Delwiche Publications, including links to data, and PDFs where permitted.

Updated 5.26.2009

Note: alignments and other supporting materials may be viewed or downloaded for several of these articles. If you work with these data, please cite the appropriate article, and send me a pdf or reprint of any articles that make use of these data.

Hoppenrath, M., Bachvaroff, T.R., Handy, S.M., Delwiche, C.F., and Leander, B.S. 2009. Molecular phylogeny of ocelloid-bearing dinoflagellates (Warnowiidae) as inferred from SSU and LSU rDNA sequences. BMC Evol. Biol. 9:116-x. (in press)

Handy SM, Bachvaroff TR, Timme RE, Coats DW, Kim S, Delwiche CF. 2009. Phylogeny of four Dinophysiacean genera (Dinophyceae, Dinophysiales) based on rDNA sequences from single cells and environmental sample. J. Phycol. 45:x (in press)


Sánchez-Puerta, M. V., and Delwiche, C. F. 2008. A hypothesis for plastid evolution in chromalveolates. J. Phycol. 44:1097-1107. DOI: 10.1111/j.1529-8817.2008.00559.x

Hall, J. D., McCourt, R.M., and Delwiche, C.F. 2008. Patterns of cell division in the filamentous Desmidiaceae, close green algal relatives of land plants. Amer. J. Bot. 95:643-654. doi:10.3732/ajb.2007210

Palenik, Brian, Jane Grimwood, Andrea Aerts, Pierre Rouze, Asaf Salamov, Nicholas Putnam, Chris Dupont, Richard Jorgensen, Evelyne Derelle, Stephane Rombauts, Kemin Zhou, Robert Otillar, Sabeeha Merchant, Sheila Podell, Terry Gaasterland, Carolyn Napoli, Karla Gendler, Andrea Manuell, Vera Tai, Olivier Vallon, Gwenael Piganeau, Séverine Jancek, Marc Heijde, Kamel Jabbari, Chris Bowler, Martin Lohr, Steven Robbens, Gregory Werner, Inna Dubchak, Gregory J Pazour, Qinghu Ren, Ian Paulsen, C F. Delwiche, Jeremy Schmutz, Daniel Rokhsar, Yves Van de Peer, Hervé Moreau, and Igor Grigoriev. 2007. Tiny eukaryotes provide genomic insights into the Paradox of the Plankton. Proc. Natl. Acad. Sci. USA. 7705-7710. doi: 10.1073/pnas.0611046104

Sánchez-Puerta, M. V., T. R. Bachvaroff, and C. F. Delwiche. 2007. Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids. Mol. Phylog. Evol. 44:885-897.

Hall, John D., Kenneth G. Karol, Richard M. McCourt and Charles F. Delwiche 2008 Phylogeny of the conjugating green algae based on chloroplast and mitochondrial nucleotide sequence data. J. Phycol. 95:643-654. doi: 10.1111/j.1529-8817.2008.00485.x

Johnson, M. D., Oldach, D., Delwiche, C. F., and Stoecker, D. K. 2007. Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra. Nature 445, 426-428. doi:10.1038/nature05496

Sanchez-Puerta, M. V., Lippmeier, J. C., Apt, K. E., and Delwiche, C. F. 2007. Plastid genes in a non-photosynthetic dinoflagellate. Protist 158, 105-117. doi:10.1016/j.protis.2006.09.004

Delwiche, C. F., 2007. Algae in the warp and weave of life: bound by plastids. In Unraveling the Algae: The Past, Present, and Future of Algal Systematics (J. Brodie, and J. Lewis, eds.), pp. 7-20. Taylor and Francis Group LLC, Boca Raton, FL.

Hall, J.D., and C.F. Delwiche. 2007. In the shadow of giants: the charophyte green algae. In Unraveling the Algae: The Past, Present, and Future of Algal Systematics (J. Brodie, and J. Lewis, eds.), pp. 155-170. Taylor and Francis Group LLC, Boca Raton, FL.

Delwiche, C. F. (2007). The origin and evolution of dinoflagellates. In Evolution of Primary Producers of the Sea (P. G. Falkowski, and A. H. Knoll, eds.), pp 193-205. Elsevier, New York, NY.

Shalchian-Tabrizi, K., Skanseng, M., Ronquist, F., Klaveness, D., Bachvaroff, T. R., Delwiche, C. F., Botnen, A., Tengs, T., and Jakobsen, K. S. 2006. Heterotachy Processes in Rhodophyte-Derived Secondhand Plastid Genes: Implications for Addressing the Origin and Evolution of Dinoflagellate Plastids. Mol Biol Evol 23, 1504-1515. doi:10.1093/molbev/msl011

Bachvaroff, T. R., Sanchez-Puerta, M. V., and Delwiche, C. F. 2006. Rate variation as a function of gene origin in plastid-derived genes of peridinin-containing dinoflagellates. J. Mol. Evol. 62, 42-52.

