Abstract
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 pattern 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 dataset 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 Au. afarensis; Au. garhi is ancestral to Homo; H. antecessor is ancestral to H. heidelbergensis, which in turn is ancestral to both H. sapiens and H. neanderthalensis. These results show a benefit of accommodating direct ancestry in phylogenetics. By so doing, quantitative results align more closely with previous qualitative expectations.
Author contributions
CPF designed and implemented the ML stratocladistic procedure, performed analyses, interpreted results, and drafted the manuscript. DCF made conceptual contributions to the stratocladistic approach developed here, contributed to the manuscript, and helped interpret results. EG gathered temporal occurrence ranges, helped interpret results, and edited the manuscript. LMM helped focus the scope of the hominin analysis, helped interpret results, and contributed to the manuscript.
Acknowledgments
CPF would like to thank JW Brown, CW Dick, M Friedman, SA Smith, and GW Stull for helpful discussion of the manuscript and method.
Footnotes
Supplementary data: Software used in this study is implemented in the mandos package and is available on GitHub (github.com/carolinetomo/mandos). All trees tested using the stratocladistic likelihood procedure and their associated AIC scores are available on GitHub (WEB ADDRESS—will upload prior to submission). This repository also contains the morphological matrix and stratigraphic range files and all scripts needed to reproduce results. Stratigraphic occurrences and their associated citations are provided as supplementary information. The supplement also includes an online appendix that describes and tests the morphological likelihood calculation on trees containing anagenetic relationships.