Publications

2017

Morrow, J.M., Castiglione, G.M., Dungan, S.Z. Tang, P.L., Bhattacharyya, N., Hauser F.E. and B.S.W. Chang (2017). An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease. FEBS Letters, DOI: 10.1002/1873-3468.12637.

Dungan, S.Z. and B.S.W. Chang (2017). Epistatic interactions influence terrestrial–marine functional shifts in cetacean rhodopsin. Proceedings of the Royal Society B, 284: 20162743. PDF

Schott, R.K., Panesar, B., Card, D.C., Preston, M., Castoe, T.A., and B.S.W. Chang (2017). Targeted capture of complete coding regions across divergent species. Genome Biology and Evolution, evx005. PDF

Morrow, J.M., Lazic, S., Dixon Fox, M., Kuo, C., Schott, R.K., Gutierrez, E.A., Santini, F., Tropepe, V., and Belinda S. W. Chang (2017). A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. Journal of Experimental Biology, PDF

2016

Luk, H.L., Bhattacharyya, N., Montisci, F., Morrow, J.M., Melaccio, F., Wada, A., Sheves, M., Fanelli, F., Chang, B.S.W., and M. Olivucci (2016). Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins. Scientific Reports, 6:38425. PDF Suppl

Di Roberto, R.B., Chang, B., Trusina, A., and Sergio G. Peisajovich (2016). Evolution of a G protein-coupled receptor response by mutations in regulatory network interactions. Nature Communications, 7:12344. PDF

van Hazel, I., Dungan, S.Z., Hauser, F.E., Morrow, J.M., Endler, J.A., and B.S.W. Chang (2016). A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics. Protein Science, 25 (7): 1308-1318. PDF

Elbassiouny, A.A., Schott, R.K., Waddell, J.C., Kolmann, M.A., Lehmberg, E.S., Van Nynatten, A., Crampton, W.G.R., Chang, B.S.W., and N.R. Lovejoy (2016). Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes). Mitochondrial DNA Part B: Resources, 1 (1): 401-403. PDF

Gutierrez, E.A., Van Nynatten, A., Lovejoy, N.R., and B.S.W. Chang (2016). Sensory Systems: Molecular Evolution in Vertebrates. In The Encyclopedia of Evolutionary Biology, Kliman, R.M. (ed.), Oxford: Academic Press, vol. 4, pp. 33–40. PDF

Dungan, S.Z., Kosyakov, A., and B.S.W. Chang (2016). Spectral tuning of killer whale (Orcinus orca) rhodopsin: Evidence for positive selection and functional adaptation in a cetacean visual pigment. Molecular Biology and Evolution, 33 (2): 323-336. PDF Suppl

Hauser, F.E., Schott, R.K., Castiglione, G.M., Van Nynatten, A., Kosyakov, A., Tang, P.L., Gow, D.A., and B.S.W. Chang (2016). Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations. Visual Neuroscience, 33: e002. PDF

Schott, R.K., Müller, J., Clement Y.G.Y., Bhattacharyya, N., Chan, N., Xua, M., Morrow, J.M., Ghenu, A.H., Loew, E.R., Tropepe, V., and B.S.W. Chang (2016). Evolutionary transformation of rod photoreceptors in the all-cone retina of a diurnal garter snake. Proceedings of the National Academy of Sciences of the United States of America, 113(2): 356-361. PDF Suppl

2015

Bickelmann, C., Morrow, J.M, Du, J., Schott, R.K., van Hazel, I., Lim, S., Müller, J., and B.S.W. Chang (2015). The molecular origin and evolution of dim-light vision in mammals. Evolution, 69(11): 2995-3003. PDF Suppl

Bloch, N.I., Price, T.D., and B.S.W. Chang (2015). Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga). Molecular Ecology, 24(10): 2449-2462. PDF Suppl

Morrow, J.M. and B.S.W. Chang (2015). Comparative mutagenesis studies of retinal release in light-activated zebrafish rhodopsin using fluorescence spectroscopy. Biochemistry, 54(29):4507-4518. PDF

