EXPLOSIVE RADIATION OR CRYPTIC MASS EXTINCTION? INTERPRETING SIGNATURES IN MOLECULAR PHYLOGENIES

Beerling, 2007, The emerald planet: how plants changed Earth's history, 10.1093/oso/9780192806024.001.0001

Benton, 1995, Diversification and extinction in the history of life, Science, 268, 52, 10.1126/science.7701342

Benton, 2007, How did life become so diverse? The dynamics of diversification according to the fossil record and molecular phylogenetics, Palaeontology, 50, 23, 10.1111/j.1475-4983.2006.00612.x

Boatwright, 2007, Systematic position of the anomalous genus Cadia and the phylogeny of the tribe Podalyrieae (Fabaceae), Syst. Bot., 33, 133, 10.1600/036364408783887500

Bromham, 2003, Molecular clocks and explosive radiations, J. Mol. Evol., 57, S13, 10.1007/s00239-003-0002-7

Conway Morris, 2006, Darwin's dilemma: the realities of the Cambrian ‘explosion’, Philos. Trans. R. Soc. Lond., B, 361, 1069, 10.1098/rstb.2006.1846

Cooper, 1998, Evolutionary explosions and the phylogenetic fuse, Trends Ecol. Evol., 13, 151, 10.1016/S0169-5347(97)01277-9

Crisp, 2003, Molecular evidence for definition of genera in the Oxylobium group (Fabaceae: Mirbelieae), Syst. Bot., 28, 705

Crisp, 2003, Advances in legume systematics, part 10. higher level systematics, 253

Crisp, 2003, Phylogeny and evolution of anomalous roots in Daviesia (Fabaceae: Mirbelieae), Int. J. Plant Sci., 164, 603, 10.1086/375318

Crisp, 2007, A congruent molecular signature of vicariance across multiple plant lineages, Mol. Phylogenet. Evol., 43, 1106, 10.1016/j.ympev.2007.02.030

Crisp, 2004, Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?, Philos. Trans. R. Soc. Lond., B, Biol. Sci., 359, 1551, 10.1098/rstb.2004.1528

Doyle, 1991, Molecular techniques in taxonomy, 283, 10.1007/978-3-642-83962-7_18

Foote, 1996, Fossil preservation and the stratigraphic ranges of taxa, Paleobiology, 22, 121, 10.1017/S0094837300016134

Harvey, 1994, Phylogenies without fossils, Evolution, 48, 523, 10.1111/j.1558-5646.1994.tb01341.x

Ho, 2005, Accuracy of rate estimation using relaxed-clock models with a critical focus on the early Metazoan radiation, Mol. Biol. Evol., 22, 1355, 10.1093/molbev/msi125

Jablonski, 1995, Extinction rates, 25

Jablonski, 2005, Mass extinctions and macroevolution, Paleobiology, 31, 192, 10.1666/0094-8373(2005)031[0192:MEAM]2.0.CO;2

Klak, 2004, Unmatched tempo of evolution in Southern African semi-desert ice plants, Nature, 427, 63, 10.1038/nature02243

Lavin, 2005, Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary, Syst. Biol., 54, 575, 10.1080/10635150590947131

Lawver, 2003, Evolution of Cenozoic seaways in the circum-Antarctic region, Palaeogeogr. Palaeoclimatol. Palaeoecol., 198, 11, 10.1016/S0031-0182(03)00392-4

Lovette, 1999, Explosive speciation in the New World Dendroica warblers, Proc. R. Soc. Lond., B, 266, 1629, 10.1098/rspb.1999.0825

May, 1995, Extinction rates, 1

McElwain, 2007, Mass extinction events and the plant fossil record, Trends Ecol. Evol., 22, 548, 10.1016/j.tree.2007.09.003

McKenna, 2006, Tropical forests are both evolutionary cradles and museums of leaf beetle diversity, Proc. Natl. Acad. Sci. USA, 103, 10947, 10.1073/pnas.0602712103

McPeek, 2008, The ecological dynamics of clade diversification and community assembly, Am. Nat., 172, E270, 10.1086/593137

Moore, 2007, Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations, Am. Nat., 170, S28, 10.1086/519460

Nee, 2006, Birth-death models in macroevolution, Annu. Rev. Ecol. Syst., 37, 1, 10.1146/annurev.ecolsys.37.091305.110035

Nee, 1995, Extinction rates, 164

Niklas, 1997, The evolutionary biology of plants

Orthia, 2005, Bush peas: a rapid radiation with no support for monophyly of Pultenaea (Fabaceae: Mirbelieae), Aust. Syst. Bot., 18, 133, 10.1071/SB04028

Peters, 2002, Determinants of extinction in the fossil record, Nature, 416, 420, 10.1038/416420a

Poe, 2004, Birds in a bush: five genes indicate explosive evolution of avian orders, Evolution, 58, 404, 10.1111/j.0014-3820.2004.tb01655.x

Posada, 1998, MODELTEST: testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817

Rabosky, 2006, LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies, Evol. Bioinform., 257

Rabosky, 2006, Likelihood methods for detecting temporal shifts in diversification rates, Evolution, 60, 1152, 10.1111/j.0014-3820.2006.tb01194.x

Rambaut, A. 1996. Se-Al: sequence alignment editor. Available at http://evolve.zoo.ox.ac.uk/, Univ. of Oxford, Department of Zoology.

Rambaut, 2002, Phyl-O-Gen: phylogenetic tree simulator package

Raup, 1976, Species diversity in the Phanerozoic: an interpretation, Paleobiology, 2, 289, 10.1017/S0094837300004929

Raup, 1991, Extinction-bad genes or bad luck, New Scientist, 131, 46

Ree, 2005, Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis, Evolution, 59, 257, 10.1111/j.0014-3820.2005.tb00986.x

Ricklefs, 2007, History and diversity: explorations at the intersection of ecology and evolution, Am. Nat., 170, S56, 10.1086/519402

Rokas, 2005, Animal evolution and the molecular signature of radiations compressed in time, Science, 310, 1933, 10.1126/science.1116759

Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180

Sanderson, 2003, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, 19, 301, 10.1093/bioinformatics/19.2.301

Sanderson, 1984, A kinetic-model of Phanerozoic taxonomic diversity .3. Post-Paleozoic families and mass extinctions, Paleobiology, 10, 246, 10.1017/S0094837300008186

Smith, 2007, Marine diversity through the Phanerozoic: problems and prospects, J. Geol. Soc. Lond., 164, 731, 10.1144/0016/76492006-184

Turgeon, 2005, Simultaneous quaternary radiations of three damselfly clades across the Holarctic, Am. Nat., 165, E78, 10.1086/428682

Zachos, 2001, Trends, rhythms, and aberrations in global climate 65 Ma to present, Science, 292, 686, 10.1126/science.1059412

Zwickl, 2006, Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion