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Contact Information

P: 864-656-2328

Campus Location

132 Long Hall, Clemson, SC 29634


Monday - Friday:
8 a.m. - 4:30 p.m.


Profile Photo

Susan Chapman

Biological Sciences

Associate Professor

Long Hall 340 [Office]

Educational Background

Ph.D., Developmental Neurobiology, Kings College London, 2002
B.Sc., Neuroscience, University College London, 1998
B.Sc., Science, Open University, 1999

Research Interests


This project combines paleontology and developmental biology to study bird evolution from avian dinosaurs to extant birds. Multiple skeletal adaptations separated birds from their avian dinosaur ancestors. Our focus is on the Cretaceous transition from long- to short-tailed birds and fusion events within the axial skeleton. Cretaceous short-tailed birds and modern avians share a truncated tail with the fusion of distal caudal vertebrae into a pygostyle (a bony rod that supports the tail fan feathers) and the synsacrum. These transitions were so advantageous that birds, arguably the most successful terrestrial vertebrates, have maintained the same configuration for 125 million years. Our studies aim to understand the morphogenesis and molecular mechanisms of avian axial skeletal development and correlate that information with the fossil record.


We study the axial skeleton intending to understand normal and pathogenic processes of axial extension and fusion processes. Using RNAseq analysis, we have identified novel lncRNA molecules regulating Hox gene family member expression. Hox genes are essential for imparting positional identity to somites, which are the precursors of the vertebrae. We are conducting functional experiments designed to elucidate the global regulatory mechanism governing Hox gene expression. Additionally, our RNAseq data has identified immune signals of the complement cascade in the skeletal remodeling process. Degeneration of the nucleus pulposus and intervertebral discs (IVDs) is required to fuse the pygostyle and synsacrum regions. We are further interested in the crossover between normal fusion, traumatic injury, and disease processes. Bone fracture healing and Ankylosing spondylitis (AS) are examples of inflammation-driven fusion events. We use chicken and mouse models to identify the triggering and molecular mechanism governing changing morphogenesis during normal and disease state, thereby informing therapeutic and clinical approaches.

Courses Taught

BIOL4400, H4400, 6400, Developmental Animal Biology, S15, S16, S17
BIOL4610, H4610, 6610, Cell Biology, F14-ongoing
BIOL4930, Senior Seminar, Cognitive Developmental Defects, F15
BIOL4940, Creative Inquiry, F13-ongoing
BIOL4910, Undergraduate Research
BIOL8070, Graduate course, MCDB Journal Club, S09, F14, F18
BIOL8070, Graduate core course, MCDB, F18, F20
BIOL8910, M.S. Graduate Research
BIOL9910, Ph.D. Graduate Research

Selected Publications

Since 2008

23: Reshaping the Tree of Life: Ecological Implications of Evolution in the Anthropocene. Krista Capps, Susan Chapman, Keith Clay, Jonathan Fresnedo-Ramirz, Daniel L. Potts. Frontiers in Ecology and the Environment. In Press.

22: The long and the short of tails. Dana J. Rashid and Susan C. Chapman. Developmental Dynamics. 2021 Feb. doi:10.1002/dvdy.311.

21: Pygostyle development and variation in avian distal spinal nerves. Dana J. Rashid, Roger Bradley, Alida M. Bailleul, Kevin Surya, Holly Ballard, Ping Wu, Yun-Hsin (Becky) Wu, Cheng-Ming Chuong, Douglas B. Menke, Sergio G. Minchey, Ben Parrott, Samantha L. Bock, Christa Merzdorf, Emma Narotzky, Nathan Burke, John R. Horner*, and Susan C. Chapman* (Joint senior authors). Scientific Reports. 2020 Apr 14;10(1):6303. doi: 10.1038/s41598-020-63264-5. PMID: 32286419.

20: Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. Rooksana E. Noorai, Vijay Shankar, Nowlan H. Freese, Christopher Gregorski, and Susan C. Chapman. 2019. PLoS ONE 14(12): e0225834. PMID: 31821332.

