Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Homo naledi is a recently discovered species of fossil hominin from South
Africa. A considerable amount is already known about H. naledi but some
important questions remain unanswered. Here we report a study that
addressed two of them: “Where does H. naledi fit in the hominin
evolutionary tree?” and “How old is it?” We used a large supermatrix of
craniodental characters for both early and late hominin species and
Bayesian phylogenetic techniques to carry out three analyses. First, we
performed a dated Bayesian analysis to generate estimates of the
evolutionary relationships of fossil hominins including H. naledi. Then we
employed Bayes factor tests to compare the strength of support for
hypotheses about the relationships of H. naledi suggested by the
best-estimate trees. Lastly, we carried out a resampling analysis to
assess the accuracy of the age estimate for H. naledi yielded by the dated
Bayesian analysis. The analyses strongly supported the hypothesis that H.
naledi forms a clade with the other Homo species and Australopithecus
sediba. The analyses were more ambiguous regarding the position of H.
naledi within the (Homo, Au. sediba) clade. A number of hypotheses were
rejected, but several others were not. Based on the available craniodental
data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo
floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon
of H. naledi. According to the dated Bayesian analysis, the most likely
age for H. naledi is 912 ka. This age estimate was supported by the
resampling analysis. Our findings have a number of implications. Most
notably, they support the assignment of the new specimens to Homo, cast
doubt on the claim that H. naledi is simply a variant of H. erectus, and
suggest H. naledi is younger than has been previously proposed.