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Thomas Stewart

Thomas Stewart

· Assistant Professor of BiologyVerified

Pennsylvania State University · Biosciences

Active 1986–2025

h-index14
Citations1.2k
Papers6910 last 5y
Funding
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Research topics

  • Medicine
  • Geography
  • Biology
  • Gastroenterology
  • Evolutionary biology
  • Genetics
  • Immunology
  • Zoology
  • Geology
  • Paleontology
  • Internal medicine
  • Oceanography

Selected publications

  • Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition

    Nature Communications · 2025-05-29 · 2 citations

    articleOpen access

    The mechanisms of the pectoral girdle transformation at the origin of terrestrial locomotion in vertebrates remain an outstanding problem. The loss of intramembranous bones and the enlargement of endochondral bones resulted in the disarticulation of the pectoral girdle from the skull and the formation of the neck during the fish-to-tetrapod transition. Despite the functional implications of this skeletal shift in the emergence of terrestrial vertebrates, the underlying genetic-developmental alterations have remained enigmatic. Here, we show that in zebrafish pectoral girdle mesodermal cells expressing gli3, a transcription factor gene in the Hedgehog signaling pathway, differentiate into both intramembranous and endochondral bones. Intriguingly, Gli and Hedgehog compound knockout fish exhibited an unexpected combination of actinopterygian fish and stem-tetrapod pectoral girdle characteristics. These ontogenetic and anatomical data suggest that a trade-off between the two distinct ossification pathways is a deeply embedded developmental program in bony fishes and that tuning of this trade-off can generate novel pectoral girdle akin to those of stem-tetrapods at the dawn of vertebrate terrestrialization.

  • Plasticity in the pectoral fin skeleton is induced by altered foraging regime in a South American cichlid

    bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-24

    preprintOpen accessSenior authorCorresponding

    ABSTRACT The fins of fishes are remarkably diverse, and this variation is tied to the ecology and locomotor mode of a species. While numerous genetic factors are known to pattern fins in development, it is unclear how developmental plasticity shapes the fin skeleton. Here, we analyze the cichlid Satanoperca daemon , raised under three distinct feeding regimes, and show that plasticity is pervasive across the pectoral fin skeleton with foraging mode impacting patterning of both the endoskeleton and dermal skeleton. Radials and fin rays were µCT scanned and analyzed using a combination of linear measures and geometric morphometrics. Anteroposterior patterning of both radials and fin rays are affected by feeding regime. Notably, S. daemon pectoral fin rays show distinct patterns of fin ray branching between treatments, suggesting altered fin stiffness. We argue that the observed changes in the fin likely reflect developmental plasticity resultant from altered swimming behaviors when fishes are challenged to forage in different ways. These data show how non-genetic mechanisms can shape both the endoskeleton and dermal skeleton of fins, and that foraging mode can induce plastic changes in skeletal elements that do not directly interface with food items.

  • Integration Investigation: Feeding Regime Alters Patterns of Integration in Cichlids

    2024-01-01

    articleOpen accessSenior author
  • The axial skeleton of <i>Tiktaalik roseae</i>

    Proceedings of the National Academy of Sciences · 2024-04-02 · 11 citations

    articleOpen access1st authorCorresponding

    The axial columns of the earliest limbed vertebrates show distinct patterns of regionalization as compared to early tetrapodomorphs. Included among their novel features are sacral ribs, which provide linkage between the vertebral column and pelvis, contributing to body support and propulsion by the hindlimb. Data on the axial skeletons of the closest relatives of limbed vertebrates are sparce, with key features of specimens potentially covered by matrix. Therefore, it is unclear in what sequence and under what functional context specializations in the axial skeletons of tetrapods arose. Here, we describe the axial skeleton of the elpistostegalian Tiktaalik roseae and show that transformations to the axial column for head mobility, body support, and pelvic fin buttressing evolved in finned vertebrates prior to the origin of limbs. No atlas–axis complex is observed; however, an independent basioccipital–exoccipital complex suggests increased mobility at the occipital vertebral junction. While the construction of vertebrae in Tiktaalik is similar to early tetrapodomorphs, its ribs possess a specialized sacral domain. Sacral ribs are expanded and ventrally curved, indicating likely attachment to the expanded iliac blade of the pelvis by ligamentous connection. Thus, the origin of novel rib types preceded major alterations to trunk vertebrae, and linkage between pelvic fins and axial column preceded the origin of limbs. These data reveal an unexpected combination of post-cranial skeletal characters, informing hypotheses of body posture and movement in the closest relatives of limbed vertebrates.