19: Embryonic Exposure to 2,2,3,5,6-pentachlorobiphenyl (PCB-95) Causes Developmental Malformations in Zebrafish. Prabha Wijesinghe, Susan C. Chapman, Cindy Lee. Environmental Toxicology and Chemistry. 2019. DOI: 10.1002/etc.4587. PubMed PMID: 31499578.

18: Avian tail ontogeny, pygostyle formation, and interpretation of juvenile Mesozoic specimens. Dana J. Rashid, Kevin Surya, Luis M. Chiappe, Nathan Carroll, Kimball Garrett, Bino Varghese, Alida Bailleul, Jingmai K. O'Connor, Susan C. Chapman*, and John R. Horner* (Joint senior authors). 2018; 8:9014 | DOI:10.1038/s41598-018-27336-x. PubMed PMID: 29899503.

17: Lectin staining selectively highlights tissues within the embryonic chicken head. Poulomi Ray*, Ami L Hughes, Misha Sharif**, Susan C Chapman. Journal of Anatomy. 2016. DOI: 10.1111/joa.12565 PMID: 27861854

16: Fgf3 and Fgf16 expression patterns define spatial and temporal domains in the developing chick inner ear. Daniel Olaya-Sánchez, Luis Óscar Sánchez- Guardado, Sho Ohta, Susan C. Chapman, Gary C. Schoenwolf, Luis Puelles, and Matías Hidalgo-Sánchez. Brain, Structure and Function. 2016. DOI 10.1007/s00429-016-1205-12015 PMID: 26995070

15: Cytoskeletal Reorganization Drives Mesenchymal Condensation and Regulates Downstream Molecular Signaling. Poulomi Ray* and Susan C. Chapman. PLoS One. 2015 Aug 3;10(8):e0134702. doi: 10.1371/journal.pone.0134702. eCollection 2015. PMID: 26237312, PMCID: PMC4523177

14: Daniel Olaya-Sanchez, Luis Oscar Sanchez-Guardado, Sho Ohta, Susan C. Chapman, Gary C. Schoenwolf, Luis Puelles, Matıas Hidalgo-Sanchez. Fgf3 and Fgf16 expression patterns define spatial and temporal domains in the developing chick inner ear. Brain Struct Function. 2016 Mar 19: DOI 10.1007/s00429-016-1205-1. Pubmed PMID: 26995070

13: Ray P, Chapman SC. Cytoskeletal Reorganization Drives Mesenchymal Condensation and Regulates Downstream Molecular Signaling. PLoS One. 2015 Aug 3;10(8):e0134702. doi: 10.1371/journal.pone.0134702. eCollection 2015. PubMed PMID: 26237312; PubMed Central PMCID: PMC4523177.

12: Galli LM, Munji RN, Chapman SC, Easton A, Li L, Onguka O, Ramahi JS, Suriben R, Szabo LA, Teng C, Tran B, Hannoush RN, Burrus LW. Frizzled10 mediates WNT1 and WNT3A signaling in the dorsal spinal cord of the developing chick embryo. Dev Dyn. 2014 Jun;243(6):833-43. doi: 10.1002/dvdy.24123. Epub 2014 Apr 1. PubMed PMID: 24599775; PubMed Central PMCID: PMC4031291.

11: Kucukkal TG, Yang Y, Chapman SC, Cao W, Alexov E. Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci. 2014 May 30;15(6):9670-717. doi: 10.3390/ijms15069670. Review. PubMed PMID: 24886813; PubMed Central PMCID:PMC4100115.

10: Rashid DJ, Chapman SC, Larsson HC, Organ CL, Bebin AG, Merzdorf CS, Bradley R, Horner JR. From dinosaurs to birds: a tail of evolution. Evodevo. 2014 Jul 29;5:25. doi: 10.1186/2041-9139-5-25. eCollection 2014. Review. PubMed PMID:25621146; PubMed Central PMCID: PMC4304130.

