Today's post will explore the pathogens that cause Malaria, and how they reached America.
A paper published in April 2021 (Population genomic evidence of a Southeast Asian origin of Plasmodium vivax J. Daron, A. Boissière, L. Boundenga, B. Ngoubangoye, S. Houze, C. Arnathau, C. Sidobre, J.-F. Trape, P. Durant, F. Renaud, M.C. Fontaine, F. Prugnolle, V. Rougeron. bioRxiv 2020.04.29.067439; doi: https://doi.org/10.1101/2020.04.29.067439 Now published in Science Advances doi: 10.1126/sciadv.abc3713) proposed a Southeast Asian origin (below we will see two other papers, one, suggesting an African origin, the other an Asian one.)
The paper includes the following phylogenetic tree. Notice how America forms one of the three branches, with two separate clades, and the other two branches are: Most Asian countries, and India, Madagascar and Africa (perhaps linked by trade across the Indian Ocean).
For America the authors suggest two possible explanations: "Across the Americas, P. vivax strains were structured in two distinct ancestral populations (Fig. 3, B to D). This is consistent with two putative evolutionary scenarios of the parasite in America. The first scenario hypothesizes that both ancestral populations originated from the isolation between Amazonian and non-Amazonian populations, after a single introduction during the European colonization in the 15th century. In the second scenario, two distinct waves of introduction occurred from the same or from different sources. Disentangling these two hypotheses will require more samples and statistical population genetic modeling."
The original online publication in Bioarxiv included text that was ommitted in the Science publication:
"Across the Americas, P. vivax strains were structured into two distinct ancestral populations. This is consistent with recent findings suggesting two successive migratory waves responsible for the introduction of P. vivax in America (37). The first wave has been suggested to occur following a reverse Kon-Tiki route, with a long-range oceanic crossing from the Western Pacific to the Americas. The second wave, has been recently attributed to an introduction by the European colonization of the Americas during the 15th century, and represents the major genetic contributors to the New World P. vivax lineages."
The paper cited as (37) is the following: Rodrigues, P. T., Valdivia, H. O., De Oliveira, T. C., Alves, J. M. P., Duarte, A. M. R., Cerutti-Junior, C., ... & Ferreira, M. U. (2018). Human migration and the spread of malaria parasites to the New World. Scientific reports, 8(1), 1993.🔓
The paper analyzes the genetics and relationship between the different lineages of malaria-causing parasites. It says it originated in Africa ("Plasmodium falciparum is currently hypothesized to have originated from a lateral transfer from gorillas to humans in Western Africa between 10,000 and 100,000 years ago" and spread globally.
In the case of American variants it notes that: "The TMRCA estimates for SAM populations of P. falciparum (37,002 years; 95% HPD interval, 21,385–56,606 years before present) and P. vivax (52,149 years; 95% HPD interval, 29,896–60,659 years before present) indicate that the hypothetical most recent common ancestor of New World malaria parasites largely predates the first human migrations to the continent."
Ah! the question of the arrival in America makes them say that being 37 or 52 ky old means that they "predate the first human migration" into America. Why not accept the facts, and suppose that there were humans in America 37-52 ky ago and that these parasites evolved there, in America?
They continue the analysis looking at the African variant (AFR) and point out that "Moreover, these estimates are rather similar to those obtained for populations of AFR P. falciparum (35,384 years; 95% HPD interval, 21,101–54,974 years before present) and P. vivax (41,685 years; 95% HPD interval, 28,630-57,563 years before present). Therefore, skyline analysis and TMRCA estimates argue against a severe population bottleneck associated with the recent malaria parasite migration to the Americas; to the contrary, SAM lineages appear to have retained much of the diversity that preexisted in their ancestral populations." Which is interesting: the parasite didn't have a bottleneck like the one that is always argued, happened to the humans that peopled America -and carried it there. And also, that the American variant is as old as the Old World African clade.
The paper concludes that slave trade and European navigation brought malaria parasites from Africa to America, and from India and Asia via Madagascar, and South Africa. There may have been a transpacific route from Asia to Central America. They also note that Melanesian variants could have also reached America in pre-Hispanic times: "We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans... While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax."
However, the great diversity observed in America surprises them and they try to explain it as sampling errors or, the successive waves from different places: "The lack of an apparent bottleneck in South American populations of P. falciparum is somewhat surprising. Not only parasite migration events, but also selective sweeps induced by large-scale antimalarial use in more recent years could have drastically reduced parasite diversity in this continent. We argue, however, that the current diversity levels have originated from the very many introductions of this parasite into the continent over centuries, from several different source populations in Africa. The substantial differentiation between present-day SAM and AFR lineages of P. falciparum likely results from the fact that we have not sampled all potential AFR source populations (Supplementary Fig. 15) or all P. falciparum subpopulations currently found in the Americas."
But looking at the phylogenetic tree from this paper, below, we see that the American (and the Atlantic rainforest simian variety) clades clearly are nested within the SE Asian and Melanesian clades, while the African and some other Asian clades form a different branch (with some -few- American samples, these surely came with the Slave Trade.
Polynesian - Melanesian migration?
As mentioned above, this paper also mentions the transpacific route and also adds: "Carter has speculated that a relapsing parasite such as P. vivax might have survived long-range, pre-Columbian oceanic crossings from the Western Pacific to the Americas through a reverse Kon-Tiki route." citing: Carter, R. Speculations on the origins of Plasmodium vivax malaria. Trends Parasitol. 19, 214–219 (2003).🔒
Carter suggests a South Asian origin for P. vivax" from where it moved aroun 1 million years ago into Europe and Africa, surviving in warm, humid places until humans were infected some 10 to 20 ky ago.
Closing Comments
There are three separate clusters, or branches on the malaria pathogen tree: Africa, Asia, and America. If the parasites originated in Asia and moved to Africa 20-50,000 years ago (or vice versa) and originated a seprate branch there, it took 20 to 50 ky to acquire its present diversity. So, why are we expected to imagine that these same pathogens came to America barely 400 years ago and suddenly evolved into another separate branch with equally enormous diversity?
Perhaps the pathogens reached America 50 ky (or even 100, or 200 ky earlier, via a migration from Asia by infected Neanderthals, Denisovans, or even older hominins like H. erectus then they diversified there, in the New World, where they infected monkeys in the Brazilian rainforests.
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