The Red Ape Returns & Willi Hennig Superstar!

20 years ago Jeffrey Schwartz published The Red Ape, making the case that humanity's closest extant relatives within the animal kingdom were orangutans, not chimpanzees. This was contemporaneous with the media hullabaloo around African Eve, so either you could say that Schwartz's timing was perfect, or it was disastrous. Certainly he was swimming against the spirit of the age, and I recall assuming that The Red Ape was a piece of crankery when I first heard about it, its thesis was so outrageous. But historically the idea that humanity descends from Asian apes is less anomalous, and many scientists of Charles Darwin's time did not agree with his model of an African origin for humanity. The skepticism of this idea persisted deep into the 20th century, one reason that Raymond Dart's discovery of Australopithecus africanus was met with less interest than we might assume. Only with further discoveries of numerous early hominids in East Africa by luminaries such as Richard Leaky and Donald Johanson did our probabilistic framework shift so that the unearthing of a wide range of extinct African apes elicit excitement. After all, one of these (or many) are likely to be the possible precursor to the most important species which walks the earth!

But Jeffrey Schwartz is not deterred, and continues to throw stones at the idols of the age. A few years ago he came out with a second issue of The Red Ape. Today I noticed that he has also coauthored a new paper putting forward the model that orangutans are our closest relatives, Evolution of the second orangutan: phylogeny and biogeography of hominid origins:

Our analyses support the following hypotheses: (1) the living largebodied hominoids represent a monophyletic group comprising two sister clades: humans + orangutans, and chimpanzees (including bonobos) + gorillas (collectively, the African apes); and (2) the human–orangutan clade (dental hominoids) includes fossil hominids (Homo, australopiths, Orrorin) and the Miocene-age apes Hispanopithecus, Ouranopithecus, Ankarapithecus, Sivapithecus, Lufengpithecus, Khoratpithecus and Gigantopithecus (also Plio-Pleistocene of eastern Asia). We also demonstrate that the distributions of living and fossil genera are largely vicariant, with nodes of geographical overlap or proximity between Gigantopithecus and Sivapithecus in Central Asia, and between Pongo, Gigantopithecus, Lufengpithecus and Khoratpithecus in East Asia. The main massing is represented by five genera and eight species in East Asia. The dental hominoid track is spatially correlated with the East African Rift System (EARS) and the Tethys Orogenic Collage (TOC).

Monophyletic simply means that of the set of terminal branches all descend from a common ancestral node. To the left you see the blue highlighting a monophyletic clade: reptiles + birds. Reptiles themselves are not monophyletic, because the class excludes birds, who are descended from the common ancestor of all reptiles. In fact, birds cluster together with crocodiles, alligators, etc., as a monophyletic clade! We don't need molecular biology to know this, it is clear from morphological characters, and has long been so. In fact that's why the hypothesis emerged and became dominant that birds are the last extant lineage of theropod dinosaurs long before the rise of molecular techniques (birds can be shown to be closely related to crocodiles even without the extraction of biological material from fossils).

Though most people do not know what a monophyletic lineage is, the intuition that chimpanzees are our closet relatives in the animal world has sunk deep into the public consciousness. So deeply that Jared Diamond wrote a book which was titled The Third Chimpanzee, implying that humans should be viewed as the third chimpanzee species after the common chimp and the bonobo. The use of these two species as analogs to our own lineage has resulted in warring conceptions of human nature. The authors of The Demonic Males looked to common chimps as an echo of the human ancestor and primal condition, while others suggest bonobos might tell us more. Focusing on orangutans would change the whole playing field and upturn a great deal of reasoning which is predicated on our closer connection to chimpanzees (as well as gorillas).

Figure 2a from the paper, to the left, illustrates the main result. I'm not showing you the rest because it relates to Miocene apes and such which I don't know much about. When it comes to fossils Kambiz Kamrani or John Hawks might add some value, but I certainly won't. The way the cladogram was generated is pretty easy to communicate though, they just looked as informative morphological characters (e.g., teeth) and used cladistic methods to generate the most parsimonious tree. The principle of parismony is of course smiled upon in science, and in the context of cladistics what you are trying to explain are synapomorphies, shared derived traits.That is, traits which two lineages exhibit because of common descent, but which other lineages do not because they do not share common descent from the ancestor which originated that trait. Not all traits are created equal when it comes to giving us information which allows one to distinguish between clusters of species which form clades, who we presume emerged over evolutionary time in a contingent manner.