Van Nynatten, A. Bloom, D., Chang. B.S.W., and N. Lovejoy (2015). Out of the Blue: adaptive visual pigment evolution accompanies Amazon invasion. Biology Letters, 11(7):20150349. PDF

Bloch, N.I., Morrow, J.M., Chang, B.S.W., and T.D. Price (2015). SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers. Evolution, 69(2):341-356. PDF

2014

Hauser, F.E., van Hazel, I., and B.S.W. Chang (2014). Spectral tuning in vertebrate short wavelength sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data? Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 322(7):529-539. PDF

Du, J., Dungan, S.Z., Sabouhanian, A., and B.S.W. Chang (2014). Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes. BMC Evolutionary Biology, 14:96. PDF Suppl 1 Suppl 2 Suppl 3

Lovejoy, D.A., Chang, B.S.W., Lovejoy, N.R., and J. del Castillo (2014). Molecular evolution of GPCRs: CRH/CRH receptors. Journal of Molecular Endocrinology, 52:T43-60. PDF

Schott, R.K., Refvik, S.P., Hauser, F.E., Lopez-Fernandez, H., and B.S.W. Chang (2014). Divergent Positive Selection in Rhodopsin from Lake and Riverine Cichlid Fishes. Molecular Biology and Evolution, 31(5):1149-1165. PDF Suppl. Info

B.S.W. Chang (2014). Ancient insights into uric acid metabolism in primates. Proceedings of the National Academy of Sciences of the United States of America, 111(10):3657-3658. PDF

Williams, R., Ma, X., Schott, R.K., Mohammad, N., Ho, C.Y., Li, C.F., Chang, B.S.W., Demetriou, M., and J.W. Dennis (2014). Encoding Asymmetry of the N-Glycosylation Motif Facilitates Glycoprotein Evolution. PLoS ONE, 9(1):e86088. PDF

2013

Castoe, T.A., … Schott R.K., Chang, B.S.W., … Pollock, D.D. (2013). The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America, 110(51):20645-20650. PDF

van Hazel, I., Sabouhanian, A., Day, L., Endler, J.A., and B.S.W. Chang (2013). Functional characterization of spectral tuning mechanisms in the great bowerbird short-wavelength sensitive visual pigment (SWS1) and the origins of UV/violet vision in passerines and parrots. BMC Evolutionary Biology, 13:250. PDF Suppl. Info

Lin, Y.G., Weadick, C.J., Santini, F., and B.S.W. Chang (2013). Molecular Evolutionary Analysis of Vertebrate Transducins: A Role for Amino Acid Variation in Photoreceptor Deactivation. Journal of Molecular Evolution, 77(5-6):231-245. PDF

2012

Weadick, C.J., and B.S.W. Chang (2012). Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses. BMC Evolutionary Biology, 12:206. PDF

Weadick, C.J., Loew, E.R., Rodd, F.H., and B.S.W. Chang (2012). Visual pigment molecular evolution in the Trinidadian pike cichlid (Crenicichla frenata): A less colourful world for Neotropical cichlids? Molecular Biology and Evolution, 29(10):3045-3060. PDF

Bickelmann, C., Morrow, J.M, Müller, J., and B.S.W. Chang (2012). Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal. Visual Neuroscience, 29:211-217. PDF

Weadick, C.J., and B.S.W. Chang (2012). An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes. Molecular Biology and Evolution, 29(5):1297-1300. PDF Errata

Chang, B.S.W., Du, J., Weadick, C., Müller, J., Bickelmann, C., Yu, D.D., and J.M. Morrow (2012). The future of codon models in studies of molecular evolution: Ancestral reconstruction, and clade models of functional divergence. In Codon Evolution: Mechanisms and Models, G.M. Cannarozzi, A. Schneider (eds.), Oxford University Press, pp. 145-163. PDF