9: Freese NH, Lam BA, Staton M, Scott A, Chapman SC. A novel gain-of-function mutation of the proneural IRX1 and IRX2 genes disrupts axis elongation in the Araucana rumpless chicken. PLoS One. 2014 Nov 5;9(11):e112364. doi:10.1371/journal.pone.0112364. eCollection 2014. PubMed PMID: 25372603; PubMed Central PMCID: PMC4221472.

8: Kumar M, Chapman SC. Cloning and expression analysis of Fgf5, 6 and 7 during early chick development. Gene Expr Patterns. 2012 Aug-Sep;12(7-8):245-53. doi:10.1016/j.gep.2012.05.002. Epub 2012 May 24. PubMed PMID: 22634565; PubMed Central PMCID: PMC3434314.

7: Kumar M, Ray P, Chapman SC. Fibroblast growth factor and bone morphogenetic protein signaling are required for specifying prechondrogenic identity in neural crest-derived mesenchyme and initiating the chondrogenic program. Dev Dyn. 2012 Jun;241(6):1091-103. doi: 10.1002/dvdy.23768. Epub 2012 Mar 29. PubMed PMID:22411638; PubMed Central PMCID: PMC3354026.

6: Noorai RE, Freese NH, Wright LM, Chapman SC, Clark LA. Genome-wide association mapping and identification of candidate genes for the rumpless and ear-tufted traits of the Araucana chicken. PLoS One. 2012;7(7):e40974. doi:10.1371/journal.pone.0040974. Epub 2012 Jul 23. PubMed PMID: 22844420; PubMed Central PMCID: PMC3402462.

5: Chapman SC. Can you hear me now? Understanding vertebrate middle ear development. Front Biosci (Landmark Ed). 2011 Jan 1;16:1675-92. Review. PubMed PMID: 21196256; PubMed Central PMCID: PMC3065862.

4: Bleyl SB, Saijoh Y, Bax NA, Gittenberger-de Groot AC, Wisse LJ, Chapman SC, Hunter J, Shiratori H, Hamada H, Yamada S, Shiota K, Klewer SE, Leppert MF, Schoenwolf GC. Dysregulation of the PDGFRA gene causes inflow tract anomalies including TAPVR: integrating evidence from human genetics and model organisms. Hum Mol Genet. 2010 Apr 1;19(7):1286-301. doi: 10.1093/hmg/ddq005. Epub 2010 Jan 13. PubMed PMID: 20071345; PubMed Central PMCID: PMC2838537.

3: Wood JL, Hughes AJ, Mercer KJ, Chapman SC. Analysis of chick (Gallus gallus) Middle ear columella formation. BMC Dev Biol. 2010 Feb 16;10:16. doi:10.1186/1471-213X-10-16. PubMed PMID: 20158901; PubMed Central PMCID: PMC2834582.

2: Paxton CN, Bleyl SB, Chapman SC, Schoenwolf GC. Identification of differentially expressed genes in early inner ear development. Gene Expr Patterns. 2010 Jan;10(1):31-43. doi: 10.1016/j.gep.2009.11.002. Epub 2009 Nov 11. PubMed PMID: 19913109; PubMed Central PMCID: PMC2818654.

1: Warren M, Puskarczyk K, Chapman SC. Chick embryo proliferation studies using EdU labeling. Dev Dyn. 2009 Apr;238(4):944-9. doi: 10.1002/dvdy.21895. PubMed PMID: 19253396; PubMed Central PMCID: PMC2664394.


Professional Memberships
2018- Fellow, Royal Society of Biology
2009- Member, ASCB
2007- Member, AAAS
2002- Member, Society for Developmental Biology
2001- Member, Genetics Society
2000- Fellow, Anatomical Society
1996- Member, British Society for Developmental Biology

Contact Information

P: 864-656-2328

Campus Location

132 Long Hall, Clemson, SC 29634


Monday - Friday:
8 a.m. - 4:30 p.m.