Research Themes

How and why does animal form evolve?

I integrate evidence from the fossil record with data on the anatomy, development, functional morphology, physiology, and ecology of living animals to investigate
how animal form has changed through evolution and why it has evolved in particular directions.

In particular, by linking developmental processes, ecology and function, interindividual phenotypic variation, and evolvability, I aim to empirically elucidate the patterns of morphological evolution and the mechanisms and constraints that generate them.

1. From development to deep time
A Paleo-Evo-Devo approach to morphological evolution

I integrate developmental processes in living animals with morphological transformations preserved in the fossil record to investigate how novel forms have arisen during evolution.

I am particularly interested in osteological correlates, such as processes, foramina, grooves, and rugosities of bones that are associated with particular soft tissues. Using comparative anatomical and developmental data from living animals, I investigate which soft tissues correspond to these skeletal features and how they arise during ontogeny. By integrating these observations with the fossil record, I aim to reconstruct the developmental mechanisms and constraints underlying morphological evolution.

My previous work has examined the diversification of cranial morphology through comparative analyses of skull development in turtles（Tkita, Watanabe et al., 2021）, as well as the evolution of the jaw joint and middle ear along the dinosaur–bird lineage by integrating fossil evidence with comparative developmental analyses of reptile and bird embryos（Watanabe et al., 2026）.

2. Evolution of musculoskeletal and sensory systems during ecological transitions

How do adaptation and constraint shape morphological evolution?

Tetrapods have colonized a wide range of environments—including terrestrial, aquatic, arboreal, subterranean, and aerial habitats—and have undergone extensive modifications of their musculoskeletal and sensory systems in the process. I am interested not only in associations between morphology and ecology, but also in how ecological adaptation interacts with phylogenetic and developmental constraints to channel morphological evolution.

I focus particularly on structures that have received relatively little attention during major ecological transitions, as well as on the evolutionary coupling of multiple organ systems. By considering morphological integration, modularity, developmental constraints, phenotypic plasticity, and related factors, I seek to understand which structures are more evolutionarily labile and which remain comparatively conservative under similar environmental pressures.

I am currently investigating the evolutionary reorganization of auditory systems associated with secondary aquatic adaptation, with a particular focus on turtles.

3. Evolutionary phenomics of Cenozoic mammals
How has the potential for morphological evolution changed through deep time?

Understanding morphological evolution requires more than tracking changes in mean morphology. It is also important to understand the phenotypic variation present among individuals and how different traits covary. I use large-scale morphological datasets from fossil and extant mammals to investigate how phenotypic variation, morphological integration, and modularity have changed over geological timescales.

Cenozoic mammals are particularly suitable for this approach because they have a rich fossil record that can be directly compared with extant species. Some taxa are represented by assemblages containing large numbers of individuals, while extensive morphological datasets have also accumulated through research in paleoecology, conservation paleobiology, and related fields.

By comparing these data through time, I aim to determine how the magnitude and covariance structure of phenotypic variation changed in association with environmental change, ecological transitions, and extinction events. Ultimately, this work seeks to understand long-term changes in the evolutionary constraints that shape morphology and in the underlying evolvability of morphological systems.

4. Taxonomy, evolution, and paleoecology of fossil decapod crustaceans

Re-examining fossil crustaceans through digital morphology

Decapod crustaceans, including crabs and shrimps, are major components of present-day aquatic ecosystems. However, relatively few paleontologists specialize in their fossil record, and the taxonomy and morphology of some fossil groups remain insufficiently understood. Japan has a particularly rich fossil record of decapod crustaceans, especially from the Cenozoic, while older deposits also contain specimens that are difficult to accommodate within existing taxonomic frameworks.

I apply approaches developed through my research on vertebrate morphology—including micro-CT scanning, 3D visualization, and fine-scale morphological analysis—to fossil decapod crustaceans. My work reassesses characters traditionally used in classification and explores previously overlooked morphological information that may provide new diagnostic characters.

By establishing a stronger morphological and taxonomic foundation and integrating these data with information on geological age and depositional environments, I aim to better understand the evolution, paleoecology, and biogeographic history of decapod crustaceans.

5. 3D Digital Natural History and Inquiry-Based Learning

Connecting field observation, digital archiving, and scientific inquiry

Inquiry-based learning has become increasingly important in school education, while advances in technologies such as photogrammetry have made it much easier to record and share natural objects and environments as three-dimensional digital data.

Three-dimensional data offer new possibilities not only for preserving digital records of natural environments and natural history materials for the future, but also for observing specimens and landscapes from multiple perspectives and for sharing students' discoveries and research outcomes online.

I aim to develop ways of making these technologies accessible not only to professional researchers, but also to elementary and secondary school students conducting inquiry-based learning and independent research projects. Through educational practices that combine field observation and question development with 3D digital archiving, I explore new approaches to observing, documenting, comparing, and sharing natural history materials.

I also develop 3D archiving methods and educational resources that can be used by school teachers and students in museum studies and curator-training programs, with the goal of integrating field-based natural history with digital technologies in education and museum practice.

Part of this project is currently supported by the Nature Experience Activity Support Program of the Ando Foundation.

Research Approaches

Methods

Gross dissection and morphometric analysis
Experimental developmental biology, including staining techniques and histological analyses
Acquisition and analysis of 3D morphological data
(micro-CT, DiceCT, photogrammetry, 3D scanning, Avizo / Amira / 3D Slicer, and confocal laser scanning microscopy)
Image analysis using ImageJ and related software
Statistical analyses in R / RStudio
Phylogenetic comparative and evolutionary analyses, including ancestral-state reconstruction
Field and collections research, including museum specimen surveys and fieldwork in Japan and abroad

Study Organisms

My research primarily focuses on extant and fossil vertebrates—including reptiles such as dinosaurs, birds, amphibians, and mammals—with particular emphasis on the evolution of cranial morphology, especially craniofacial and auditory structures.

I also study fossil invertebrates, particularly decapod crustaceans such as crabs and shrimps from Japan.

My research and educational activities are conducted in collaboration with universities, museums, research institutions, local organizations, and other partners in Japan and abroad.

Research Collaborations

Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo
Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo
College of Media and Communications, Edogawa University
National Museum of Nature and Science, Japan — Evolutionary Paleontology Research Group
National Museum of Nature and Science, Japan — Human Evolution Research Group
Natural History Museum and Institute, Chiba — Earth Sciences Research Group
Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” / CONICET, Argentina

Research Cooperation and Specimen Access

The University Museum, The University of Tokyo
National Museum of Nature and Science, Japan — Vertebrate Zoology Research Group
Kanagawa Prefectural Museum of Natural History — Zoology Group
Natural History Museum and Institute, Chiba — Zoology Research Group
Natural History Museum and Institute, Chiba — Museum Studies Research Group
Abiko City Museum of Birds
Adachi Park of Living Things
Institute of Island Biology Co., Ltd.
Kiyama Farm Co., Ltd.
Yusuhara Gibier no Sato Co., Ltd.
Ogasawara Wildlife Research Society
Mizumoto Nature Project
Katsushika Biodiversity Promotion Council
Regional offices of the Ministry of the Environment, Japan
Local government departments responsible for nature conservation

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