2008
Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. [Systematic Biology, In press]
Ane, C., O. Eulenstein, R. Piaggio-Talice, and M. J. Sanderson. Groves of phylogenetic trees. Annals of Combinatorics. In press.
2007
Sanderson, M. J., C. Ane, O. Eulenstein, D. Fernandez-Baca, J. Kim, M. M. McMahon, and R. Piaggio-Talice. 2007. Fragmentation of large data sets in phylogenetic analyses. Pp. 199-216 in (M. Steel and O. Gascuel, eds.) Reconstructing Evolution: New Mathematical and Computational Advances. Oxford University Press.
Sanderson, M. J. 2007. Construction and annotation of large phylogenetic trees. Australian Systematic Botany 4:287-301.
Sanderson, M. J., and M. M. McMahon. 2007. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology, 7 (suppl. 1): S3.		Link to Data	Link to Software
2006
Chen, D., O. Eulenstein, D. Fernandez-Baca, and M. J. Sanderson. 2006. Minimum flip supertrees: complexity and algorithms. IEEE Trans. Comp. Biology & Bioinformatics 3:165-173.
Burleigh, J. G., A. C. Driskell,, and M. J. Sanderson. 2006. Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst. Biol. 55:426-440.		Link to Data
Smythe, A. B., M. J. Sanderson, and S. A. Nadler. 2006. Nematode small subunit phylogeny correlates with alignment. Syst. Biol., 55:972-992.
McMahon, M. M., and M. J. Sanderson. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Systematic Biology, 55:818-836.		Link to Data
Sanderson, M. J. 2006. Paloverde: an OpenGL 3-D phylogeny browser. Bioinformatics, 22:1004-1006.		Link to Software
2005
Yan, C. H., J. G. Burleigh, and O. Eulenstein. 2005. Identifying optimal incomplete phylogenetic data sets from sequence databases. Molecular Phylogenetics and Evolution 35:528-535.
Ane, C., and M. J. Sanderson. 2005. Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories. Syst. Biol., 54:146-157.
Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol., 22:914-924.
Sanderson, M. J. 2005. Bean Trees: Advances in Legume Systematics. Part 10.  Higher Level Systematics.- B. B. Klitgaard and A. Bruneau (eds.). Syst. Biol., in press. [Book Review]
Magallon, S., and M. J. Sanderson. 2005. Angiosperm divergence times: the effects of genes, codon positions, and time constraints. Evolution 59:1653-1670.

2004 and earlier

Driskell, A. C., C. Ané, J. G. Burleigh, M. M. McMahon, B. O’Meara, and M. J. Sanderson. 2004. Prospects for building the tree of life from large sequence databases. Science, 306:1172-1174.

Scotland, R., and M. J. Sanderson. 2004. The significance of few versus many in the tree of life. Science, 303:643..

Eulenstein, O., D. Chen, J. G. Burleigh, D. Fernández-Baca, and M. J. Sanderson. 2004. Performance of a flip-supertree heuristic. Syst. Biol. 53:299-308.

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

Grotkopp, E., M. Rejmanek, M. J. Sanderson, and T. L. Rost. 2004. Evolution of genome size in pines (Pinus) and its life-history correlates: supertree analysis. Evolution, 58:1705-1729.

Wojciechowski, M. F., M. Lavin, and M. J. Sanderson. 2004. A phylogeny of legumes (Leguminosae) based on the plastid matK gene resolves many well-supported subclades within the family. Amer. J. Bot., 91:1846-1862.

Near, T. J., and M. J. Sanderson. 2004. Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Phil. Trans. R. Soc. London 359:1477-1483.

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

Chen, D, L. Diao, O. Eulenstein, D. Fernandez-Baca, and M. J. Sanderson. 2003. Flipping: a supertree construction method. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. 61:135-160.

Sanderson, M. J., A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley. 2003. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20:1036-1042.

Piel, W. H. , M. J. Sanderson, and M. J. Donoghue. 2003. The small-world dynamics of tree networks and data mining in phyloinformatics. Bioinformatics. 19:1162-1168.

Sanderson, M. J., and A. C. Driskell. 2003. The challenge of constructing large phylogenetic trees. Trends in Plant Science. 8:374-379.

 

Sanderson, M. J. 2002. Homoplasy. In M. Pagel, ed. The Encyclopedia of Evolution. Oxford Univ. press.

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

Hu, J.-M., M. Lavin, M. F. Wojciechowski and M. J. Sanderson. 2002. Phylogenetic analysis of nuclear ribosomal ITS/5.8S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclobium, the core Millettieae, and the Callerya group. Syst. Bot. 27:722—733.