Cladists are almost messianic in their zeal for synapomorphies. There's a reason. A phylogeneticist who collaborated with Allan Wilson's group during the early years of molecular evolution once explained to me that before the cladistic paradigm came to the fore systematics was a total mess with no common currency. Sometimes it was an entertaining mess, such as Ernst Haeckel's famous diagrams, and sometimes an authoritative mess as evidenced by Ernst Mayer's attempts at evolutionary systematics. But arguments always ended with "I said so!" How exactly could one objectively discern right from wrong when intuition ruled the day? Enter Willi Hennig and the cladist revolution, which introduced a genuine system to systematics, so to speak. Using Karl Popper's criterion of falsification and the principle of parsimony a process emerged to clear out the debris of opinion which riddled taxonomy. Modern phylogenetics was born, and the basic ideas were also applied in a molecular context (though from the beginning molecular biologists did not always rely on cladist frameworks, as noted by Schwartz in this paper, nor do they today).

At this point I'll interject something personal. A good friend of mine was trained as a taxonomist, and she told me once that one of the members of her group gave a presentation which did not hue to the strict cladist line. After the talk a cladist approached her privately and berated her for not using "strict Popperian methods." The point here is not the substance but the style. Hennig's ideas added a great deal of rigor and precision, but many people feel that they go too far, and confuse Karl Popper's philosophy of science with science itself. My friend was predominantly a cladist, but her attitude was that there are more things in heaven and earth than only synapomorphies. Taxonomy needed some boundaries in the 20th century, but some cladists are strangling good science in the name of a straightjacket framework.

Jeffrey Schwartz's fixation on morphological characters and dismissal of the sometimes ad hoc and philosophically sloppy molecular methods strikes me as exhibiting this sort of narrowness. The main reason that molecular phylogenetics is viewed as authoritative in evolutionary paleontology is that in the 1970s the fossils and the molecules disagreed, and in the 1980s the fossils came into line with the molecules. There simply aren't that many fossils, and in previous eras the interpretation left much to be desired. With computational methods this is changing, but the reality is that molecular methods in the study of human evolution has withstood the test of time. This simply isn't fleshed out in the paper, which objects to molecular methods in a more general sense.

I don't find Schwartz's objections to the molecular data persuasive. There're the ones I would expect, and I won't go into them because i don't want to get into discussions about the molecular clock and what not. Obviously coalescent theory and such need to be questioned and examined, and models may not be as robust as one would like, but I don't personally find Schwartz's proffered alternative, rejecting most molecular methods as philosophically incoherent, as viable. Morphological characters used in analyses as in the paper above are a small finite subset of the total set of possible characters. In contrast, with the short-term likelihood of a large number of total genomes for both humans and other primates, and computational power to analyzes those genomes, there won't be the problem of methodological bias in terms of characters which are selected for analysis.

I think it is actually of interest to see how human traits and specific genes do not map onto the affinities of total genome content across taxa. In fact, it is interesting to see how this works within human populations. After all, the darkest skinned populations in the world, those of India, Melanesia and Africa, are not a monophyletic group. Rather, Indians and Melanesians cluster with non-Africans generally, light or dark. This is a trivial example, but illustrates that characters which do not map onto general phylogenies are significant and may tell us a great deal of & about the nature of adaptation. My attitude toward the "Red Ape Hypothesis" was that though I dismissed the model I thought the collection of traits where humans resembled orangutans were of interest, note and worthy of further exploration. As it is, Schwartz seems intent on overturning the credibility of molecular systematics itself to stack the odds in favor of his ideas about the origins of humanity. I wouldn't take that bet personally. This might not rank with Fred Hoyle's stubborn adherence to Steady State Theory, but I think the same basic issues are at work. When it comes to models of molecular evolution, mend it, don't end it. We need a diversity of methods, and for many questions fossils offer no answers because of the
small number of remains. The issues relating to this paper are worthwhile because putting a spotlight on the characteristics which can't be predicted by shared descent is going to tell us a lot about evolution, especially adaptation. But these sorts of really radical revisionisms shouldn't lead us to dismissing the traits outside of the main trendline; and yes, genetic sequences are traits too.

Related: For a more detailed review of the paper itself, see The New Scientist.

Note: It seems that to some extent ancient DNA might be a check on some of the molecular evolutionary models which Schwartz contends are not falsifiable.

Cite: Journal of Biogeography (J. Biogeogr.) (2009), Evolution of the second orangutan: phylogeny and biogeography of hominid origins, John R. Grehan and Jeffrey H. Schwartz,