Origins and Diversity of Land Plants

 

Course Bibliography 2004: A summary of the recent literature.

 

 

Introductory and Overview Literature

 

Feild, T. S. 2002. Plant evolution viewed through a functional and paleoclimatic prism. Amer. J. Bot. 89: 2034–2036.

 

Palmer, J. D., D. E. Soltis, and M. W. Chase 2004. The plant tree of life: an overview and some points of view. Amer. J. Bot. 91: 1437–1445.

 

Primers on Phylogenetic Theory

 

Baldauf, S. L. 2003. Phylogeny for the faint of heart: a tutorial. Trends in Genetics 19: 345–351.

 

Lewis, P. O. 2001. Phylogenetic systematics turns over a new leaf. Trends in Ecology and Evolution 16: 30–37.

 

Extinction

 

Benton, M. J. 1995. Diversification and extinction in the history of life. Science 268: 52–58.

 

Solé, R. V., J. M. Montoya, and D. H. Erwin 2002. Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics. Phil. Trans. R. Soc. Lond. 357: 697–707.

 

Wilf, P. and K. R. Johnson 2004. Land plant extinction and the end of the Cretaceous: a quantitative analysis of the North Dakota megafloral record. Paleobiology 30: 347–368.

 

Wilf, P., K. R. Johnson, and B. T. Huber 2003. Correlated terrestrial and marine evidence for global climate changes before mass extinction at the Cretaceous–Paleogene boundary. PNAS 100: 599–604.

 

Evolutionary Divergence and Estimates of Time

 

Benton, M. J. and F. J. Ayala 2003. Dating the tree of life. Science 300: 1698–1700.

 

Hedges, S. B. and S. Kumar 2003. Genomic clocks and evolutionary timescales. Trends in Genetics 19: 200–206.

 

Hedges, S. B. and S. Kumar 2004. Precision of molecular time estimates. Trends in Genetics 20: 242–247.

 

Rodríguez–Trelles, F., R. Tarrío, and F. J. Ayala 2002. A methodological bias toward overestimation of molecular evolutionary time scales. PNAS 99: 8112–8115.

 

Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19: 101–109.

 

Sandeson, M. J. 2003. Molecular data from 27 proteins do not support a Precambrian origin of land plants. Amer. J. Bot. 90: 954–956.

 

Sanderson, M. J., J. L. Thorne, N. Wikström, and K. Bremer 2004. Molecular evidence on plant divergence times. Amer. J. Bot. 91: 1656–1665.

 

Soltis, P. S., D. E. Soltis , V. Savolainen, P. R. Crane, and T. G. Barraclough 2002. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. PNAS 99: 4430–4435.

 

Morphology and Development

 

Endress, P. K. 2003. Morphology and angiosperm systematics in the molecular era. Bot. Rev. 68: 545–570.

 

Friedman, W. E., R. C. Moore, and M. D. Purugganan 2004. The evolution of plant development. Amer. J. Bot. 91: 1726–1741

 

Kaplan, D. R. 2001. The science of plant morphology: definition, history, and the role in modern biology. Amer J. Bot. 88: 1711–1741.

 

Raven, J. A. and D. Edwards 2001. Roots: evolutionary origins and biogeochemical significance. J. Experimental Bot. 52: 381–401.

 

Plant Cells and Biochemistry

 

Cook, M. E., L. E. Graham, C. E. J. Botha, and C. A. Lavin 1997. Comparative ultrastructure of plasmodesmata of Chara and selected bryophytes: toward an elucidation of the evolutionary origin of plant plasmodesmata. Amer. J. Bot. 84: 1169–1178.

 

Popper, Z. A. and S. C. Fry 2003. Primary cell wall composition of bryophytes and charophytes. Annals of Botany 91: 1–12.

 

Raven, J. A. 2000. Land plant biochemistry. Phil. Trans. R. Soc. Lond. 255: 833–846.

 

Southworth, D. and M. Cresti 1997. Comparison of flagellated and nonflagellated sperm in plants. Amer. J. Bot. 84: 1301–1311.

 

Progenitors of Land Plants

 

Cook, M. E. 2004 Cytokinesis in Coleochaete orbicularis (Charophyceae): an ancestral mechanism inherited by plants. Amer. J. Bot. 91: 313–320.

