The mite on your face and the early peopling of America

Earlier this year I wrote a post about some tiny, minute mites that live inside the hair follicles of humans (and almost all mammals), the Demodex; in my post I suggested that they would be a useful tool to trace human migrations and the links between extant human populations. Yesterday I came across a very recent paper (M. Palopoli et al., 2001 [1]), whose findings I want to share with you in today's post.

The repulsive Demodex folliculorum mites

These mites are microscopic eight-legged creatures that are symbionts. They live on us, and we carry them with us and, as this pape [1] shows, the mites live for years on their hosts without moving. People get them from their immediate family environment (parents) or they may move between mates. As African Americans born in America carry the "A" clade which is mostly African and not found in Europe instead of the "D" clade which is very common in Europeans and white Americans, it is clear that these people still carry the mites that their ancestors brought with them from Africa to America when they were enslaved many generations ago.

Demodex and human migrations

The paper [1] detected "four deeply divergent lineages", which they named A, B, C and D. Each of these had a very high level of diversity, which implies that they have colonized their human hosts long ago, in other words "D. folliculorum has had a long association with humans."

Almost all Europeans belong to clade D clade (D is also found in all other regions and all other populations). A and B are common in Asia and Latin America. C is found in Africa and America, with a small share in Europe

An unexpected finding is that the high diversity found "suggest that D. folliculorum has not been through a severe population bottleneck in the recent past, despite evidence for a recent bottleneck among human populations...". This is interesting, as one of the typical arguments is that Amerindians and all non-Africans have gone through bottlenecks that reduced their genetic diversity, how could we go through a bottleneck and our symbionts remained unscathed? No explanation is given.

The genetic variability among Demodex is also interesting as shown in the paper's Table 1. Guess where diversity among Demodex is higest? Africa? No, actually it is lowest there. Asia? No. It is highest in America!:

• "h" Haplotype Diversity, that is the proportion of individuals carrying unique hapotypes, is highest in America and its value is 1 (i.e. 100% which means each individual sampled had a unique haplotype!).
• "π" Nucleotide Diveristy is highest in Asia and America with 0.06. This measures the differences between sequences. Africa's value is a bit lower 0.05.

So Demodex,unlike the usual Out of Africa theory, is different, it is more diverse out of Africa...

Nevertheless, the authors report that: "the observed patterns of mite diversity are consistent with an out-of-Africa model of human migration. As predicted by this model, the hosts of African descent harbored a very diverse sample of mite haplotypes..." [1]. They add in proof that as Africans have all clades present while "Only a subset of this variation was present on hosts of either Asian or European descent", these derive from an African origin. The revealing part is that Latin Americans have all four subsets too.

The authors put it this way: "One complexity that is not well accounted for by the out-of-Africa diversity model is that hosts from Latin America harbored a broad diversity of mites from all four divergent clades...". They attribute it to the slave trade that brought Africans to the New World, plus the European admixture with Native Americans.

Age

By using the average arthropod molecular clock, they estimate the duration of the mite relationship with humans: "... the time back to the most recent common ancestor of mitochondrial clades A, B, and C is more than 3 Mya, with a 95% highest posterior density (HPD) interval of 2.4–3.8 Mya. This date roughly corresponds with the origin of the genus Homo...".

They also consider that the clock may not be applicable to Demodex and add: "If such were the case for D. folliculorum, then the actual divergence times between lineages could be much more recent than found here. However, a rate 10 times as fast would still place D. folliculorum lineage divergences more than 200,000 y ago, before the estimated origin of modern H. sapiens."

This is a very interesting suggestion hinting at a pre-sapiens relationship. Could Demodex have arisen among our Homo erectus relatives? Let's look at the information in their Table S2 (supplemental information in [2]):

Table S2. Time to common ancestry of mitochondrial clades in D. folliculorum based on divergence in COIII

• D: 3.2 Mya CI 2.4 - 3.8 Mya
• B: 2.2 Mya CI 1.6 - 2.7 Mya
• C: 1.1 Mya CI 0.7 - 1.4 Mya
• A: 0.8 Mya CI 0.4 - 1.2 Mya

The oldest clade, D, is found all over the world, followed by B unique to Africa, Asia and Latin America. The next oldest clade C is found in Africa America and Europe but not in Asia. While the youngest clade A is unique to Africa, Asia and Latin America.

Of course the confidence intervals overlap but not entirely. Interestingly A and B have together, have a TCA of 3.2 Mya while A and B together have 2.8 Mya.

Can we make sense of this?

Let's take a look at the unrooted tree from Fig S.2 in [1]. It is quite clear that these clades are very distinct from each other.

Clade D has many branches, perhaps due to a bias in the sampling (most people sampled had a European origin) the second largest sample, Asians also had a large share of D followed by B, hence the quantity of branches on B is larger than that of A or C, which are mostly Africans and Latin Americans. So the branching cannot tell us much.

However the root of the tree as per Fig S.1. in [1], shown below, is located between A & B on one side and C & D on the other:

Looking at the outer circle (origin of the host's ancestors) and not the dots (place of birth of the hosts), a pattern emerges:

• A is roughly 1/3 each, African, Asian, Latin American
• B is mostly Asian, actually the "African" case has a Kenyan father and an Indian mother, who probably passed the mite to her child.
• C is mostly African
• D is mostly European

And when whe check the origin of the Asian populations (in the supplemental information), another pattern arises

Clade D Asians are roughly 50% Chinese and the others are Taiwanese (25%), and the balance from Nepal and Phillipines.

Clade B Asians are from Thailand 60% and India 40%. This does not include the "Kenyan" whose mother was Indian. In America it was found in a Colombian.

Clade A Asians are Indian and non-specified Asian 50 ⁄50.

The Latin Americans belonging to Clade A include a Brazilian,a Colombian, a Costa Rican and a Mayan. The first two may have African slave genes but the Mayan? Surely not.

A Hypothesis

Could A clade represent a very first ancient migration into America? It is not found among modern Europeans, only in Africa, America and Asia (Indians). As the Afro sample is actually Afro-American the data is scarce! But one could imagine Homo erectus carrying pre-Clade A mites into Asia from Africa.(Those that remained behind would evolve into Clade C in Africa). And their trek through Southern Asia (what will PNG mites tell us when they are sequenced?) and north into China (where they left no trace) and onwards into the New World.

Clade A then branched into Clade B in Asia in the southeastern region from India to Thailand, and it did not backflow into Europe or Africa but did find its way into America.

The C clade evolved in Africa and spread into Europe and (slave trade?) America. In Europe it was found in a Belgian (probable Congo admixture?).

D clade, the global one, found all over the world,in Asia a clearly Sino-Himalayan (Nepal, Taiwan, China), insular Asean (Phillipines) trait, and then in Africa, Europe and America. Could it represent the dispersal of Homo sapiens in Eurasia and later, white Europeans in America? It appears there in Peru and Mexico (Spanish conquest?) in Africa one is from Morocco.

A sampling including the mtDNA and Y Hg of the hosts plus a Papua New Guinea - Australia and Siberia sample would give a much better picture.

Source
[1] Michael F. Palopoli, et al., (2015), Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages doi: 10.1073/pnas.1512609112, doi: 10.1073/pnas.1512609112

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