M J Sanderson

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint The challenge of constructing large phylogenetic trees
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Trends Plant Sci 8:374-9. 2003
  2. ncbi request reprint Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
    M J Sanderson
    Section of Evolution and Ecology, University of California at Davis, 95616, USA
    Mol Biol Evol 17:782-97. 2000
  3. ncbi request reprint Paloverde: an OpenGL 3D phylogeny browser
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, CA, USA
    Bioinformatics 22:1004-6. 2006
  4. ncbi request reprint Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
    Mol Biol Evol 19:101-9. 2002
  5. ncbi request reprint Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae)
    M J Sanderson
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Syst Biol 49:671-85. 2000
  6. ncbi request reprint r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    Michael J Sanderson
    Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, CA 95616, USA
    Bioinformatics 19:301-2. 2003
  7. ncbi request reprint Obtaining maximal concatenated phylogenetic data sets from large sequence databases
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 20:1036-42. 2003
  8. ncbi request reprint Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes
    Michelle M McMahon
    Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
    Syst Biol 55:818-36. 2006
  9. ncbi request reprint Prospects for building the tree of life from large sequence databases
    Amy C Driskell
    Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
    Science 306:1172-4. 2004
  10. ncbi request reprint Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
    J Gordon Burleigh
    Section of Evolution and Ecology, University of California, J G B, Davis, CA 95616, USA
    Syst Biol 55:426-40. 2006

