Angielczyk, K. D. Dimetrodon is not a dinosaur: using tree thinking to understand the ancient relatives of mammals and their evolution. Evolution: Education & Outreach. in press.
Bardack D. First fossil hagfish (Myxinoidea): a record from the Pennsylvanian of Illinois. Science. 1991;254:701–3.
Bardack D, Richardson ES Jr. New agnathous fishes from the Pennsylvanian of Illinois. Fieldiana Geol. 1977;33:489–510.
Bardack D, Zangerl R. First fossil lamprey: a record from the Pennsylvanian of Illinois. Science. 1968;162:1265–7.
Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature. 2006;444:85–8.
Bourlat SJ, Nielsen C, Economou AD, Telford MJ. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol Phylogen Evol. 2008;49:23–31.
Chang M-M, Zhang J, Miao DA. Lamprey from the Cretaceous Jehol biota of China. Nature. 2006;441:972–4.
Conway Morris S. A redescription of a rare chordate, Metaspriggina walcotti Simonetta and Insom, from the Burgess Shale (Middle Cambrian), British Columbia, Canada. J Paleontol. 2008;82:424–30.
Delarbre C, Barriel V, Janvier P, Gachelin G. Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly. Mol Phylogen Evol. 2002;22:184–92.
Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 2006;439:965–8.
Dominguez P, Jacobson AG, Jefferies RPS. Paired gill slits in a fossil with a calcite skeleton. Nature. 2002;417:841–4.
Donoghue PCJ, Purnell MA. Genome duplication, extinction and vertebrate evolution. Trends Ecol Evol. 2005;20:312–9.
Donoghue PCJ, Purnell MA. Distinguishing heat from light in debate over controversial fossils. BioEssays. 2009;31:178–89.
Donoghue PCJ, Smith MP. The anatomy of Turinia pagei (Powrie) and the phylogenetic status of the Thelodonti. Trans R Soc Edinb Earth Sci. 2001;92:15–37.
Donoghue PCJ, Forey PL, Aldridge RJ. Conodont affinity and chordate phylogeny. Biol Rev. 2000;75:191–251.
Donoghue PCJ, Graham A, Kelsh RN. The origin and evolution of the neural crest. BioEssays. 2008;30:530–41.
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008;452:745–9.
Forey PL. Agnathans recent and fossil, and the origin of jawed vertebrates. Rev Fish Biol Fisheries. 1995;5:267–303.
Gans C, Northcutt RG. Neural crest and the origin of the vertebrates: a new head. Science. 1983;220:268–74.
Gee H. Before the backbone: views on the origin of the vertebrates. London: Chapman & Hall; 1996.
Gess RW, Coates MI, Rubidge BS. A lamprey from the Devonian period of South Africa. Nature. 2006;443:981–4.
Heimberg AM, Sempere LF, Moy VN, Donoghue PCJ, Peterson KJ. MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A. 2008;105:2946–50.
Holland PWH, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Development. 1994;1994 Supplement:125–33.
Huxley-Jones J, Robertson DL, Boot-Handford RP. On the origins of the extracellular matrix in vertebrates. Matrix Biol. 2007;26:2–11.
Janvier P. The phylogeny of the Craniata, with particular reference to the significance of fossil “agnathans”. J Vertebr Paleontol. 1981;1:121–59.
Janvier P. The dawn of the vertebrates: characters versus common ascent in the rise of current vertebrate phylogenies. Palaeontology. 1996;39:259–87.
Janvier P. Ostracoderms and the shaping of the gnathostome characters. In: Ahlberg PE, editor. Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development. London: Taylor and Francis; 2001. p. 172–86.
Janvier P, Lund R. Hardistiella montanensis n. gen. et sp. (Petromyzontida) from the Lower Carboniferous of Montana, with remarks on the affinities of lampreys. J Vertebr Paleontol. 1983;2:407–13.
Jefferies RPS. The Ordovician fossil Lagynocystis pyramidalis (Barrande) and the ancestry of amphioxus. Philos Trans R Soc Lond Series B. 1973;265:409–69.
Jefferies RPS, Brown NA, Daley PEJ. The early phylogeny of chordates and echinoderms and the origin of chordate left–right asymmetry and bilateral symmetry. Acta Zool (Stockh). 1996;77:101–22.
