Michael J Sanderson

Summary

Affiliation: University of Arizona
Country: USA

Publications

  1. 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
  2. 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
  3. pmc Phylogenomics with incomplete taxon coverage: the limits to inference
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    BMC Evol Biol 10:155. 2010
  4. doi request reprint Terraces in phylogenetic tree space
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Science 333:448-50. 2011
  5. 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
  6. ncbi 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
  7. pmc Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference
    Joel O Wertheim
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Syst Biol 59:1-8. 2010
  8. pmc Diversity and evolution of a trait mediating ant-plant interactions: insights from extrafloral nectaries in Senna (Leguminosae)
    Brigitte Marazzi
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Ann Bot 111:1263-75. 2013
  9. 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
  10. 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

Detail Information

Publications27

  1. 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...
  2. 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...
  3. pmc Phylogenomics with incomplete taxon coverage: the limits to inference
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    BMC Evol Biol 10:155. 2010
    ..We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa...
  4. doi request reprint Terraces in phylogenetic tree space
    Michael J Sanderson
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Science 333:448-50. 2011
    ..Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space...
  5. 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...
  6. ncbi 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...
  7. pmc Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference
    Joel O Wertheim
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Syst Biol 59:1-8. 2010
    ..We also compared the quality of inference between Bayesian and maximum likelihood time-free inference models and found them to be qualitatively similar...
  8. pmc Diversity and evolution of a trait mediating ant-plant interactions: insights from extrafloral nectaries in Senna (Leguminosae)
    Brigitte Marazzi
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Ann Bot 111:1263-75. 2013
    ..In this study the evolution of EFN diversity is explored by focusing on the legume genus Senna, in which EFNs underwent remarkable morphological diversification and occur in over 80 % of the approx. 350 species...
  9. 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
    ....
  10. 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...
  11. doi request reprint Locating evolutionary precursors on a phylogenetic tree
    Brigitte Marazzi
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 8572, USA
    Evolution 66:3918-30. 2012
    ..The model generates explicit hypotheses about the phylogenetic location of hypothetical precursors, which may help guide future studies of molecular genetic pathways underlying nectary position, development, and function...
  12. doi request reprint Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries
    Brigitte Marazzi
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Evolution 64:3570-92. 2010
    ..EFNs may have promoted the colonization of new habitats appearing with the early uplift of the Andes. This would explain the distinctive geographic concentration of the EFN clade in South America...
  13. pmc Estimating diversification rates: how useful are divergence times?
    Joel O Wertheim
    Department of Pathology, University of California, San Diego, California 92103, USA
    Evolution 65:309-20. 2011
    ..Finally, because Bayesian and frequentist methods provided similar assessments of error, novel Bayesian approaches may provide a useful framework for tests of diversification rates in more complex contexts than are addressed here...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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
  21. 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...
  22. 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...
  23. 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
    ....
  24. 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...
  25. 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...
  26. 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...
  27. 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...