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Extended Distance-based Phylogenetic Analyses Applied to 3D Homo Fossil Skull Evolution

This article shows how 3D geometric morphometric data can be analyzed using newly developed distance-based evolutionary tree inference methods, with extensions to planar graphs. Application of these methods to 3D representations of the skullcap (calvaria) of 13 diverse skulls in the genus Homo, ranging from Homo erectus (ergaster) at about 1.6 mya, all the way forward to modern humans, yields a remarkably clear phylogenetic tree. Various evolutionary hypotheses are tested. Results of these tests include rejection of the monophyly of Homo heidelbergensis, the Multi-Regional hypothesis, and the hypothesis that the unusual 12,000 year old (12kya) Iwo Eleru skull represents a modern human. Rather, by quantitative phylogenetic analyses the latter is seen to be an old (200-400kya) lineage that probably represents a novel African species, Homo iwoelerueensis. It diverged after the lineage leading to Neanderthals, and may have been driven to extinction in the last 10kya by modern humans, Homo sapiens, another African species of Homo that appeared about 100kya. Another enigmatic skull, Qafzeh 6 from the Middle East about 90kya, appears to be a hybrid of two thirds near, but not, anatomically modern human and one third of an archaic lineage diverging close to classic European Neanderthals. Overall, the tree clearly implies an accelerating rate of skullcap shape change, and by extension, change of the underlying brain, over the last 400kya in Africa. This acceleration may have extended right up to the origin of modern humans. Methods of distance-based evolutionary tree inference are refined and extended, with particular attention to diagnosing the model and achieving a better fit. This includes power transformations of the input data which favor root Procrustes distances.