RESEARCH and review ARTICLES
|
Bonett, R.M., E. L. Bierbaum, A. J. Hess, S. D. Trame, C. W. Eckhardt, M. A. Herrboldt, C. N. McGouran, A. D. Kolozsvary, S. Sowell, A. M. Flusche and R. McGlone 2025. Compounding heterochrony shapes the salamander visual system across adaptive zones. Proceedings of the Royal Society, B 292:20250910.
|
|
Herrboldt, M. A., C. N. C. Wright, and R. M. Bonett 2024. Seasonal heterochrony of reproductive development and gene expression in a polymorphic salamander. Developmental Dynamics 10.1002/dvdy.744.
| ||
|
Bonett, R. M., and N. M. Ledbetter 2022. Paedomorphic salamanders are larval in form and patterns of limb emergence inform life cycle evolution. Developmental Dynamics 251:934-941.
| ||
|
Bonett, R. M., N. M. Ledbetter, A. J. Hess, M. A. Herrboldt, and M. Denoël 2022. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development. Developmental Dynamics 251:957-972.
| ||
|
Herrboldt, M. A., M. A. Steffen, C. N. McGouran, and R. M. Bonett 2021. Pheromone gene diversification and the evolution of courtship glands in plethodontid salamanders. Journal of Molecular Evolution 89:576-587.
| ||
|
Bonett, R. M., A. J. Hess, and N. M. Ledbetter 2020. Facultative transitions have trouble committing, but stable life cycles predict salamander genome size evolution. Evolutionary Biology 47:111-122.
| ||
|
Clay, T. A., M. A. Steffen, M. L. Treglia, D. T. Torres, A. L. Trujano-Alvarez, and R. M. Bonett 2019. Multiple stressors produce differential transcriptomic patterns in a stream-dwelling
salamander. BMC Genomics 20:482,1-13. | ||
|
Ledbetter, N. M. and R. M. Bonett. 2019. Terrestriality constrains salamander limb diversification: Implications for the evolution of pentadactyly. Journal of Evolutionary Biology 32:642-652.
| ||
|
Bonett, R. M., J. G. Phillips, N. M. Ledbetter, S. D. Martin, and L. Lehman. 2018. Rapid phenotypic evolution following shifts in life cycle complexity. Proceedings of the Royal Society, B 285:20172304.
| ||
|
Bonett, R. M. 2018. Heterochrony. In Evolutionary Developmental Biology,
Edited by: L. Nuño de la Rosa, G.B. Müller; Springer International Publishing. 1-14. | ||
|
Bonett, R. M. and A. L. Blair. 2017. Evidence for complex life cycle constraints on
salamander body form diversification Proceedings of the National Academy of Science U.S.A. 114:9936-9941. | ||
|
Phillips, J. G., D. B. Fenolio, S. L. Emel, and R. M. Bonett. 2017. Hydrologic and geologic history of the Ozark Plateau drive phylogenomic patterns in a cave-obligate salamander. Journal of Biogeography 44:2463-2474.
| ||
|
Beachy, C. K., T. J. Ryan, and R. M. Bonett. 2017. How metamorphosis is different in plethodontids: larval life history perspectives on life-cycle evolution. Herpetologica 73:252-258.
Symposium Volume from Plethodontid Conference, Highlands, NC. | ||
|
Bonett, R. M. 2016. Analyzing endocrine system conservation and evolution.
General and Comparative Endocrinology 234:3-9. Symposium Volume from the 3rd NASCE Conference, Ottawa, ON. | ||
|
Bonett, R. M. 2016. An integrative endocrine model for the evolution of developmental timing and life history of plethodontids and other salamanders. Copeia 104:209-221.
Symposium Volume from the 6th Conference on Plethodontid Salamanders, Tulsa, OK. | ||
|
Kyono, Y., A. Subramani, P. Ramadoss, A. N. Hollenberg, R. M. Bonett, and R. J. Denver. 2016. Liganded thyroid hormone receptors transactivate the DNA Methyltransferase 3a gene in mouse neuronal cells. Endocrinology 157:3647-3657.
| ||
|
Martin, S. D., D. B. Shepard, M. A. Steffen, J. G. Phillips, and R. M. Bonett. 2016. Biogeography and colonization history of plethodontid salamanders from the Interior Highlands of eastern North America. Journal of Biogeography 43:410-422.
| ||
|
Martin, S. D. and R. M. Bonett. 2015. Biogeography and divergent patterns of body size disparification in North American minnows. Molecular Phylogentics and Evolution 93:17-28.
| ||
|
Bagamasbad, P. D., R. M. Bonett, L. Sachs, N. Buisine, S. Raj, J. R. Knoedler, Y. Kyono, Y. Ruan, X. Ruan, and R. J. Denver. 2015. Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module. Molecular Endocrinology 29:856-72.