 

Delwiche, C. F., K. G. Karol, M. T. Cimino, and K. J. Sytsma 2002. Phylogeny of the genus Coleochaete (Coleochaetales, Charophyta) and related taxa infered by analysis of the chloroplast gene rbcL. J. Phycol. 38: 394–403.

 

Karol, K. G., R. M. McCourt, M. T. Cimino, and C. F. Delwiche 2001. The closest living relatives of land plants. Science 294: 2351–2353.

 

Lewis, L. A. and R. M. McCourt 2004. Green algae and the origin of land plants. Amer. J. Bot. 91: 1535–1556.

 

Turmel, M., C. Otis, and C. Lemieux 2003. The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell 15: 1888–1903.

 

Coevolution of Fungi and Land Plants

 

Brundrett, M. C. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275–304.

 

Heckman, D. S., D. M. Geiser, B. R. Eidell, R. L. Stauffer, N. L. Kardos, and S. B. Hedges 2001. Molecular evidence for the early colonization of land by fungi and plants. Science 293: 1129–1133.

 

Read, D. J., J. G. Duckett, R. Francis, R. Ligrone, and A. Russel 2000. Symbiotic fungal associations in 'lower' land plants. Phil. Trans. R. Soc. Lond. 355: 815–831.

 

Fossil Record

 

Cheng–Sen, L. and D. Edwards 1997. A new microphyllous plant from the Lower Devonian of Yunnan Province, China. Amer. J. Bot. 84: 1441–1448.

 

Crane, P. R., P. Herendeen, and E. M. Friis 2004. Fossils and plant phylogeny. Amer. J. Bot. 91: 1683–1699.

 

Crepet, W. L., K. C. Nixon, and M. A. Gandolfo 2004. Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits. Amer. J. Bot. 91: 1666–1682.

 

Dilcher, D. 2000. Toward a new synthesis: Major evolutionary trends in the angiosperm fossil record. PNAS 97: 7030–7036.

 

Edwards, D. 2000. The role of Mid–Paleozoic mesofossils in the detection of early bryophytes. Phil. Trans. R. Soc. Lond. 355: 733–755.

 

Gottschling, M. and H. H. Hilger 2003. First fossil record of transfer cells in Angiosperms. Amer. J. Bot. 90: 957–959.

 

Graham, A. 2003. The concepts of deep-time floras and paleobotanical hot–spots. Syst. Bot. 28: 461–464.

 

Kodner, R. B. and L. E. Graham 2001. High-temperature, acid-hydrolyzed remains of Polytrichum (Musci, Polytrichaceae) resemble enigmatic Silurian-Devonian tubular microfossils. Amer. J. Bot. 88: 462–466.

 

Kotyk, M. E., J. F.Basinger, P. G. Gensel, and T. A. de Freitas 2002. Morphologically complex plant microfossils from the Late Silurian of Arctic Canada. Amer. J. Bot. 89: 1004–1013.

 

Poort,  R. J., H. Visscher, and D. L. Dilcher 1996. Zoidogamy in fossil gymnosperms: The centenary of a concept, with special reference to prepollen of late Paleozoic conifers. PNAS 93: 11713–11717.

 

Roth–Nebelsick, A., G. Grimm, V. Mosbrugger, H. Hass, and H. Kerp 2000. Morphometric analysis of Rhynia and Asteroxylon: testing functional aspects of early land plant evolution. Paleobiology 26: 405–418.

 

Wellman, C. H. and J. Gray 2000. The microfossil record of early land plants. Phil. Trans. R. Soc. Lond. 355: 717–732.

 

Wellman, C. H., P. L. Osterloff, and U. Mohiuddin 2003. Fragments of the earliest land plants. Nature 425: 282–285.

 

Emergence of Land Plants

 

Bateman, R. M. and W. A. DiMichele 2003. Genesis of phenotypic and genotypic diversity in land plants: the present as the key to the past. Systematics and Biodiversity 1: 13–28.

 

Blackwell, W. H. 2003. Two theories of the origin of the land plant sporophyte: which is left standing? Bot. Rev. 69: 125–148.

 

Cooke, T. J., D. Poli, and J. D. Cohen 2003. Did auxin play a crucial role in the evolution of novel body plans during the Late Silurian-Early Devonian radiation of land plants? Chapter 5 in, The Evolution of Plant Physiology, A. Hemsley and I. Poole (eds.). Academic Press.

 

Duff, R. J. and D. L. Nickrent 1999. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences. Amer. J. Bot. 86: 372–386.

