Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record

Probabilistic approaches to phylogenetic inference have recently gained
traction in paleontological studies. Because they directly model processes
of evolutionary change, probabilistic methods facilitate a deeper
assessment of variability in evolutionary patterns by weighing evidence
for competing models. Although phylogenetic methods used in
paleontological studies have generally assumed that evolution proceeds by
splitting cladogenesis, extensions to previous models help explore the
potential for morphological and temporal data to provide differential
support for contrasting modes of evolutionary divergence. Recent
methodological developments have integrated ancestral relationships into
probabilistic phylogenetic methods. These new approaches rely on
parameter-rich models and sophisticated inferential methods, potentially
obscuring the respective contributions of data and models. In this study,
we describe a simple likelihoodist approach that combines probabilistic
models of morphological evolution and fossil preservation to reconstruct
both cladogenetic and anagenetic relationships. By applying this approach
to a data set of fossil hominins, we demonstrate the capability of
existing models to unveil evidence for anagenesis presented by
morphological and temporal data. This evidence was previously recognized
by qualitative assessments, but largely ignored by quantitative
phylogenetic analyses. For example, we find support for directly ancestral
relationships in multiple lineages: Sahelanthropus is ancestral to later
hominins; Australopithecus anamensis is ancestral to Australopithecus
afarensis; Australopithecus garhi is ancestral to Homo; Homo antecessor is
ancestral to Homo heidelbergensis, which in turn is ancestral to both Homo
sapiens and Homo neanderthalensis. By accommodating direct ancestry in
phylogenetics, quantitative results align more closely with previous
qualitative expectations.