Phylogenetic Systematics and the Origin of the Novel Coronavirus

Once thrown into purgatory by the present pandemic, I decided to teach myself population genetics and phylogenetic systematics. Now it so happens that the question of the origins of the novel coronavirus (SARS-CoV-2) responsible for COVID-19 essentially boils down to nailing the phylogenetic systematics of the novel coronavirus. It was not my intention to pursue this question at all. Instead, I was interested in developing a better understanding of what the hell was going on in molecular paleoanthropology; particularly with regard to Neanderthals, Denisovans, and other vanished populations. But hey, the great joy of learning is that you get so much else for free!

The modern way of thinking about systematics is due in great measure to the German entomologist Willi Hennig (1913-1976). Hennig saw action in the Soviet-German War, got wounded in 1942 and subsequently transferred to the quiet Italian front. In the summer of 1945 he was captured by the British Army and held for six months as a prisoner-of-war. It was during his captivity that he nailed down his most important contribution to systematics. He had revolutionized and modernized the field practically overnight. But his ideas would not penetrate the Anglo-Saxon world until the publication (in English) of Phylogenetic Systematics in 1966. In the meantime, biologists in the Anglo-Saxon world, particularly in America, led by Ernst Mayr, were sorting out the systematics of the lower taxa. Mayr (1942, 1963) had done most to clarify the process of speciation and therefore the origin of species — that Darwin had promised in the title of his famous monograph but failed to deliver. And he simplified the classification of hundreds of genera — largely by identifying geographic races or allopatric subspecies that that hitherto been wrongly classified as full species, thereby taming the uncontrolled proliferation of species. But Mayr and other workers in the Anglo-Saxon world, had no idea how to think about the origins of the higher taxa, as he confessed in Animal Species and Evolution (1963). Hennig would solve that problem in the most straightforward way possible.

Hennig’s core idea was that the main point of systematics was to forge a general reference system for the biological sciences. For this purpose, homology (the similarity of characters) was not only not useful but actually misleading. He argued that there is a natural system of classification intrinsic to the process of biological diversification. Specifically, he agreed with Mayr that new species arose through what he called species cleavage — by a single population splitting into two or more genetically isolated populations.

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He agreed with Mayr that the motor driving this fission was geographic isolation, understood broadly. But he went a decisive step further than Mayr and argued the same process of fission was responsible for the origins of the higher taxa as well: genera emerged from the fission of stem species further back in time; orders too emerged from stem species even further back in time, and so on and so forth, back to the very root of the tree of life. Phylogenetic systematics, Hennig argued convincingly, must classify monophyletic groups (all decedents of a single species) together, endowed with the hierarchical ordering induced by phylogenetic relationships (the family tree of the species if you will), and then you are done. In order to do so, the overall similarly of characters was irrelevant, he argued. Instead, in order to identify monophyletic groups what mattered was synapomorphies — derived characters shared by two of three taxa but not the third.


It is now well understood that the tree of life is not so neat after all. There are complications; particularly, at the root; where it seems that there may have been horizontal transfer of genes. Yet, by and large, Hennig’s ideas have prevailed comprehensively. No biologist today would care to challenge the classification of monophyletic groups together, or phylogenetic systematics as the general reference system of biology.

Hennig is to systematics what Einstein is to physics. It is a terrible tragedy that the only English-language biography of Willi Hennig that exists fails to engage properly with the intellectual revolution unleashed by his work. When molecular anthropologists talk of haplogroup this haplogroup that (such as those found exclusively in European or Asian populations), what they have in mind are synapomorphies of molecular markers. His influence has been extraordinary. Hennig’s influence is comparable to — if not more important than — Haldane, Fisher, Wright, Huxley, Dobzhansky, Mayr, and the other heavy weights of modern biology.

Enough preliminaries, Policy Tensor! Where did the damn pandemic originate?

The scenario of a deliberately lab-designed virus cannot be ruled out with complete confidence. There are four genera of coronaviruses (alpha, beta, gamma and delta). SARS-CoV-2, the coronavirus responsible for COVID-19 is a betacoronoravirus. Had it been engineered in a lab, whether with military purposes in mind, or inadvertently in the course of scientific investigations, one of the ‘reverse-genetic systems’ for betacoronaviruses would’ve been used. But the genome of SARS-CoV-2 is not derived from any of them. SARS-CoV-2 is therefore almost certainly of zoonotic origin. So which species did it jump to us from?

Here is where phylogenetic systematics comes in. Initially, the similarity of the SARS-CoV-2 genome with a coronavirus endemic in bats seemed to suggest that it originated there. However, molecular phylogenetic analysis by Zhang et al. (2020) suggest that it originated in Pangolins.

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Phylogenetic systematics of two coronavirus genera. Source: Zhang et al. (2020).




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