23-8 Building Phenotypic Character Matrices for Phylogenetic Inference: an Exploration of 35 Years of Practice

Session: Phylogenetic and Computational Approaches in Paleobiology and Paleoecology, Part I

Presenting Author:

Mark Nikolic

Authors:

Hopkins, Melanie J.¹, Nikolic, Mark C.², Holmes, James D.³, Monti, Daniela S.⁴, Vargas-Parra, Ernesto E.⁵, Bicknell, Russell D. C.⁶, Edgecombe, Gregory D.⁷, Jordan-Burmeister, Katherine⁸, Paterson, John R. ⁹, Srivastava, Shravya¹⁰

(1) Division of Paleontology (Invertebrates), American Museum of Natural History, New York, NY, USA, (2) Department of Earth and Planetary Sciences, Stanford University, Stanford, CA, USA; Division of Paleontology, American Museum of Natural History, New York City, NY, USA, (3) Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden; Palaeoscience Research Centre, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia, (4) Instituto de Ecología, Genética y Evolución de Buenos Aires, Facultad de Ciencias Exactas y Naturales, CONICET-UBA, Buenos Aires, Argentina, (5) Department of Earth and Planetary Sciences, University of California, Riverside, Riverside, CA, USA; Division of Paleontology, American Museum of Natural History, New York City, NY, USA, (6) Division of Paleontology, American Museum of Natural History, New York City, NY, USA; Palaeoscience Research Centre, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia, (7) The Natural History Museum, London, United Kingdom, (8) Department of Earth, Environmental, and Planetary Sciences, University of Tennessee-Knoxville, Knoxville, TN, USA, (9) Palaeoscience Research Centre, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia, (10) Department of Earth and Planetary Sciences, University of California, Riverside, Riverside, CA, USA,

Abstract:

Recent methodological developments in phylogenetic inference have focused predominantly on molecular data. However, renewed interest in other datatypes, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. Attention has largely focused on the improvement in models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference, particularly in fossil taxa. We present a meta-analysis of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods, the trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Unsurprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data is missing for many tips, providing support against the exclusion of characters because of missing data. We identify and recommend several avenues for increasing the quality and quantity of morphological character data in phylogenetic analyses and discuss how advances in the study of developmental biology and variational complexity can contribute to this.

Geological Society of America Abstracts with Program. Vol. 57, No. 6, 2025

doi: 10.1130/abs/2025AM-9689

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