Jeffery WR. Ascidian neural crest-like cells: phylogenetic distribution, relationship to larval complexity, and pigment cell fate. J Exp Zool B Mol Dev Evol. 2006;306B:470–80.
Jeffery WR, Strickler AG, Yamamoto Y. Migratory neural crest-like cells form body pigment in a urochordate embryo. Nature. 2004;431:696–9.
Jenner RA. When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss. Evol Dev. 2004;6:372–8.
Jenner RA, Schram FR. The grand game of metazoan phylogeny: rules and strategies. Biol Rev. 1999;74:121–42.
Kemp TS. The origin of higher taxa: macroevolutionary processes, and the case of the mammals. Acta Zoologica. 2007;88:3–22.
Lartillot N, Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans Royal Soc B Biol Sci. 2008;363:1463–72.
Le Douarin NM, Kalcheim C. The neural crest. Cambridge: Cambridge University Press; 1999.
Løvtrup S. The phylogeny of the Vertebrata. New York: Wiley; 1977.
Mallatt J, Chen J-Y. Fossil sister group of craniates: predicted and found. J Morphol. 2003;258:1–31.
Mallatt J, Winchell CJ. Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogen Evol. 2007;43:1005–22.
Mallatt J, Chen JY, Holland ND. Comment on “A new species of yunnanozoan with implications for deuterostome evolution”. Science. 2003;300:1372.
Martinez-Morales JR, Henrich T, Ramialison M, Wittbrodt J. New genes in the evolution of the neural crest differentiation program. Genome Biology. 2007;8(R36).
Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM. Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev Biol. 2005;282:494–508.
McLennan D. The concept of co-option: why evolution often looks miraculous. Evo Edu Outreach. 2008;1:247–58.
Meyer SC. The origin of biological information and the higher taxonomic categories. Proc Biol Soc Wash. 2004a;117:213–39.
Meyer SC. The Cambrian information explosion: evidence for intelligent design. In: Dembski WA, Ruse M, editors. Debating design: from Darwin to DNA. Cambridge: Cambridge University Press; 2004b. p. 371–91.
Padian K, Chiappe LM. The origin and early evolution of birds. Biol Rev. 1998;73:1–42.
Prohaska SJ, Stadler PF. The duplication of the Hox gene clusters in teleost fishes. Theory Biosci. 2004;123:89–110.
Raineri M. Are protochordates chordates? Biol J Linn Soc. 2006;87:261–84.
Shu D-G. A paleontological perspective of vertebrate origin. Chin Sci Bull. 2003;48:725–35.
Shu D-G, Conway Morris S. Response to comment on “A new species of Yunnanozoon with implications for deuterostome evolution”. Science. 2003;300:1372d.
Shu D-G, Conway Morris S, Zhang X-L. A Pikaia-like chordate from the Lower Cambrian of China. Nature. 1996a;384:157–8.
Shu D-G, Zhang X, Chen L. Reinterpretation of Yunnanozoon as the earliest known hemichordate. Nature. 1996b;380:428–30.
Shu D-G, Luo H-L, Conway Morris S, Zhang X-L, Hu S-X, Chen L, et al. Lower Cambrian vertebrates from south China. Nature. 1999;402:42–6.
Shu D-G, Conway Morris S, Han J, Zhang Z-F, Yasui K, Janvier P, et al. Head and backbone of the Early Cambrian vertebrate Haikouichthys. Nature. 2003a;421:526–9.
Shu D-G, Conway Morris S, Zhang ZF, Liu JN, Han J, Chen L, et al. A new species of Yunnanozoon with implications for deuterostome evolution. Science. 2003b;299:1380–4.
Shu D-G, Conway Morris S, Han J, Zhang Z-F, Liu J-N. Ancestral echinoderms from the Chengjiang deposits of China. Nature. 2004;430:422–8.
Sidow A. Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev. 1996;6:715–22.
Smith AB. The pre-radial history of echinoderms. Geol J. 2005;40:255–80.
Smith AB. Deuterostomes in a twist: the origins of a radical new body plan. Evolut Develop. 2008;10:493–503.
Sweet WC, Donoghue PCJ. Conodonts: past, present and future. J Paleontol. 2001;75:1174–84.
Wagner GP, Amemiya C, Ruddle F. Hox cluster duplications and the opportunity for evolutionary novelties. Proc Natl Acad Sci U S A. 2003;100:14603–6.