RESEARCH ARTICLE Morphoscopic ancestry estimates in Filipino crania using multivariate probit regression models Matthew C. Go 1,2 | Joseph T. Hefner 3 1 Department of Anthropology, University of Illinois at Urbana-Champaign, 109 Davenport Hall, 607 South Mathews Avenue, Urbana, Illinois 2 SNA International, supporting the Department of Defense POW/MIA Accounting Agency, 590 Moffet Street, Building 4077, Joint Base Pearl Harbor- Hickam, Hawaii 3 Department of Anthropology, Michigan State University, 655 Auditorium Drive, East Lansing, Michigan Correspondence Matthew C. Go, Department of Anthropology, University of Illinois at Urbana-Champaign Email: mgo4@illinois.edu Funding information National Institute of Justice, Grant/Award Numbers: 2015-DN-BX-K012, 2017-IJ-CX- 0008; Social Sciences and Humanities Research Council of Canada, Grant/Award Number: 752-2016-0221 Abstract Objectives: Probit has not been applied to ancestry estimation in forensic anthropology. The goals of this study were to: (1) evaluate the performance of probit analysis as a clas- sification tool for ancestry estimation using ordinal data and (2) expand our current understanding of human cranial variation for an understudied population. Methods: Multivariate probit models were used to classify the ancestral affiliation of Filipino crania using morphoscopic traits. Ancestral reference populations represen- ted Africa, Asia, and Europe in a three-group model, with the addition of Hispanics in a four-group model. Posterior probabilities across these groups were interpreted as admixture proportions of an individual. Model performance was also evaluated for individuals with missing data. Results: The overall correct classification rates for the three-group and four-group models were 72.1% and 68.6%, respectively. Filipinos classified as Asian 52.9% of the time using three ancestral reference groups and 48.6% using four groups. A large portion of Filipinos also classified as African. There were no significant differences in classification trends or accuracy rates between complete crania and crania with at least one missing variable. Conclusions: Multivariate probit models using morphoscopic traits perform well when populations are represented in both training and test samples. Probit can also accommodate individuals with missing data. Classifying Filipinos showed only moder- ate success. Filipinos are more phenotypically similar to Africans than the other Asian samples used here, but still affiliate most closely as Asian. Ancestry methods would benefit from including Filipinos as a reference sample given the additional variation they provide to the continental category of Asian. KEYWORDS ancestry estimation, forensic anthropology, nonmetric traits, ordinal categorical data, Philippines 1 | INTRODUCTION The advent of several federal court rulings on the admissibility of evidence and expert testimony (i.e., the Daubert Trilogy) played a major role in the push for more statistically empirical approaches to biological profile estimation (Christensen, 2004; Christensen & Crowder, 2009; Grivas & Komar, 2008; Holobinko, 2012; Saks & Koehler, 2005). Estimation methods using ordinal categorical data abound in forensic anthropology yet have lagged behind in statistical rigor versus more computationally manageable osteometric data. In this regard, cranial morphoscopic traits useful in ancestry estimation have generally seen the least progress in statistical validation versus Received: 14 August 2019 Revised: 19 November 2019 Accepted: 2 January 2020 DOI: 10.1002/ajpa.24008 386 © 2020 Wiley Periodicals, Inc. Am J Phys Anthropol. 2020;172:386–401. wileyonlinelibrary.com/journal/ajpa