2011

Hult E.F., Tobe S.S., and B.S.W. Chang (2011). Molecular evolution of ultraspiracle protein (USP/RXR) in insects. PLoS ONE, 6(8): e23416. PDF

Morrow, J.M., Lazic, S., and B.S.W. Chang (2011). A novel rhodopsin-like gene expressed in zebrafish retina. Visual Neuroscience, 28:325-335. PDF

Martínez-Pérez, F., Bendena, W.G., Chang, B.S.W., and S.S. Tobe (2011). Influence of codon usage bias in FGLamide-Allatostatin mRNA secondary structure. Peptides, 32:509-517. PDF

2010

Morrow, J.M., and B.S.W. Chang (2010). The p1D4-hrGFP II expression vector: a tool for expressing and purifying visual pigments and other G protein-coupled receptors. Plasmid, 64(3):162-169. PDF

Wong, L., Weadick, C.J., Kuo, C., Chang, B.S.W., and V. Tropepe (2010). Duplicate dmbx1 genes regulate progenitor cell cycle and differentiation during zebrafish midbrain and retinal development. BMC Developmental Biology, 10:100. PDF

2009

Koehler, A., Desser, S., Chang, B., MacDonald, J., Tepass, U., and M. Ringuette (2009). Molecular evolution of SPARC: absence of the acidic module and expression in the endoderm of the starlet sea anemone, Nematostella vectensis. Development, Genes and Evolution, 219:509-521. PDF

Weadick, C.J. and B.S.W. Chang (2009). Molecular evolution of the βγ lens crystallin superfamily: evidence for a retained ancestral function in γN crystallins? Molecular Biology and Evolution 26:1127-1142. PDF

Martinez-Perez, F., Bendena, W.G., Chang, B.S.W., and S.S. Tobe (2009). FGLamide-Allatostatin gene in Arthropoda: Introns early or late? Peptides 30(7):1241-1248. PDF

2008

Hult, E.F., Weadick, C.J., Chang, B.S.W., and S.S. Tobe (2008). Reconstruction of ancestral FGLamide-type insect allatostatins: A novel approach to the study of allatostatin function and evolution. Journal of Insect Physiology 54(6):959-968. PDF

Lenkic, L.E., Wolfe, J., Chang, B.S.W., and S.S. Tobe (2008). Endocrine and reproductive differences and genetic divergence in two populations of the cockroach Diploptera punctata. Journal of Insect Physiology 54(6):931-938. PDF

2007

Weadick, C.J., and B.S.W. Chang (2007). Long-wavelength sensitive visual pigments of the guppy (Poecilia reticulata): six opsins expressed in a single individual. BMC Evolutionary Biology, 7 (Suppl. 1):S11. PDF

Chang, B.S.W., Matz, M.V., Field, S.F., Müller, J., and I. van Hazel (2007). Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: Examples from ancestral visual pigments and GFP-like proteins. In Ancestral Sequence Reconstruction, D.A. Liberles (ed.), Oxford University Press. PDF

Pollock, D.D., and B.S.W. Chang (2007). Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution. In Ancestral Sequence Reconstruction, D.A. Liberles (ed.), Oxford University Press. PDF

2006

Kuang, D., Yao, Y., MacLean, D., Wang, M., Hampson, D.R., and B.S.W. Chang (2006). Ancestral reconstruction of the ligand binding pocket of family C G-protein coupled receptors. Proceedings of the National Academy of Sciences of the United States of America, 103(38):14050-14055. PDF

van Hazel, I., Santini, F., Müller, J. and B.S.W. Chang (2006). Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics. BMC Evolutionary Biology, 6:97. PDF

2005

Chang B.S.W., Ugalde J.A., and Matz M.V. (2005). Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins. Methods in Enzymology, 395: 652-670. PDF

2004

Ugalde J.A., Chang B.S., Matz M.V. (2004). Evolution of coral pigments recreated. Science 305(5689):1433. PDF

