative ones in the human genome. In most of Eurasia the the Duffy negative null allele* is present at very low frequencies, less than 5%, and often simply absent. In contrast, in Sub-Saharan Africa the Duffy negative variant reaches frequencies as high as 95% in West Africa, and and 90% in many other regions. In North Africa and the Middle East the frequencies are intermediate, likely due to the necessity for local adaptation to malaria in many regions, and the historical introduction of the Duffy negative allele via the slave trade.
Before genomics, looking at the Duffy locus was one simple way that geneticists ascertained the proportion of white admixture in the African American population. The Duffy negative allele was nearly absent in Europeans, and present in frequencies of ~95% in West Africa. Therefore, the ~70% frequency in African Americans indicates what we know from other sources, a substantial minority European contribution to their ancestry. The people of Madagascar are similar insofar as they are a byproduct of admixture between African and non-African populations. The source of the non-African ancestry is rather easy to determine, unlike most African countries Madagascar has one language, Malagasy, and it is of the Barito family of languages. Aside from Malagasy the Barito languages are spoke only in a small region of southern Borneo in Indonesia. There are other aspects of the Malagasy culture which make their Southeast Asian provenance clear. The photo above is of Andry Rajoelina, the current President of Madagascar. Two aspects of his visage are salient, his youth (he used to be a disk jockey!), and the fact that his features do not seem typical Sub-Saharan African. Many of the leaders of Madagascar, including the former royal family, are from the highlands where Asiatic features and folkways are more prevalent.
But there is also a clear African component to the Malagasy, more obvious among coastal populations, but also possibly dominant in a genetic sense in terms of proportion to the Asian according to research using uniparental markers. An analysis of Y lineage Fst genetic distances suggests that the Malagasy are, on the whole, somewhat closer to East Africans than to people from Borneo. I stipulate on the whole because as implied above there seems to be regional variation, which Southeast Asian ancestry and culture least hybridized with a Sub-Saharan African in the central highlands, likely for ecological reasons.