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

Chen, D, O. Eulenstein, D. Fernandez-Baca, and M. J. Sanderson. 2002. Supertrees by flipping. Pp. 391-400 in COCOON (Computing and Combinatorics, 8th Annual Conference), O. H. Ibarra and L. Zhang, eds. Springer-Verlag (Lecture notes in computer science no. 2387).

Sanderson, M. J. 2003. r8s; inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.

Sanderson, M. J., and H. B. Shaffer. 2002. Troubleshooting molecular phylogenetic analysis. Ann. Rev. Ecol. Syst. 33:49-72.

Bininda-Emonds, O. R. P., S. G. Brady, J. Kim, and M. J. Sanderson. 2001. Scaling of accuracy in extremely large phylogenetic trees. Pacific Symposium on Biocomputing 6:547-558.

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.

Bininda-Emonds, O., and M. J. Sanderson. 2001. An assessment of the accuracy of MRP supertree construction. Syst. Biol. 50:565-579.

Piel, William H., Michael J. Donoghue, and Michael J. Sanderson. 2002. TreeBASE: a database of phylogenetic knowledge. Pp. 41-47. In: Shimura, J., K. L. Wilson, and D. Gordon, eds. To the interoperable "Catalog of Life". Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.

Magallón, S., and M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762—1780.

Lavin, M., M. F. Wojciechowski, A. Richman, M. Sanderson. 2001. Identifying Tertiary radiations of Fabaceae in the Greater Antilles: alternatives to cladistic vicariance analysis. Int. J. Plant Sci. 162:S53-S76.

Hu, J. M., M. Lavin, M. F. Wojciechowski, and M. J. Sanderson. 2000. Molecular systematics of the tribe Millettieae (Fabaceae) and its implications for character evolution. Amer. J. Bot. 87:418-430.

Sanderson, M. J., and M. F. Wojciechowski. 2000. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49:671-685.

Sanderson, M. J., M. F. Wojciechowski, J.-M. Hu, T. Sher Khan, and S. G. Brady. 2000. Error, bias, and long branch attraction in data for two chloroplast photosystem genes in seed plants. Mol. Biol. Evol. 17:782-797.

Sanderson, M. J., and J. Kim. Parametric phylogenetics? 2000. Syst. Biol. 49:817-829.

Wojciechowski, M. F., M. J. Sanderson, K. P Steel and A. Liston. 2000. Molecular phylogeny of the "temperate herbaceous tribes" of papilionoid legumes: a supertree approach. Advances in Legume Systematics, vol. 9. Pp. 277-298.

 

Wojciechowski, M. F., M. J. Sanderson, and J. M. Hu. 1999. Evidence on the monophyly of Astragalus and its major subgroups based on nuclear ribosomal DNA ITS and chloroplast DNA trnL intron data. Syst. Bot. 24:409-437.

Wagstaff, S. J., P. B. Heenan, and M. J. Sanderson. 1999. Classification, origins, and patterns of diversification in New Zealand Carmichaelinae (Fabaceae). Amer. J. Bot. 86:1346-1356.

Sanderson, M. J. 1998. Reappraising adaptive radiation [review of Molecular Evolution and Adaptive Radiation.] Amer. J. Bot. 85:1650-1655.

Sanderson, M. J. 1998. Estimating rate and time in molecular phylogenies: beyond the molecular clock? Pp. 242-264 in Plant Molecular Systematics, 2nd. ed. (P. Soltis, D. Soltis, and J. Doyle, eds.), Chapman and Hall.

Baldwin, B. and M. J. Sanderson. 1998. Age and rate of diversification of the Hawaiian silversword alliance. Proc. Natl. Acad. Sci., USA 95:9402-9406.

Sanderson, M. J., A. Purvis, and C. Henze. 1998. Phylogenetic supertrees: Assembling the trees of life. Trends. Ecol. Evol., 13:105-109.

Sanderson, M. J. 1997. Review of "New Uses for New Phylogenies". Trends. Ecol. Evol. 12:201.

Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol., 14:1218-1231.

Sanderson, M. J., and L. Hufford, eds. 1996. Homoplasy: The Recurrence of Similarity in Evolution. Academic Press, New York.

Sanderson, M. J., and L. Hufford. 1996. Homoplasy and the evolutionary process: An afterword. Pp. 327-330 in Homoplasy: The Recurrence of Similarity in Evolution (M. J. Sanderson and L. Hufford, eds.), Academic Press, New York,.

Sanderson, M. J., and M. J. Donoghue. 1996. The relationship between homoplasy and confidence in phylogenetic trees. Pp. 67-89 in Homoplasy: The Recurrence of Similarity in Evolution (M. J. Sanderson and L. Hufford, eds.), Academic Press, New York.

Sanderson, M. J. 1996. How many species must be sampled to identify the root node of a large clade? Syst. Biol. 45:168-173.