Yan, E.C.Y., Ganim, Z., Kazmi, M.A., Chang, B.S.W., Sakmar, T.P., and R.A. Mathies (2004). Resonance Raman analysis of the mechanism of energy storage and chromophore distortion in the primary visual photoproduct. Biochemistry, 43:10867-10876. PDF

2003

Chang, B.S.W. (2003). Ancestral gene reconstruction and synthesis of ancient rhodopsins in the laboratory. Integrative and Comparative Biology, 43:500-507. PDF

Yan, E.C.Y., Kazmi, M.A., Ganim, Z., Hou, J.-M., Pan, D., Chang, B.S.W., Sakmar, T.P., and R.A. Mathies (2003). Counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin. Proceedings of the National Academy of Sciences of the United States of America, 100(16):9262-9267. PDF
Commentary by Robert R. Birge and Barry E. Knox. PDF

2002

Chang, B.S.W., Jönsson, K., Kazmi, M.A., Donoghue, M.J., and T. P. Sakmar (2002). Recreating a functional ancestral archosaur visual pigment. Molecular Biology and Evolution, 19(9):1483-1489. PDF

Chang, B.S.W., Kazmi, M.A., and T.P. Sakmar (2002). Synthetic gene technology: Applications to ancestral gene reconstruction and structure-function studies of receptors. Methods in Enzymology, 343:274-294. PDF

Yan, E.C.Y., Kazmi, M.A., De, S., Chang, B.S.W., Seiburt, C., Marin, E.P., Mathies, R.A., and T.P. Sakmar (2002). Function of extracellular loop 2 in rhodopsin: Glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II. Biochemistry, 41(11):3620-3627. PDF

2001

Lindahl, P.A., and B.S.W. Chang (2001). Evolution of acetyl-CoA synthase. Origins of Life and Evolution of the Biosphere, 31(4/5): 403-434. PDF

Hsu, R., Briscoe, A.D., Chang, B.S.W., and N.E. Pierce (2001). Molecular evolution of a long wavelength-sensitive opsin in mimetic Heliconius butterflies (Lepidoptera: Nymphalidae). Biological Journal of the Linnaean Society, 72:435-449. PDF

2000

Chang, B.S.W., and D.L. Campbell (2000). Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Molecular Biology and Evolution, 17(8):1220-1231. PDF

Chang, B.S.W. and M.L. Donoghue (2000). Recreating ancestral proteins. Trends in Ecology and Evolution, 15(3):109-114. PDF

Hughes, L., Chang, B.S.W., Wagner, D., and N.E. Pierce (2000). Effects of mating history on ejaculate size, fecundity, longevity, and copulation duration in the ant-tended lycaenid butterfly, Jalmenus evagoras. Behavioral Ecology and Sociobiology, 47:119-128. PDF

Pre-2000

JNeurosci-coverTownson, S.M., Chang, B.S.W., Salcedo, E., Chadwell, L., Pierce, N.E., and S.G. Britt (1998). Isolation and physiological characterization of the genes encoding the blue and ultraviolet sensitive opsins of the honeybee, Apis mellifera. Journal of Neuroscience, 18(7):2412-2422. PDF

Chang, B.S.W., Ayers, D., Smith, W.C., and N.E. Pierce (1996). Cloning of the gene encoding honeybee long-wavelength rhodopsin: a new class of insect visual pigments. Gene, 173:215-219. PDF

Chang, B.S.W., Crandall, K.A., Carulli, J.P., and D.L. Hartl (1995). Opsin phylogeny and evolution: a model for blue shifts in wavelength regulation. Molecular Phylogenetics and Evolution, 4(1):31-43. PDF

Ayala, F.J., Chang, B.S.W., and D.L. Hartl (1993). Molecular evolution of the Rh3 gene in Drosophila. Genetica, 92(1):23-32. PDF

Ruvolo, M., Zehr, S., von Dornum, M., Pan, D., Chang, B., and J. Lin (1993). Mitochondrial COII sequences and modern human origins. Molecular Biology and Evolution, 10(6):1115-1135. PDF