Basal vertebrates
2015.7.1. Revised

Sister group of vertebrates
Yue JX, Yu JK, Putnam NH, Holland LZ. 2014.
The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution. Genome Biology and Evolution 6:2681-2696.

Edgecombe GD, et al . 2011.
Higher-level metazoan relationships: recent progress and remaining questions. Organisms Diversity & Evolution 11:151-172.

Peterson KJ, Cotton JA, Gehling JG, Pisani D. 2008.
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society B-Biological Sciences 363:1435–1443.

Delsuc, F. et al. (2006)
Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965–968

Divergence time estimation for basal vertebrates

Wang Z,et al. 2013.
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics.

Crottini al.2012.
Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K–T boundary in Madagascar. PNAS.

Inoue, JG
, M Miya, K Lam, BH Tay, JA Danks, J Bell, TI Walker, B Venkatesh. 2010.
Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): A Mitogenomic Perspective. Molecular Biology and Evolution 27:2576-2586.

Alfaro, ME, F Santini, C Brock, H Alamillo, A Dornburg, DL Rabosky, G Carnevale, LJ Harmon. 2009.
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences of the United States of America 106:13410-13414.

Hallström, B. M., and A. Janke. 2009.
Gnathostome phylogenomics utilizing lungfish EST sequences. Mol. Biol. Evol 26:463-471.

Hugall, A. F., R. Foster, and M. S. Y. Lee. 2007.
Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Systematic Biology 56:543-563.

Hedges SB, Kumar S [Review]
Vertebrate genomes compared
SCIENCE 297 (5585): 1283-1285 AUG 23 2002

Hedges SB, Kumar S
Genomic clocks and evolutionary timescales
TRENDS IN GENETICS 19 (4): 200-206 APR 2003

Kumar S, Hedges SB
A molecular timescale for vertebrate evolution
NATURE 392 (6679): 917-920 APR 30 1998

Review of basal vertebrate phylogenetics
Meyer, A, R Zardoya. 2003.
Recent advances in the (molecular) phylogeny of vertebrates. Annu. Rev. Ecol. Evol. Syst. 34:311-338.

Cloutier R, Ahlberg P.E. 1996.
Interrelationships of basal sarcopterygians. In: Stiassny MLJ, Parent LR, J GD, editors. Interrelationships of Fishes. San Diego: Academic Press. p. 445–479.

Phylogenetics of basal vertebrates

Chen M, Zou M, Yang L, & He SP (2012)
Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing. Plos One 7(4).

Kikugawa, K., S. Katoh, S. Kuraku, H. Sakurai, O. Ishida, N. Iwabe and T. Miyata. 2004.
Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.
BMC Biology 2: Art. No. 3 MAR 11.

Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Klein J
Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes.
Mol Biol Evol 2003, 20:287-292.

Zardoya, R., E. Malaga-Trillo, M. Veith, A. Meyer. 2003.
Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani.
Gene 317: 17-27.

Meyer, A., and R. Zardoya. 2003. [Review]
Recent advances in the (molecular) phylogeny of vertebrates.
Annual Review of Ecology, Evolution, and Systematics 34: 311-338.

Hedges SB
Molecular evidence for the early history of living vertebrates.
Major Events in Early Vertebrate Evolution Edited by Ahlberg PE. London: Taylor & Francis; 2001:119-134.

Martin A
The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications
for comparative studies.
Genetica 2001, 111:349-357.

Venkatesh B, Erdmann MV, Brenner S., 2001
Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates.
Proc Natl Acad Sci USA, 98:11382-11387.

Arnason U, Gullberg A, Janke A
Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage.
Zool Scripta 2001, 30:249-249.

Zardoya R, Meyer A
Vertebrate phylogeny: limits of inference of mitochondrial genome and nuclear rDNA sequence data due to an adverse phylogenetic signal/noise ratio.
Major Events in Early Vertebrate Evolution Edited by: Ahlberg PE. London: Taylor & Francis; 2001:135-155.

Rasmussen AS, Arnason U. 1999.
Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree.
Proc. Natl. Acad. Sci. USA 96: 2177-82.

Rasmussen AS, Arnason U
Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes.

Cao Y, Waddell PJ, Okada N, Hasegawa M
The complete mitochondrial sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates.
Mol Biol Evol 1998, 15:1637-1646.

Le, H. L. V., Lecointre, G., and Perasso, R. 1993
A 28S rRNA-based phylogeny of the gnathostomes: First steps in the analysis of conflict and congruence with morphologically based cladograms.
Mol. Phylogenet. Evol. 2, 31-51.

Origin of tetrapods

Brinkmann, H., Denk, A., Zitzler, J., Joss, J. J., and Axel Meyer. 2004.
Complete mitochondrial genome sequences of the south American and the Australian lungfish: testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships.
J. Mol. Evol. 59: 834-848.

Brinkmann, H., Venkatesh, B., Brenner., S. and Axel Meyer. 2004.
Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates.
Proc. Natl. Acad. Sci. USA 101: 4900-4905.

Zardoya R, Cao Y, Hasegawa M, et al.
Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

Zardoya R, Meyer A
Molecular phylogenetic information on the identity of the closest living relative(s) of land vertebrates
NATURWISSENSCHAFTEN 84 (9): 389-397 SEP 1997