 

Graham, L. E., M. E. Cook, and J. S. Busse 2000. The origin of plants: body plan changes contributing to a major evolutionary radiation. PNAS 97: 4535–4540.

 

Graham, L. K. E. and L. W. Wilcox 2000. The origin of alternation of generations in land plants: a focus on matrotrophy and hexose transport. Phil. Trans. R. Soc. Lond. 355: 757–767.

 

Kenrick, P. and P. R. Crane 1997. The origin and early evolution of plants on land. Nature 389: 33–39.

 

Nickrent, D. L., C. L. Parkinson, J. D. Palmer, R. J. Duff  2000. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17: 1885–1895.

 

Renzaglia, K. S., R. J. Duff, D. L. Nickrent, and D. J. Garbary 2000. Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny. Phil. Trans. R. Soc. Lond. 355: 769–793.

 

Soltis, P. S., D. E. Soltis, P. G. Wolf, D. L. Nickrent, S. Chaw, and R. L. Chapman 1999. The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol. Biol. Evol. 16: 1774–1784.

 

Bryophtyes and Land Plant Evolution

 

Carafa, A., J. G. Duckett, and R. Ligrone 2003. The placenta in Monoclea forsteri Hook. and Treubia lacunosa (Col.) Prosk: insights into placental evolution in liverworts. Annals of Botany 92: 299–307.

 

Henschel, K., R. Kofuji, M. Hasebe, H. Saedler, T. Münster, and G. Theißen 2002. Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens. Mol. Biol. Evol. 19: 801–814.

 

Kugita, M., A. Kaneko, Y. Yamamoto, Y. Takeya, T. Matsumoto and K. Yoshinaga 2003. The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Research 31: 716–721.

 

Mishler, B. D. 2001. The biology of bryophytes: bryophytes aren't just small tracheophytes. Amer. J. Bot. 88: 2129–2131.

 

Newton, A. E., C. J. Cox, J. G. Duckett, J. A. Wheeler, B. Goffinet, T. A. J. Hedderson, and B. D. Mishler 2000. Evolution of the major mosslineages: phylogenetic analyses based on multiple gene sequences and morphology. Bryologist 103: 187–211.

 

Renzaglia, K. S., K. D. McFarland, and D. K. Smith 1997. Anatomy and ultrastrcuture of the sporophyte of Takakia ceratophylla (Bryophyta). Amer. J. Bot. 84: 1337–1350.

 

Shaw, J., C. J. Cox, and S. B. Boles 2003. Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots? Amer. J. Bot. 90: 1778–1787.

 

Shaw, J. and K. Renzaglia 2004. Phylogeny and diversification of bryophytes. Amer. J. Bot. 91: 1557–1581.

 

Wheeler, J. A. 2000. Molecular phylogenetic reconstructions of the marchantioid liverwort radiation. Bryologist 103: 314–333.

 

Tracheophyte Evolution

 

Carlquist, S. and E. L. Schneider 1997. SEM studies on vessels in ferns. 2. Pteridium. Amer. J. Bot. 84: 581–587.

 

Carlquist, S. and E. L. Schneider 1999. SEM studies on vessels in ferns. 12. Marattiaceae, with comments on vessel patterns in eusporangiate ferns. Amer. J. Bot. 86: 457–464.

 

Carlquist, S. and E. L. Schneider 2001. Vessels in ferns: structural, ecological, and evolutionary significance. Amer. J. Bot. 88: 1–13.

 

Carlquist, S. and E. L. Schneider 2002. The trachied-vessel element transition in angiosperms involves multiple independent features: cladistic consequences. Amer. J. Bot. 89: 185–195.

 

Ligrone, R., J. G. Duckett, and K. S. Renzaglia 2000. Conducting tissues and phyletic relationships of bryophytes. Phil. Trans. R. Soc. Lond. 355: 795–813.

 

Friedman, W. E. and M. E. Cook 2000. The origin and early evolution of tracheids in vascular plants: integration of palaeobotanical and neobotanical data. Phil. Trans. R. Soc. Lond. 355: 857–868.

 

Kenrick, P. 2000. The relationships of vascular plants. Phil. Trans. R. Soc. Lond. 355: 847–855.

 

Schneider, E. L. and S. Carlquist 2001. SEM studies on vessels in ferns. 17. Psilotaceae. Amer. J. Bot. 87: 176–181.