| ||
|
Bonett, R. M., M. A. Steffen, and G. A. Robison. 2014. Heterochrony repolarized: a phylogenetic analysis of developmental timing in plethodontid salamanders. EvoDevo 5:27,1-18.
| ||
|
Bonett, R. M., M. A. Steffen, S. M. Lambert, J. J. Wiens, and P. T. Chippindale. 2014. Evolution of paedomorphosis in plethodontid salamanders: ecological correlates and re-evolution of metamorphosis. Evolution 68:466-482.
| ||
|
Aran, R. P., M. A. Steffen, S. D. Martin, O. I. Lopez, and R. M. Bonett. 2014. Reduced effects of thyroid hormone on gene expression and metamorphosis in a paedomorphic plethodontid salamander. Journal of Experimental Zoology (Mol. Dev. Evol.) 322B:294–303.
Fenolio, D. B., M. L. Niemiller, R. M. Bonett, G. O. Graening, B. A. Collier, and J. F. Stout. 2014. Life history, demography, and the influence of cave-roosting bats on a population of the Grotto Salamander (Eurycea spelaea) from the Ozark Plateaus of Oklahoma (Caudata: Plethodontidae). Herpetological Conservation and Biology 9:394-405.
| ||||
|
Steffen, M. A., K. J. Irwin, A. L. Blair, and R. M. Bonett. 2014. Larval masquerade: a new species of paedomorphic salamander (Caudata: Plethodontidae: Eurycea) from the Ouachita Mountains of North America. Zootaxa 3786:423-442.
| ||
|
Bonett, R. M., A. L. Trujano-Alvarez, M. J. Williams, and E. K. Timpe. 2013. Biogeography and body size shuffling of aquatic salamander communities on a shifting refuge. Proceedings of the Royal Society, B 280:20130200.
| ||
|
Rovito, S. M., G. Parra-Olea, J. Hanken, R. M. Bonett, and D. B. Wake. 2013. Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius). Biological Journal of the Linnean Society 109:622-643.
| ||
|
Elmer, K. R., R. M. Bonett, D. B. Wake, and S. C. Lougheed. 2013. Early Miocene origin and cryptic diversification of South American salamanders. BMC Evolutionary Biology 13:59, 1-16.
| ||
|
Bagamasbad, P., T. Ziera, S. A. Borden, A. Rozeboom, A. Seasholtz, R. M. Bonett, and R. J. Denver. 2012. Molecular basis for glucocorticoid induction of the Krüppel-like factor 9 gene in hippocampal neurons. Endocrinology 153:5334-5345.
| ||
|
Martin, S. D., B. A. Harris, J. R. Collums, and R. M. Bonett. 2012. Life between predators and a small space: substrate selection of an interstitial space-dwelling stream salamander. Journal of Zoology 287:205-214.
| ||
|
Denver, R. J., R. M. Bonett, and G. C. Boorse. 2011. Evolution of leptin structure and function. Neuroendocrinology 94:21-38.
| ||
|
Emel, S. L. and R. M. Bonett. 2011. Considering alternative life history modes and genetic divergence in conservation: a case study of the Oklahoma salamander. Conservation Genetics 12:1243-1259.
| ||
|
Bonett, R. M., M. A. Steffen, A. L. Trujano-Alvarez, S. D. Martin, C. T. McAllister, and C. R. Bursey. 2011. Distribution, intensity, and genetic diversity of Clinostomum metacercariae (Trematoda: Digenea), in a modified Ozark stream system. Journal of Parasitology 97:177-184.
| ||
|
Bonett, R. M., E. D. Hoopfer, and R. J. Denver. 2010. Molecular mechanisms of corticosteroid synergy with thyroid hormone during tadpole metamorphosis. General and Comparative Endocrinology 168:209-219.
| ||
|
Bonett, R. M., P. T. Chippindale, P. A. Moler, R. W. Van Devender, and D. B. Wake. 2009. The evolution of gigantism in amphiuma salamanders. PLoS One 4:5,1-10.
| ||
|
Timpe, E. K., S. P. Graham, and R. M. Bonett. 2009. Phylogeography of the Brownback salamander reveals patterns of local endemism in Southern Appalachian springs. Molecular Phylogenetics and Evolution 52: 368-376.
| ||
|
Bonett, R. M., F. Hu, P. Bagamasbad, and R. J. Denver. 2009. Stressor and glucocorticoid-dependent induction of the immediate early gene Krüppel-like factor 9 (KLF9): implications for neural development and plasticity. Endocrinology 150: 1757-1765.
| ||
|
Zelditch, M. L., A. R. Wood, R. M. Bonett, and D. L. Swiderski. 2008. Modularity of the rodent mandible: Integrating bones, muscles and teeth. Evolution and Development 10: 756-768.