Sanderson, M. J., and M. F. Wojciechoswki. 1996. Diversification rates in a temperate legume clade: Are there "so many species" of Astragalus? Amer. J. Bot., 83:1488-1502.

Sanderson, M. J., and M. J. Donoghue. 1996. Reconstructing shifts in diversification rates on phylogenetic trees. Trends Ecol. Evol. 11: 15-20.

Sanderson, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol., 44:299-320.

Baldwin, B. G. , C. S. Campbell, J. M. Porter, M. J. Sanderson, M. F. Wojciechowski, and M. J. Donoghue. 1995. Utility of nuclear ribosomal DNA ITS sequences in phylogenetic analyses of angiosperms. Annals of the Missouri Bot. Garden, 82:247-277.

Sanderson, M. J., and M. J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science, 264:1590-1593.

Sanderson, M. J. 1994. Reconstructing the evolution of genes and organisms using maximum likelihood. Pp. 13-26 in Molecular Evolution of Physiological Processes (D. Fambrough, ed.), Rockefeller University Press, New York.

Donoghue, M. J., and M. J. Sanderson. 1994. Homology and complexity in plants. Pp. 393-421 in Homology, Brian Hall (Ed.), Academic Press, San Diego.

Sanderson, M. J., and A. Liston. 1995. Molecular phylogenetic systematics of Galegeae, with special reference to the genus Astragalus. Pp. 331-350 in Proceedings of the Third Int'l Legume Conference (R. M. Polhill and J. J. Doyle, eds.). Royal Botanic Gardens, Kew.

Sanderson, M. J. 1993. Review of "MacClade vers. 3.0". Syst. Biol.: 42:218-220.

Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, C. von Dohlen, D. Ferguson, J. M. Porter, M. F. Wojciechowski, and M. J. Donoghue. 1993. The growth of phylogenetic information, and the need for a phylogenetic data base. Syst. Biol., 42:562-568.

Sanderson, M. J., and J. J. Doyle. 1993. Chloroplast DNA relationships in North American Astragalus: Syst. Bot.: 18:395-408.

Wojciechowski, M., M. J. Sanderson, B. G. Baldwin, and M. J. Donoghue. 1993. Nuclear ribosomal ITS sequence data support the monophyly of aneuploid Astragalus. Amer. J. Bot., 80:711-722.

Sanderson, M. J. and G. Bharathan. 1993. Does cladistic information affect inferences about branching rates? Syst. Biol., 42:1-17.

Sanderson, M. J. 1993. Maximum likelihood estimation of gain/loss bias in cladograms derived from parsimony. Evolution, 47:236-252.

Donoghue, M. J., and M. J. Sanderson. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pp. 340-368 in Plant Molecular Systematics (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall.

Sanderson, M. J., and J. J. Doyle. 1992. Reconstruction of organismal and gene phylogenies from data on multigene families: Concerted evolution, homoplasy, and confidence. Syst. Biol. 41:4-17.

Sanderson, M. J. 1991. In search of homoplastic tendencies: Statistical tests for patterns in the topological distribution of homoplasy. Evolution 45:351-358

Sanderson, M. J. 1991. Phylogenetic relationships within North American Astragalus L. (Fabaceae). Syst. Bot.16:414-430.

Sanderson, M. J. 1990. Flexible phylogeny reconstruction: A review of phylogenetic inference packages using parsimony. Syst. Zool. 39:414-420.

Sanderson, M. J. 1990. Estimating rates of speciation and evolution: A bias due to homoplasy. Cladistics 6:387-391.

Sanderson, M. J. 1989. Astragalus nutriosensis: A new species from Eastern Arizona. Madrono 35:325-329.

Sanderson, M. J. 1989. Confidence limits on phylogenies: The bootstrap revisited. Cladistics 5:113-129.

Sanderson, M. J., and M. J. Donoghue. 1989. Patterns of variation in levels of homoplasy. Evolution 43:1781-1795.

Hopf, F., R. E. Michod, and M. J. Sanderson [authorship alphabetical]. 1988. The effect of reproductive system on mutation load. Theor. Pop. Biol. 33:243-265.

Michod, R. E., and M. J. Sanderson. 1985. Interaction structure and the evolution of social behavior. In P. J. Greenwood and M. Slatkin (eds.), Evolution - Essays in Honour of John Maynard Smith, chapter 7, pp. 95-104. Cambridge University Press.

Sanderson, M. J., and R. E. Michod. 1983. Review of Cultural Transmission and Evolution by L. L. Cavalli-Sforza and M. Feldman. Animal Behavior 31:956-958.

Brown, J. S., M. J. Sanderson, and R. E. Michod. 1982. Evolution of social behavior by reciprocation. J. Theor. Biol. 99:319-339.