 

Lycophyte Evolution

 

Gensel, P. G. and C. M. Berry 2001. Early lycophyte evolution. Amer. Fern. J. 91: 74–98.

 

Grauvogel-Stamm, L. and B. Lugardon 2001. The Triassic lycopsids Pleuromeia and Annalepis: relationships, evolution, and origin. Amer. Fern J. 91: 115–149

 

Pigg, K. B. 2001. Isoetalean lycopsid evolution: from the Devonian to the present. Amer. Fern J. 91: 99–114.

 

Svensson, M. E. and P. Engström 2002. Closely related MADS-box genes in club moss (Lycopodium) show broad expression patterns and are structurally similar to, but phylogenetically distinct from, typical seed plant MADS-box genes. New Phytologist 154: 439–450.

 

Whittier, D. P. and J. E. Braggins 2000. Observations on the mature gametophyte of Phylloglossum (Lycopodiaceae). Amer. J. Bot. 87: 920–924.

 

Wikström, N. 2001. Diversification and relationships of extant homosporous lycopods. Amer. Fern J. 91: 150–165.

 

Monilophyte Evolution

 

Des Marais, D. L., A. R. Smith, D. M. Britton, and K. M. Pryer 2003. Phylogenetic relationships and evolution of extant horsetails, Equisetum, based on chloroplast DNA sequence data (rbcL and trnL-F). Int. J. Plant Sci. 164: 737–751.

 

Pryer, K. M. 1999. Phylogeny of marsileaceous ferns and relationships of the fossil Hydropteris pinnata reconsidered. Int. J. Plant Sci. 160: 931–954.

 

Pryer, K. M., H. Schneider, A. R. Smith, R. Cranfill, P. Wolf, J. S. Hunt, and S. D. Sipes 2001. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409: 618–622.

 

Pryer, K. M., E. Schuettpelz, P. Wolf, H. Schneider, A. R. Smith, and R. Cranfill 2004. Phylogeny and evolution of ferns (Monilophytes) with a focus on the early leptosporangiate divergences. Amer. J. Bot. 91: 1582–1598.

 

Schneider, H., E. Schuettpelz, K. M. Pryer, R. Cranfill, S. Magallón, and R. Lupia 2004. Ferns diversified in the shadow of angiosperms. Nature 428: 553–557.

 

Spermatophytes and Gymnosperm Evolution

 

Bowe, L. M., G. Coat, and C. W. dePamphilis 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.

 

Burleigh J. G. and S. Mathews 2004. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Amer. J. Bot. 91: 1599–1613.

 

Chaw, S., A. Zharkikh, H. Sung, T. Lau, and W. Li 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 14: 56–68.

 

Chaw, S., C. L. Parkinsono, Y. Cheng, T. M. Vincent, and J. D. Palmer 2000. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. PNAS 97: 4086–4091.

 

Crane, P. 1985. Phylogenetic analysis of seed plants and the origin of angiosperms. Ann. Missouri Bot. Gard. 72: 716–793.

 

Gugerli, F., C. Sperisen, U. Büchler, I. Brunner, S. Brodbeck, J. D. Palmer, and Y. Qiu 2001. The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny. Mol. Phyl. Evol. 21: 167–175.

 

Kellogg, E. A. and J. L. Bennetzen 2004. The evolution of nuclear genome structure in seed plants. Amer. J. Bot. 91: 1709–1725.

 

Cycads, Ginkgo and Gymnosperm Evolution

 

Bogler, D. J. and J. Francisco-Ortega 2004. Molecular systematic studies in cycads: evidence from trnL intron and ITS2 rDNA sequences. Bot. Rev. 70: 260–273.

 

Brenner, E. D., D. W. Stevenson, and r. W. Twigg 2003. Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends in Plant Science 8: 446–452.

 

Dilcher, D. 2000. Toward a new synthesis: Major evolutionary trends in the angiosperm fossil record. PNAS 97: 7030–7036.

 

Dower, B. L., R. M. Bateman, and D. W. Stevenson 2004. Systematics,ontogeny,and phylogenetic implications of exceptional anatomically preserved cycadophyte leaves from the Middle Jurassic of Bearreraig Bay, Skye, Northwest Scotland. Bot. Rev. 70: 105–120.

