Opportunities and Challenges in Applying AI to Evolutionary Morphology

He, Y; Mulqueeney, J M; Watt, E C; Salili-James, A; Barber, N S; Camaiti, M; Hunt, E S E; Kippax-Chui, O; Knapp, A; Lanzetti, A; Rangel-de Lázaro, Gizeh; McMinn, J K; Minus, J; Mohan, A V; Roberts, L E; Adhami, D; Grisan, E; Gu, Q; Herridge, V; Poon, S T S; West, T; Goswami, A

Abstract

Synopsis: Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of “big data” that aligns the study of phenotypes with genomics and other areas of bioinformatics.

Citation

He, Y., Mulqueeney, J. M., Watt, E. C., Salili-James, A., Barber, N. S., Camaiti, M., Hunt, E. S. E., Kippax-Chui, O., Knapp, A., Lanzetti, A., Rangel-de Lázaro, G., McMinn, J. K., Minus, J., Mohan, A. V., Roberts, L. E., Adhami, D., Grisan, E., Gu, Q., Herridge, V., Poon, S. T. S., …Goswami, A. (2024). Opportunities and Challenges in Applying AI to Evolutionary Morphology. Integrative Organismal Biology, 6(1), Article obae036. https://doi.org/10.1093/iob/obae036

• Journal Article Type: Article
• Acceptance Date: Sep 20, 2024
• Publication Date: Sep 23, 2024
• Deposit Date: Oct 27, 2024
• Publicly Available Date: Oct 27, 2024
• Journal: Integrative Organismal Biology
• Electronic ISSN: 2517-4843
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 6
• Issue: 1
• Article Number: obae036
• DOI: https://doi.org/10.1093/iob/obae036
• Publisher URL: https://academic.oup.com/iob/article/6/1/obae036/7769702