Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights

Evolutionary biologists, primarily palaeoanthropologists, anatomists and ontogenists, employ modern geometric morphometrics to quantitatively analyse physical forms (e.g., skull morphology) and explore relationships, variations, and differences between samples and taxa using landmark coordinates. The standard approach comprises two steps: Generalised Procrustes Analysis (GPA) followed by Principal Component Analysis (PCA). PCA projects the superimposed data produced by GPA onto a set of uncorrelated variables, which can be visualised on scatterplots and used to draw phenetic, evolutionary, and ontogenetic conclusions. Recently, the use of PCA in genetic studies has been challenged. Due to PCAs central role in morphometrics, we sought to evaluate the standard approach and claims based on PCA outcomes. To test PCAs accuracy, robustness, and reproducibility using benchmark data of the crania of five papionin genera, we developed MORPHIX, a Python package for processing superimposed landmark data with classifier and outlier detection methods, which can be further visualised using various plots. Throughout this manuscript, we address the recent and contentious use of PCA in physical anthropology and phylogenetic inference, such as the case of Homo Nesher Ramla, an archaic hominin with a questionable taxonomy. We found that PCA outcomes are artefacts of the input data and are neither reliable, robust, nor reproducible as field members may assume. We also found that supervised machine learning classifiers are more accurate both for classification and detecting new taxa. Our findings raise concerns about PCA-based findings applied in 18,400 to 35,200 Physical anthropology studies. Our work can be used to evaluate prior and novel claims concerning the origins and relatedness of inter- and intra-species and improve phylogenetic and taxonomic reconstructions.