ZFIN Person: Mabee, Paula M.

ZFIN ID: ZDB-PERS-960805-320

ZFIN ID: ZDB-PERS-960805-320

Mabee, Paula M.

Email:	pmabee@usd.edu
URL:	http://www.usd.edu/biol/faculty/mabee/index.html
Affiliation:	Mabee Lab
Address:	Department of Biology University of South Dakota Vermillion, SD 57069 USA
Country:	United States
Phone:	(605) 677-6171
Fax:	(605) 677-6557
ORCID ID:

BIOGRAPHY AND RESEARCH INTERESTS

Skeletal development and evolution of fishes; evolution of joints from segmentation mechanisms of radials/pterygiophores in the median and paired fins; description of the development of the zebrafish axial skeleton.

PUBLICATIONS

Fernando, P.C., Mabee, P.M., Zeng, E. (2023) Protein-protein interaction network module changes associated with the vertebrate fin-to-limb transition. Scientific Reports. 13:2259422594

Fernando, P.C., Mabee, P.M., Zeng, E. (2020) Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. BMC Bioinformatics. 21:442

Edmunds, R.C., Su, B., Balhoff, J.P., Eames, B.F., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. (2016) Phenoscape: Identifying candidate genes for evolutionary phenotypes. Molecular Biology and Evolution. 33(1):13-24

Haendel, M.A., Balhoff, J.P., Bastian, F.B., Blackburn, D.C., Blake, J.A., Bradford, Y., Comte, A., Dahdul, W.M., Dececchi, T.A., Druzinsky, R.E., Hayamizu, T.F., Ibrahim, N., Lewis, S.E., Mabee, P.M., Niknejad, A., Robinson-Rechavi, M., Sereno, P.C., Mungall, C.J. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics. 5:21

Mabee, P., Balhoff, J.P., Dahdul, W.M., Lapp, H., Midford, P.E., Vision, T.J., and Westerfield, M. (2012) 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology. 28(3):300-305

Dahdul, W.M., Balhoff, J.P., Blackburn, D.C., Diehl, A.D., Haendel, M.A., Hall, B.K., Lapp, H., Lundberg, J.G., Mungall, C.J., Ringwald, M., Segerdell, E., Van Slyke, C.E., Vickaryous, M.K., Westerfield, M., and Mabee, P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 7(12):e51070

Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., and Mabee, P.M. (2010) The teleost anatomy ontology: anatomical representation for the genomics age. Systematic biology. 59(4):369-383

Dahdul, W.M., Balhoff, J.P., Engeman, J., Grande, T., Hilton, E.J., Kothari, C., Lapp, H., Lundberg, J.G., Midford, P.E., Vision, T.J., Westerfield, M., and Mabee, P.M. (2010) Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One. 5(5):e10708

Crotwell, P.L., and Mabee, P.M. (2007) Gene expression patterns underlying proximal-distal skeletal segmentation in late-stage zebrafish, Danio rerio. Developmental Dynamics : an official publication of the American Association of Anatomists. 236(11):3111-3128

Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of experimental zoology. Part B, Molecular and developmental evolution. 308(5):655-668

Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C., and Westerfield, M. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution. 22(7):345-350

Mabee, P.M., Haendel, M.A., Arratia, G., Coburn, M.M., Hilton, E.J, Lundberg, J.G, Mayden, R.L. (2006) ZFIN Anatomy Working Group: Skeletal System. Manually curated data.