Detail Information

Publications26

  1. ncbi request reprint The challenge of constructing large phylogenetic trees
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Trends Plant Sci 8:374-9. 2003
    ..A final challenge is posed by the difficulty of visualizing and making inferences from trees that might soon routinely contain thousands of species...
  2. ncbi request reprint Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
    M J Sanderson
    Section of Evolution and Ecology, University of California at Davis, 95616, USA
    Mol Biol Evol 17:782-97. 2000
    ..A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups...
  3. ncbi request reprint Paloverde: an OpenGL 3D phylogeny browser
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, CA, USA
    Bioinformatics 22:1004-6. 2006
    ..Availability: Source code, makefiles for Mac OS X and Linux and a compiled binary for Mac OS X are available at http://ginger.ucdavis.edu/paloverde/paloverde.html, along with a sample dataset...
  4. ncbi request reprint Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
    Mol Biol Evol 19:101-9. 2002
    ..The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages...
  5. ncbi request reprint Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae)
    M J Sanderson
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Syst Biol 49:671-85. 2000
    ..More accurate assessments of confidence as type I error levels (relying on iterated bootstrap methods) remove most of the monotonic decline in confidence with increasing numbers of taxa...
  6. ncbi request reprint r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    Michael J Sanderson
    Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, CA 95616, USA
    Bioinformatics 19:301-2. 2003
    ..Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions...
  7. ncbi request reprint Obtaining maximal concatenated phylogenetic data sets from large sequence databases
    Michael J Sanderson
    Section of Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 20:1036-42. 2003
    ..These upper bounds to sequence concatenation have important implications for building the tree of life from large sequence databases...
  8. ncbi request reprint Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes
    Michelle M McMahon
    Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
    Syst Biol 55:818-36. 2006
    ....
  9. ncbi request reprint Prospects for building the tree of life from large sequence databases
    Amy C Driskell
    Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
    Science 306:1172-4. 2004
    ..However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life...
  10. ncbi request reprint Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
    J Gordon Burleigh
    Section of Evolution and Ecology, University of California, J G B, Davis, CA 95616, USA
    Syst Biol 55:426-40. 2006
    ..Results from supertree bootstrapping methods, when compared to results from corresponding supermatrix bootstrapping, may provide insights into patterns of variation among genes in genome-scale data sets...
  11. ncbi request reprint Evolution of genome size in pines (Pinus) and its life-history correlates: supertree analyses
    Eva Grotkopp
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Evolution 58:1705-29. 2004
    ..Many life-history patterns are therefore indirectly, but consistently, associated with genome size...
  12. ncbi request reprint Testing for different rates of continuous trait evolution using likelihood
    Brian C O'Meara
    Center for Population Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
    Evolution 60:922-33. 2006
    ..Simulations show that these tests are more powerful than existing tests using standardized contrasts. The new approaches are distributed in an application called Brownie and in r8s...
  13. ncbi request reprint Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
    O R Bininda-Emonds
    Section of Evolution and Ecology, University of California at Davis, Davis, California 95616, USA
    Syst Biol 50:565-79. 2001
    ..Overall, our results suggest that MRP supertree construction provides a reasonable approximation of a total evidence solution and that weighted MRP should be used whenever possible...
  14. ncbi request reprint Absolute diversification rates in angiosperm clades
    S Magallón
    Section of Evolution and Ecology, University of California, Davis 95616, USA
    Evolution 55:1762-80. 2001
    ....
  15. ncbi request reprint Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae
    J M Hu
    Section of Evolution and Ecology, University of California, Davis, California 95616 USA
    Am J Bot 87:418-30. 2000
    ..trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions...
  16. ncbi request reprint Covarion structure in plastid genome evolution: a new statistical test
    Cecile Ane
    Section of Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 22:914-24. 2005
    ..The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes...
  17. ncbi request reprint Nematode small subunit phylogeny correlates with alignment parameters
    Ashleigh B Smythe
    Department of Nematology, University of California, One Shields Avenue, Davis, California 95616, USA
    Syst Biol 55:972-92. 2006
    ..Finally, we discuss the implications of conservative phylogenetic hypotheses for Nematoda produced by exploring alignment space and removing alignment ambiguous regions for SSU rDNA...
  18. pmc Inferring angiosperm phylogeny from EST data with widespread gene duplication
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    BMC Evol Biol 7:S3. 2007
    ..One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants...
  19. doi request reprint The PhyLoTA Browser: processing GenBank for molecular phylogenetics research
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Syst Biol 57:335-46. 2008
    ..Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources...
  20. ncbi request reprint Angiosperm divergence times: the effect of genes, codon positions, and time constraints
    Susana A Magallón
    Departamento de Botanica, Instituto de Biologia, Universidad Nacional Autonoma de Mexico
    Evolution 59:1653-70. 2005
    ....
  21. pmc Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
    Thomas J Near
    Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN 37669 1610, USA
    Philos Trans R Soc Lond B Biol Sci 359:1477-83. 2004
    ..In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model...
  22. ncbi request reprint Performance of flip supertree construction with a heuristic algorithm
    Oliver Eulenstein
    Department of Computer Science, Iowa State University, Ames, Iowa 50011, USA
    Syst Biol 53:299-308. 2004
    ..The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large...
  23. ncbi request reprint The significance of few versus many in the tree of life
    Robert W Scotland
    Department of Plant Sciences, Oxford University, Oxford, OX1 3RB, UK
    Science 303:643. 2004
  24. ncbi request reprint The small-world dynamics of tree networks and data mining in phyloinformatics
    William H Piel
    Institute of Evolutionary and Ecological Sciences, Kaiserstraat 63, Leiden University 2311 GP Leiden, The Netherlands
    Bioinformatics 19:1162-8. 2003
    ..Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies...
  25. doi request reprint Phylogenetic signal in the eukaryotic tree of life
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Science 321:121-3. 2008
    ..This analysis shows that a stronger sampling effort aimed at genomic depth, in addition to taxonomic breadth, will be required to build high-resolution phylogenetic trees at this scale...
  26. pmc A mathematical model of airway and pulmonary arteriole smooth muscle
    Inga Wang
    Department of Mathematics, University of Auckland, Auckland, New Zealand
    Biophys J 94:2053-64. 2008
    ..In addition, the model also predicts that oscillations in calcium concentration, commonly observed during agonist-induced smooth muscle contraction, cause a significantly greater contraction than an elevated steady calcium concentration...