Deciphering African late middle Pleistocene hominin diversity and the origin of our species

Abstract

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.

Fig. 1

Phylogenetic hypotheses and landmarks distribution on the cranium. a and b Fully resolved phylogeny of the genus Homo according to hypotheses 1 (a) and 2 (b). c Position of the 780 landmarks and semilandmarks used in the study to describe the crania of the phylogeny sample

Fig. 2

Projection of phylogenetic hypotheses 1 (black) and 2 (grey) into the morphospace. The associated shape deformations are displayed next to each PC. Each node represents estimated ancestors’ shapes along with 95% confidence envelopes. Both trees are similar on PC1 and 2, while PC3 highlights differences between both hypotheses within the modern human clade. Modern human populations as follow: 1 to 9 Sub-Saharan Africa; 10–11 Oceania, 12 North Africa, 13–14 Europe, 15 South Asia, 16 to 20 East Asia, 21 North America (see Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). Source data are provided as a Source Data file

Fig. 3

Morphology of the vLCAs and of the LMP fossils. a Norma frontalis, lateralis, verticalis, occipitalis of vLCA1 when compared to vLCA2 through a surface deviation analysis. The histogram indicates the distribution of the deviation in mm between each vertex of the 3d models. b From left to right, norma frontalis and lateralis of Omo II, LH18, Florisbad, KNM-ES 11693 (the norma lateralis view is mirrored), and Irhoud 1. Source data are provided as a Source Data file

Fig. 4

Morphospaces of the bgPCAs for analyses A (a) and B (b). The ellipses represent the 90% confidence interval for the estimated distribution of the specimens of each population. The vLCAs are closer in shape to the early H. sapiens, as well as the African LMP specimens Flosibad, KNM-ES 11693 and Omo II, while Irhoud 1 is more similar to Neandertals. Modern human populations as follow: 1 to 9 Sub-Saharan Africa; 10–11 Oceania, 12 North Africa, 13–14 Europe, 15 South Asia, 16 to 20 East Asia, 21 North America (see Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). Source data are provided as a Source Data file

Fig. 5

Morphospaces of the bgPCAs for analyses C (a) and D (b). The ellipses represent the 90% confidence interval for the estimated distribution of the specimens of each population. The vLCAs are closer in shape to the early H. sapiens, as well as the African LMP specimens Flosibad, KNM-ES 11693 and Omo II, while Irhoud 1 is more similar to Neandertals. Modern human populations as follow: 1 to 9 Sub-Saharan Africa; 10–11 Oceania, 12 North Africa, 13–14 Europe, 15 South Asia, 16 to 20 East Asia, 21 North America (see Fig. 1, Supplementary Fig. 1 and Supplementary Table 1). Source data are provided as a Source Data file