Drummond, C., Hall, J. D., Karol, K. G., Delwiche, C. F., and McCourt, R. M. 2005. Phylogeny of Spirogyra and Sirogonium (Zygnematophyceae) based on rbcL sequence data. J. Phycol. 41: 1055-1064.


Delwiche, C.F. 2005. Voyage to the Bottom of the Tree (Book Review). Science 307:676-677. Full text available online.

Sanchez Puerta, M. V., T. R. Bachvaroff, and C. F. Delwiche. 2005. Sanchez Puerta, M. V., T. R. Bachvaroff, and C. F. Delwiche. 2005. The complete plastid genome sequence of the haptophyte Emiliania huxleyi: a comparison to other plastid genomes. DNA research. 12:151-156

Bachvaroff, T.R., M.V. Sánchez Puerta & C.F. Delwiche. 2005. Chlorophyll c containing plastid relationships based on analyses of a multi-gene dataset with all four chromalveolates lineages. Mol. Biol. Evol. 22:1772-1782. Abstract and full text are available online.

Sánchez Puerta, M. V., T. R. Bachvaroff, and C. F. Delwiche. 2004. The complete mitochondrial genome of the haptophyte Emiliania huxleyi and its relation to heterokonts. DNA Research 11:1-10. Full text, and PDF are available online.

Johnson, M. D., T. Tengs, C. F. Delwiche, D. Oldach, and D. K. Stoecker. 2004. Highly divergent SSU rRNA genes found in marine ciliates Myrionecta rubra and Mesodinium pulex. Protist 155:347-359.

Delwiche, C. F. 2004  The genomic palimpsest: genomics in evolution and ecology.  BioScience 54:991-1001.

McCourt, R. M., Delwiche, C. F., and Karol, K. G.  2004.  Charophyte algae and land plant origins.  Trends. Ecol. Evol. 19:661-666.

Cimino, M. T., J. L. Reveal, and C. F. Delwiche. 2003. (1569-1570) Proposals to conserve the name Coleochaete soluta against C. prostrata and the name C. orbicularis against Phyllactidium pulchellum with a note on the name C. nitellarum (Coleochaetaceae, Chlorophyceae). Taxon 52: 133-134.

Eriksson, T., M. S. Hibbs, C. F. Delwiche, M. J. Donoghue, and A. D. Yoder. 2003. The phylogeny of Rosoideae (Rosaceae) enhanced by combining sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA with the trnL/F region of chloroplast DNA. Int. J. Plant Sci 164:197-211.

Charity, J. C., K. Pak, C. F. Delwiche, and S. W. Hutcheson. 2003. Novel exchangable effector loci associated with Pseudomonas syringae hrp pathogenicity island: evidence for integron-like assembly from transposed gene casettes. Molecular Plant Microbe Interactions 16: 495-507.

Bachvaroff, T. R., G. T. Concepcion, C. R. Rogers, E. M. Herman, and C. F. Delwiche. 2003. Dinoflagellate EST data indicate massive transfer of genes to the nuclear genome. Protist 155: 65-78. [PDF]

Cimino, M.T., and C.F. Delwiche. 2002.  Molecular and morphological data identify a cryptic species complex in endophytic members of the genus Coleochaete Breb. (Coleochaetales, Charophyta).  J. Phycol. 38:1213-1221.

Delwiche, C. F., K. G. Karol, M. T. Cimino, and K. J. Sytsma. 2002. Phylogeny of the genus Coleochaete (Charophyceae, Chlorophyta) and related taxa inferred by analysis of the chloroplast gene rbcL. Journal of Phycology 38: 394-403.

Karol, K. G., R. M. McCourt, M. T. Cimino, and C. F. Delwiche. 2001. The closest living relatives of plants. Science 294: 2351-2353. Abstract and full text available online here

Tengs, T., O. J. Dahlberg, K. Shalchian-Tabrizi, D. Klaveness, K. Rudi, C. F. Delwiche, and K. S. Jakobsen. 2000. Phylogenetic analyses indicate that the 19 ' hexanoyloxy- fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin. Molecular Biology and Evolution 17: 718-729.

Oldach, D. W., C. F. Delwiche, K. S. Jakobsen, T. Tengs, E. G. Brown, J. W. Kempton, E. F. Schaefer, H. A. Bowers, H. B. Glasgow, J. M. Burkholder, K. A. Steidinger, and P. A. Rublee. 2000. Heteroduplex mobility assay-guided sequence discovery: Elucidation of the small subunit (18S) rDNA sequences of Pfiesteria piscicida and related dinoflagellates from complex algal culture and environmental sample DNA pools. Proceedings of the National Academy of Sciences of the United States of America 97: 4303-4308.