| ||
|
Bonett, R. M., K. H. Kozak, D. R. Vieites, A. Bare, J. A. Wooten, and S. E. Trauth. 2007. The importance of comparative phylogeography in diagnosing introduced species: a lesson from the seal salamander, Desmognathus monticola. BMC Ecology 7: 7,1-11.
| ||
|
Bonett, R. M. and P. T. Chippindale. 2006. Streambed microstructure predicts evolution of development and life history mode in the plethodontid salamander, Eurycea tynerensis. BMC Biology 4: 6,1-12.
| ||
|
Vences, M., M. Thomas, R. M. Bonett, and D. R. Vieites. 2005 Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society B 360: 1859-1868.
| ||
|
Kozak, K. H., A. Larson, R. M. Bonett, and L. Harmon. 2005. Phylogenetic analysis of ecomorphological divergence, species coexistance and diversification rates in dusky salamanders (Plethodontidae: Desmognathinae). Evolution 59: 2000-2016.
| ||
|
Köhler, J., D. R. Vieites, R. M. Bonett, F. Hita García, F. Glaw, D. Steinke, and M. Vences. 2005. New amphibians and global conservation: A boost in species discoveries in a highly endangered vertebrate group. BioScience 55: 693-696.
| ||
|
Min, M. S., S.Y. Yang, R. M. Bonett, D. R. Vieites, R. A Brandon, and D. B. Wake. 2005. Discovery of the first Asian plethodontid salamander. Nature 435: 87-90.
| ||
|
Wiens, J. J., R. M. Bonett, and P. T. Chippindale. 2005. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Systematic Biology 54:91-110.
| ||
|
Chippindale P. T., R. M. Bonett, A. S. Baldwin, and J. J. Wiens. 2004 Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders. Evolution 58: 2809-2822.
| ||
|
Bonett, R. M. and P. T. Chippindale. 2004 Speciation, phylogeography and evolution of live history and morphology in the salamanders of the Eurycea multiplicata complex. Molecular Ecology 13:1189-1203.
| ||
|
Noonan, B. P. and R. M. Bonett. 2003. A new species of Hyalinobatrachium from the Highlands of Guyana. Journal of Herpetology 37: 91-97.
| ||
|
Bonett, R. M. 2002. Analysis of the contact zone between the dusky salamanders Desmognathus fuscus fuscus and Desmognathus fuscus conanti (Caudata: Plethodontidae). Copeia 2002: 344-355.
| ||
|
Bonett, R. M., T. C. LaDuke, S. G. Tilley, and T. Whitford. 2000. Allozyme analysis of dusky salamanders (Desmognathus) in northeastern Pennsylvania. Journal of the Pennsylvania Academy of Science 73: 87-91.
|
notes and accounts
|
Phillips, J. G., M. A. Steffen, and R. M. Bonett. 2014. Eurycea tynerensis (Oklahoma Salamander). Terrestrial oviposition. Herpetological Review 45:473-474.
|
|
Martin, S. D. and R. M. Bonett. 2013. Distribution Record and Range Extension for the Southern Redbelly Dace, Chrosomus erythrogaster (Actinopterygii: Cypriniformes), from Sequoyah County, Oklahoma. Proceedings of the Oklahoma Academy of Sciences 93:23-24.
|
|
McAllister, C. T., C. R. Bursey, M. A. Steffen, S. D. Martin, A. L. Trujano-Alvarez, and R. M. Bonett. 2011. Sphryanura euryceae (Trematoda: Sphyranuridae) from the Grotto Salamander, Eurycea spelaea and Oklahoma Salamander, Eurycea tynerensis (Caudata: Plethodontidae), in Northeastern Oklahoma, U.S.A. Comparative Parasitology 78: 188-192.
|
|
Fenolio, D. B. and R. M. Bonett. 2009. Recent findings about the biology, ecology, and systematics of the grotto salamander, Eurycea spelaea. Proceedings of the 15th International Congress of Speleology 1:234-237.
|
|
Bonett, R. M., R. L. Mueller, and D. B. Wake. 2005. Why should reacquisition of larval stages by desmognathine salamanders surprise us? Herpetological Review 36:112-113.
|
|
Bonett, R. M. 2005. The Oklahoma salamander, Eurycea tynerensis. Pp. 767-769. In: Amphibian declines, the conservation and status of United States species. Ed. M. Lannoo. University of California Press, Berkeley, CA.
|
|
Bonett, R. M. and P. T. Chippindale. 2005. The dwarf salamander, Eurycea quadridigitata. Pp. 759-760. In: Amphibian declines, the conservation and status of United States species. Ed. M. Lannoo. University of California Press, Berkeley, CA.
|
|
Means, D. B. and R. M. Bonett. 2005. The spotted dusky salamander, Desmognathus conanti. Pp. 705-706. In: Amphibian declines, the conservation and status of United States species. Ed. M. Lannoo. University of California Press, Berkeley, CA.
|