Crotwell, P.L., Sommervold, A.R., and Mabee, P.M. (2004) Expression of bmp2a and bmp2b in late-stage zebrafish median fin development. Gene expression patterns : GEP. 5(2):291-296

Fisher, S., and Mabee, P.M. (2004) Skeletogenesis in Zebrafish Danio rerio: Evolutionary and Developmental Aspects. In Fish Development and Genetics - the Zebrafish and Medaka Models. Gong, Z. and Korh, V., Eds. Book series of "Molecular Aspects of Fish and Marine Biology". 2

Bird, N.C. and Mabee, P.M. (2003) Developmental morphology of the axial skeleton of the zebrafish, Danio rerio (Ostariophysi: Cyprinidae). Developmental Dynamics : an official publication of the American Association of Anatomists. 228(3):337-357

Mabee, P.M., Crotwell, P.L., Bird, N.C., and Burke, A.C. (2002) Evolution of median fin modules in the axial skeleton of fishes. The Journal of experimental zoology. 294(2):77-90

Crotwell, P.L., Clark, T.G., and Mabee, P.M. (2001) Gdf5 is expressed in the developing skeleton of median fins of late-stage zebrafish, Danio rerio. Development genes and evolution. 211(11):555-558

Mabee, P.M. and Bird, N.C. (2001) A preliminary description of the anatomy and development of the zebrafish axial skeleton. ZFIN Direct Data Submission.

Mabee, P.M., Olmstead, K.L., and Cubbage, C.C. (2000) An experimental study of intraspecific variation, developmental timing, and heterochrony in fishes. Evolution; international journal of organic evolution. 54(6):2091-2106

Cubbage, C.C. and Mabee, P.M. (1996) Development of the cranium and paired fins in the zebrafish Danio rerio (Ostariophysi cyprindae). Journal of morphology. 229:121-160

Collazo, A., Fraser, S.E., and Mabee, P.M. (1994) A dual embryonic origin for vertebrate mechanoreceptors. Science (New York, N.Y.). 264:426-430

NON-ZEBRAFISH PUBLICATIONS
Mabee, P.M. 2000. Developmental data and phylogenetic systematics: evolution of the vertebrate limb. American Zoologist 40(5):789-800.

Mabee, P.M. 2000. The usefulness of ontogeny in interpreting morphological characters. In: Phylogenetic Analysis of Morphological Data. ed. J. Wiens. Smithsonian Institution Press: 84-114.

Mabee, P.M., D. Cua, S. Barlow, J.V. Helvik. 1998. Morphology of the hatching glands in Betta splendens (Teleostei: Perciformes). Copeia 1998 (4): 1021-1026.

Mabee, P.M., E. Aldridge, E. Warren, and K. Helenurm. 1998. Effect of Clearing and Staining on Fish Length. Copeia 1998 (2): 346-353.

Mabee, P.M. 1996. Reassessing the ontogenetic criterion: A response to Patterson. Cladistics 12: 586-607.

Mabee, P.M. and T.A. Trendler. 1996. Cranial development in Betta splendens (Teleostei: Percomorpha): Intraspecific variation and interspecific comparisons. J. Morph. 227: 249-287.

Mabee, P.M. 1995. The evolution of pigment pattern development in centrarchid fishes. Copeia 1995: 586-607.

Mabee, P.M. and J. Humphries. 1993. Coding polymorphic data: Examples from allozymes and ontogeny. Systematic Biology 42: 166-181.

Mabee, P.M. 1993. Phylogenetic interpretation of ontogenetic change: sorting out the actual and artefactual in an empirical case study of centrarchid fishes. Zoological Journal of the Linnean Society 107: 175-291.

Wake, D.B., P.M. Mabee, J. Hanken, G. Wagner. 1991. Development and evolution - the emergence of a new field. pp. 582-588, Vol. 1. Proceedings of the Fourth International Congress of Systematic and Evolutionary Biology (ICSEB IV), ed. E. C. Dudley. Dioscorides press: Portland, OR. ICSEB Symposium Proceedings.

Mabee, P.M. 1989. Assumptions underlying the use of ontogenetic sequences in determining character state order. Transactions of the American Fisheries Society 118: 151-158.

Mabee, P.M. 1989. An empirical rejection of the ontogenetic criterion. Cladistics 5(3): 409-416.

Mabee, P.M. 1988. Supraneural and predorsal bones in fishes: development and homologies. Copeia 1988: 827-838.