Cimino, M. T., K. G. Karol, and C. F. Delwiche. 2000. An artifact in the small subunit rDNA sequence of Chaetosphaeridium globosum (Charophyceae, Streptophyta). Journal of Phycology 36: 440-442.

Delwiche, C.F. 1999. Tracing the web of plastid diversity through the tapestry of life. American Naturalist 154:S164-S177.
Click here for a modified figure.

Roos, D., and C.F. Delwiche. 1998. Endosymbiosis: cyclical and permanent in evolution (Response). Trends Microbiol. 343:345-346.

Delwiche, C.F., and J.D. Palmer. 1997. The origin of plastids and their spread via secondary symbiosis. In: D. Bhattacharya (ed.), The Origins of Algae and their Plastids. Springer-Verlag.

Palmer, J.D., and C.F. Delwiche. 1997. The origin of plastids and their genomes. In: P.S. Soltis, D.E. Soltis, and J.J. Doyle, eds. Molecular Systematics of Plants, 2nd edition. Chapman and Hall/Kluwer.

Chapman, R.L., M.A. Buchheim, C.F. Delwiche, T. Friedl, V.A.R. Huss, K.G. Karol, L.A. Lewis, J. Manhart, R.M. McCourt, J.L. Olsen, and D.A. Waters. 1997. Molecular systematics of the green algae. In: P.S. Soltis, D.E. Soltis, and J.J. Doyle, eds. Molecular Systematics of Plants, 2nd edition. Chapman and Hall (in press).

Kohler, S., C.F. Delwiche, L.G. Tilney, P. Webster, R.J.M. Wilson, J.D. Palmer, and D.S. Roos. 1997. A plastid of probable green algal origin in apicomplexan plastids. Science 275:1485-1489. Click here for full text, the abstract, or alignment, and ancillary materials.

Palmer, J.D., and C.F. Delwiche. 1996. Second-hand chloroplasts and the case of the disappearing nucleus. (Commentary) Proc. Natl. Acad. Sci. USA 93: 7432-7435.

Delwiche, C.F., and J. D. Palmer. 1996. Rampant Horizontal Transfer and Duplication of Rubisco Genes in Eubacteria and Plastids. Mol. Biol. Evol. 13:873-882. Click here for abstract, alignment, and ancillary materials.

Barns, S.M., C.F. Delwiche, J.D. Palmer, and N.R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193. Click here for abstract, algnment, and ancillary materials

Delwiche, C. F., M. Kuhsel, and J. D. Palmer. 1995. Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol. Phylo. Evol. 4:110-128 Click here for abstract, alignment, and ancillary materials.

Mishler, B.D., L.A. Lewis, M.A. Buchheim, K. S. Renzaglia, D. J. Garbarz, C. F. Delwiche, F. W. Zechman, T. S. Kantz, and R. L. Chapman. 1994. Phylogenetic relationships of the "green algae" and "bryophytes". Ann. Missouri Bot. Gard. 81:451-483.

Delwiche, C. F. and T. D. Sharkey. 1993. Rapid appearance of 13C in biogenic isoprene when 13CO2 is fed to intact leaves. Plant, Cell, and Environment 16:587-591.

Morden, C. W., C. F. Delwiche, M. Kuhsel, and J. D. Palmer. 1992. Gene Phylogenies and the endosymbiotic origin of plastids. Biosystems 28:75-90.

Graham, L. E., C. F. Delwiche, and B. Mishler. 1991. Phylogenetic connections between the "green algae" and "bryophytes." Advances in Bryology 4:213-244.

Sharkey, T. D., F. Loreto, and C. F. Delwiche. 1991. The biochemistry of isoprene emission from leaves during photosynthesis. In: Trace Gas Emissions by Plants, T. D. Sharkey, H. A. Mooney, and E. A. Holland (eds.). Academic Press, San Diego, pp. 153-184.

Sharkey, T. D., F. Loreto, and C. F. Delwiche. 1991. High carbon dioxide and sun/shade effects on isoprene emission from oak and aspen tree leaves. Plant, Cell, and Environment 14:333-338.

Sharkey, T. D., F. Loreto, C. F. Delwiche, and I. W. Treichel. 1991. Fractionation of Carbon Isotopes during Biogenesis of Atmospheric Isoprene. Plant Physiology 97:463-466.

Delwiche, C.F., L.E. Graham and N. Thomson. 1989. Lignin-like compounds and sporopollenin in Coleochaete, an algal model for land plant ancestry. Science 245:399-401.