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López, J. A, Ryburn, J. A., Fedrigo, and Naylor, G. J. P. Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity. Molecular Phylogenetics and Evolution 52 (1): 20-60.


Naylor, G. J. P., Ryburn, J. A., Fedrigo, O., and López, A. Phylogenetic relationships among the major lineages of sharks and rays deduced from multiple genes. In Reproductive Biology and Phylogeny of Chondrichthyans (Sharks, skates, stingrays and chimaeras). W. Hamlett and B. Jamieson Eds. Univ. Queensland Press.

Collins, T. M., Fedrigo, O. and Naylor, G. J. P. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Systematic Biology, 54 (3): 493-500.

Fedrigo, O., Adams, D. C., and Naylor, G. J. P. DRUIDS-detection of regions with unexpected internal deviation from stationarity. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 304 (2): 119-28.

Krenz, J. G., Naylor, G. J. P., Shaffer, H. B., and Janzen, F. J. Molecular phylogenetics and evolution of turtles. Molecular Phylogenetics and Evolution, 37 (1): 178-191.



Fedrigo, O. and Naylor, G. A gene-specific DNA sequencing chip for exploring molecular evolutionary change. Nucleic Acids Research, 32 (3): 1208-1213.

Maisey, J. G. and Naylor, G. J. P. Mesozoic elasmobranchs, neoselachian phylogeny  and the rise of modern neoselachian diversity. In Mesozoic Fishes 3 – Systematics, Paleoenvironments and Biodiversity. G. Arratia and A. Tintori  Eds. pp. 17-56 Verlag Dr. .F. Pfeil, Munchen Germany.



Naylor, G. J. P. and Adams, D. C. Total evidence versus relevant evidence: response to O'Leary et al. Systematic Biology, 52 (6): 864-865.



Savolainen, V., Chase, M. W., Salamin, N., Soltis, D. E., Soltis, P. S., Lopez, A. J., Fedrigo, O., and Naylor, G. J. P. Phylogeny reconstruction and functional constraints in organellar genomes: plastid versus animal mitochondrion. Systematic Biology, 51 (4): 638-647. 

Schonfeld, J.
, Eulenstein, O., Vander Velden, K., and Naylor, G. J. P. Investigating evolutionary lines of least resistance using the inverse protein-folding problem. Pacific Symposium on Biocomputing.



Baccam, P., Thompson, R. J., Fedrigo, O., Carpenter, S., and Cornette, J. L. PAQ: Partition Analysis of Quasipecies. Bioinformatics, 17: 16-22. 

Naylor, G. J. P.
and Adams, D. C. Are the fossil data really at odds with the molecular data? a re-examination of the morphological evidence for Cetartiodactyla phylogeny. Systematic Biology, 50 (3): 444-453.

Tavaré, S., Adams, D. C., Fedrigo, O., and Naylor, G. J. P. A model for phylogenetic inference using structural and chemical covariates. Pacific Symposium on Biocomputing, p. 215-225. (R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, etc.). World Scientific, Singapore. 



Adams, D. C. and Naylor, G. J. P. A new method for evaluating the structural similarity of proteins using geometric morphometrics. Currents in Computational Molecular Biology. Frontiers Science Series, 30: 120-121 (S. Miyano, R. Shamir, and T. Takagi, eds.). Universal Academy Press, Tokyo. 

Adams, D. C. and Naylor, G. J. P. A comparison of methods for assessing the structural similarity of proteins. Lecture Notes in Computer Science, 2666: 109-115.

Naylor, G. J. P.
and Gerstein, M. Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the Globins. Journal of Molecular Evolution, 51: 223-233.



Grundy W. N. and Naylor, G. J. P. Phylogenetic inference from conserved sites alignments using Hidden Markov Models. Journal of Experimental Zoology, 285 (2): 128-139. 

Sullivan, J., Swofford, D., and Naylor, G. J. P. The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models. Molecular Biology and Evolution, 16 (10): 1347-1354. 



Broughton, R. E., Naylor, G.J.P., and Dowling, T. E. Conflicting phylogenetic patters caused by molecular mechanisms in mitochondrial DNA sequences. Systematic Biology, 47 (4): 696-701. 

Naylor, G. J. P.
and Brown, W. M. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Systematic Biology, 47 (1): 61-76. 

Voytas, D. F. and Naylor, G. J. P. Rapid flux in plant genomes. Nature Genetics, 20: 6-7.



Dowling, T. E. and Naylor, G. J. P. Evolutionary relationships of minnows in the genus Luxilus (Teleostei : Cyprinidae) as determined from cytochrome b sequences 
Copeia, 1997 (4): 758-765.

Naylor, G. J. P. and Brown, W. M. Structural biology and phylogenetic estimation. Nature, 388 (6642): 527-528.

Naylor, G. J. P.
, Martin, A. P., Mattison, E. G., and Brown, W. M. Interrelationships of Lamniform sharks: testing phylogenetic hypotheses with sequence data. In Molecular Systematics of Fishes. T. D. Kocher and C. A. Stepien, Eds. Academic Press.




Naylor, G. J. P., Collins, T. M., Brown, W. M. Hydrophobicity and phylogeny. Nature, 373 (6515): 565-566.





Collins, T. M, P. H. Wimberger, G. J. P. Naylor. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology, 43 (4): 482-496.

Naylor, G. J. P.
Evolutionary reconstruction using gene and protein-sequence. Journal of Neurochemistry, 62: s57-s57 suppl.


Naylor, G. J. P.
and Marcus, L. 1994. Identifying isolated shark teeth of the genus Carcharhinus to species: reference for tracking phyletic change through the fossil record. American Museum Novitates, 3109: 1-53.




Naylor, G. J. P. Plotting frequency-distributions of phylogenetic groupings found among sets of most parsimonious trees. Cladistics-the International Journal of the Willi Hennig Society, 8 (2): 161-164.


Naylor, G. J. P.
The phylogenetic-relationships among requiem and hammerhead sharks - inferring phylogeny when thousands of equally most parsimonious trees result. Cladistics-the International Journal of the Willi Hennig Society, 8 (4): 295-318.

Martin, A. P, Naylor, G. J. P., Palumbi, S. R. Rates of mitochondrial-DNA evolution in sharks are slow compared with mammals. Nature, 357 (6374): 153-155.