 

Farjon, A. and S. O. Garcia 2003. Cone and ovule development in Cunninghamia and Taiwania (Cupressaceae sensu lato) and its significance for conifer evolution. Amer. J. Bot. 90: 8-16.

 

Hernandez-Castillo, G. R., G. W. Rothwell, and G. Mapes 2001. Compound pollen cone in a Paleozoic conifer.

Amer. J. Bot. 88: 1139–1142.

 

Holt, B. F. and G. W. Rothwell 1997. Is Ginkgo biloba (Ginkgoaceae) really an oviparous plant? Amer. J. Bot. 84: 870–872.

 

Magallón, S. and M. J. Sanderson 2002. Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages. Amer. J. Bot. 89: 1991–2006.

 

Norstog, K. J., E. M. Gifford, and D. W. Stevenson 2004. Comparative development of the spermatozoids of cycads and Ginkgo biloba. Bot. Rev. 70: 5–15.

 

Poort,  R. J., H. Visscher, and D. L. Dilcher 1996. Zoidogamy in fossil gymnosperms: The centenary of a concept, with special reference to prepollen of late Paleozoic conifers. PNAS 93: 11713–11717.

 

Royer, D. L., L. J. Hickey, and S. L. Wing 2003. Ecological conservatism in the "living fossil" Ginkgo. Paleobiology 29: 84–104.

 

Yang, Y. 2004. Ontogeny of triovulate cones of Ephedra intermedia and origins of the outer envelope of ovules of Ephedraceae. Amer. J. Bot. 91: 361–368.

 

Angiosperm Origins and Evolution

 

Barkman, T. J., G. Chenery, J.R. McNeal, J. Lyons-Weiler, W. J. Ellisens, G. Moore, A. D. Wolfe, and C. W. dePamphilis 2000. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. PNAS 97: 13166–13171.

 

Bremer, K. 2000. Early Cretaceous lineages of monocot flowering plants. PNAS 97: 4707–4711.

 

Carlquist, S. and E. L. Schneider 2002. The trachied-vessel element transition in angiosperms involves multiple independent features: cladistic consequences. Amer. J. Bot. 89: 185–195.

 

Crepet, W. L. 2000. Progress in understanding angiosperm history, success, and relationships: Darwin's abominably "perplexing phenomenon." PNAS 97: 12939–12941.

 

Crepet, W. L., K. C. Nixon, and M. A. Gandolfo 2004. Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits. Amer. J. Bot. 91: 1666–1682.

 

Davies, T. J., T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and Vincent Savolainen 2004. Darwin's abominable mystery: insights from a supertree of the angiosperms. PNAS 101: 1904–1909.

 

Endress, P. K. 2001. Origins of flower morphology. J. Exper. Zool. 291: 105–115.

 

Endress, P. K. 2003. Morphology and angiosperm systematics in the molecular era. Bot. Rev. 68: 545–570.

 

Feild, T. S., N. C. Arens, J. A. Doyle, T. E. Dawson, and M. J. Donoghue 2004. Dark and disturbed: a new image of early angiosperm ecology. Paleobiology 30: 82–107.

 

Frohlich, M. W. and D. S. Parker 2000. The mostly male theory of flower evolutionary origins: from genes to fossils. Syst. Bot. 25: 155–170.

 

Judd, W. S. and R. G. Olmstead 2004. A survey of tricolpate (eudicot) phylogenetic relationships. Amer. J. Bot. 91: 1627–1644.

 

Labandeira, C. C., D. L. Dilcher, D. R. Davis, and D. L. Wagner 1994. Ninety-seven million years of angiosperm-insect association: paleobiological insights into the meaning of coevolution. PNAS 91: 12278–12282.

 

Mathews, S. and M. J. Donoghue 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947–950.

 

Sanderson, M. J. and J. A. Doyle 2001. Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Amer. J. Bot. 88: 1499–1516.

 

Soltis, D. E. and P. S. Soltis 2004. Amborella not a "basal angiosperm"? Not so fast. Amer. J. Bot. 91: 997–1001.

 

Soltis, P. S. and D. E. Soltis 2004. The origin and diversification of angiosperms. Amer. J. Bot. 91: 1614–1626.

 

Zanis, M. J., D. E. Soltis, P. S. Soltis, S. Mathews, and M. J. Donoghue 2002. The root of the angiosperms revisited. PNAS  99: 6848–6853.





Origins and Diversity of Land Plants Bibliography
Assembled by Steven L. Jessup, December 2004.