  • The origin of blinking in both mudskippers and tetrapods is linked to life on land

    Proceedings of the National Academy of Sciences · 2023 · 14 citations

    Senior authorCorresponding
    • Biology
    • Evolutionary biology
    • Zoology

    blinks more often under high-evaporation conditions to wet the eye, a blink reflex protects the eye from physical insult, and a single blink can fully clean the cornea of particulates. Thus, eye retraction in concert with a passive occlusal membrane can achieve functions associated with life on land. Osteological correlates of eye retraction are present in the earliest limbed vertebrates, suggesting blinking capability. In both mudskippers and tetrapods, therefore, the origin of this multifunctional innovation is likely explained by selection for increasingly terrestrial lifestyles.

  • Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition

    bioRxiv (Cold Spring Harbor Laboratory) · 2023-07-17 · 2 citations

    preprintOpen access

    Abstract The mechanisms of the pectoral girdle transformation at the origin of terrestrial locomotion in vertebrates remains an outstanding problem in evolutionary biology 1 . The loss of dermal bones and the enlargement of endochondral bones resulted in the disarticulation of the pectoral girdle from the skull and the formation of the neck during the fish-to-tetrapod transition 2–5 . Despite the functional implications of this skeletal shift in the emergence of terrestrial vertebrates, the underlying genetic-developmental alterations have remained enigmatic. Here, we discovered that in zebrafish pectoral girdle mesodermal cells expressing gli3 , a transcription factor in the Hedgehog signaling pathway, contribute to both dermal and endochondral bones. We show that Gli3 regulates expression of activin A receptor type 1-like , a BMP type 1 receptor lost in tetrapod lineages, and thereby determines endochondral and dermal ossification. Intriguingly, Gli and Hedgehog compound knockout fish exhibited an unexpected combination of actinopterygian fish and stem-tetrapod pectoral girdle characteristics. These ontogenetic and anatomical data suggest that a trade-off between the two distinct ossification pathways is a deeply embedded developmental program in bony fishes, with potential for tuning of this trade-off to generate novel pectoral girdle forms akin to stem-tetrapods at the dawn of vertebrate terrestrialization.

  • Axial regionalization in <i>Tiktaalik roseae</i> and the origin of quadrupedal locomotion

    bioRxiv (Cold Spring Harbor Laboratory) · 2023-01-13

    preprintOpen access1st authorCorresponding

    Summary The origin of quadrupedal locomotion in tetrapods entailed the evolution of a regionalized axial skeleton with sacral ribs. These ribs provide linkage between the pelvis and vertebral column and contribute to body support and propulsion by the hind limb. The closest relatives of limbed vertebrates are not known to possess such a connection and, therefore, have typically been described as primarily supporting their bodies against the substrate with pectoral fins. However, data on the axial skeletons of stem tetrapods are sparce, with key features of specimens potentially concealed by matrix. Here we provide micro-computed tomography data of the axial skeleton of Tiktaalik roseae and show that its vertebrae and ribs are regionalized along the craniocaudal axis, including expanded and ventrally curved ribs in the sacral region. The sacral ribs would have contacted the expanded iliac blade of the pelvis in a soft tissue connection. No atlas-axis complex is observed, however the basioccipital-exoccipital complex is deconsolidated from the rest of the neurocranium, suggesting increased mobility at occipital-vertebral junction. Thus, axial regionalization that allowed for innovations in head mobility, body support and buttressing the pelvic fin evolved prior to the origin of limbs.

  • Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition.

    Research Square · 2023-10-16

    preprintOpen access
  • Functionalized surfaces for the destruction of pathogens and organics

    OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2023-01-23

    articleOpen access1st authorCorresponding

    The disclosure is directed to a surface having a binding component applied thereto for the adsorption or capture of pathogens and organic molecules or materials. The surface may be a component of a porous or nonporous substrate. The binding component may also bind a photocatalyst to the surface for photocatalytic destruction of the captured pathogens and organic molecules or materials.

  • Meet Qikiqtania, a fossil fish with the good sense to stay in the water while others ventured onto land

    2022-07-20

    preprint1st authorCorresponding

Frequent coauthors

  • Travis M. Anderson

    Sandia National Laboratories

    8 shared
  • Wenqian Xu

    Fudan University

    8 shared
  • Joel N. Bixler

    7 shared
  • Dina Navon

    Abbott (Canada)

    6 shared
  • Neil H. Shubin

    University of Chicago

    5 shared
  • Mark A. Rodriguez

    Sandia National Laboratories

    5 shared
  • Cong Liang

    Fourth Affiliated Hospital of Guangxi Medical University

    5 shared
  • W. Brown

    Loma Linda University

    4 shared

Education

  • PhD in Integrative Biology, Organismal Biology and Anatomy

    University of Chicago

    2015
  • B.S. in Biology, Department of Biology

    Syracuse University

    2009
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