Stephen A. Smith - Publications

University of Michigan, Ann Arbor, Ann Arbor, MI 
Evolutionary Biology, Phylogenetics, Phyloinformatics, Plant evolution, Transcriptomics

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Wang N, Braun EL, Liang B, Cracraft J, Smith SA. Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree. Molecular Phylogenetics and Evolution. 107550. PMID 35691570 DOI: 10.1016/j.ympev.2022.107550  0.314
2021 Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, Yang ZY, Hu Y, Ma H, Soltis PS, Soltis DE, Li DZ, Smith SA, Yi TS. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nature Plants. PMID 34282286 DOI: 10.1038/s41477-021-00964-4  0.341
2021 Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Systematic Biology. PMID 34240209 DOI: 10.1093/sysbio/syab052  0.337
2020 Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y. Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l. Systematic Biology. PMID 32785686 DOI: 10.1093/Sysbio/Syaa066  0.809
2020 Singhal S, Colston TJ, Grundler MR, Smith SA, Costa GC, Colli GR, Moritz C, Pyron RA, Rabosky DL. Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective. Systematic Biology. PMID 32681800 DOI: 10.1093/Sysbio/Syaa054  0.674
2020 Smith SA, Walker-Hale N, Walker JF. Intragenic conflict in phylogenomic datasets. Molecular Biology and Evolution. PMID 32658966 DOI: 10.1093/Molbev/Msaa170  0.396
2020 Stull GW, Soltis PS, Soltis DE, Gitzendanner MA, Smith SA. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. American Journal of Botany. PMID 32406108 DOI: 10.1002/Ajb2.1468  0.406
2020 Larson DA, Walker JF, Vargas OM, Smith SA. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. American Journal of Botany. PMID 32350864 DOI: 10.1002/Ajb2.1469  0.451
2020 Lewis SH, Ross L, Bain SA, Pahita E, Smith SA, Cordaux R, Miska EA, Lenhard B, Jiggins FM, Sarkies P. Metagene plot of methylation within TEs and in flanking sequence for all species. Plos Genetics. DOI: 10.1371/Journal.Pgen.1008864.S002  0.324
2019 Smith SA, Walker-Hale N, Walker JF, Brown JW. PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS. Systematic Biology. PMID 31747023 DOI: 10.1093/Sysbio/Syz078  0.643
2019 Sheehan H, Feng T, Walker-Hale N, Lopez-Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, ... Smith SA, et al. Evolution of L-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales. The New Phytologist. PMID 31369159 DOI: 10.1111/Nph.16089  0.547
2019 Vargas OM, Heuertz M, Smith SA, Dick CW. Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data. Molecular Phylogenetics and Evolution. PMID 30818022 DOI: 10.1016/J.Ympev.2019.02.020  0.456
2019 Yao G, Jin JJ, Li HT, Yang JB, Shiva Mandala V, Croley M, Mostow R, Douglas NA, Chase MW, Christenhusz MJM, Soltis DE, Soltis PS, Smith SA, Brockington SF, Moore MJ, et al. Plastid phylogenomic insights into the evolution of Caryophyllales. Molecular Phylogenetics and Evolution. PMID 30735725 DOI: 10.1016/J.Ympev.2018.12.023  0.41
2019 Chang J, Rabosky DL, Smith SA, Alfaro ME. An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life Methods in Ecology and Evolution. 10: 1118-1124. DOI: 10.1111/2041-210X.13182  0.735
2019 Smith SA, Walker JF. PyPHLAWD: A python tool for phylogenetic dataset construction Methods in Ecology and Evolution. 10: 104-108. DOI: 10.1111/2041-210X.13096  0.323
2018 Allen JM, Germain-Aubrey CC, Barve N, Neubig KM, Majure LC, Laffan SW, Mishler BD, Owens HL, Smith SA, Whitten WM, Abbott JR, Soltis DE, Guralnick R, Soltis PS. Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates. Iscience. 11: 57-70. PMID 30590251 DOI: 10.1016/J.Isci.2018.12.002  0.488
2018 Wang N, Yang Y, Moore MJ, Brockington SF, Walker JF, Brown JW, Liang B, Feng T, Edwards C, Mikenas J, Olivieri J, Hutchison V, Timoneda A, Stoughton T, Puente R, ... ... Smith SA, et al. Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments. Molecular Biology and Evolution. PMID 30371871 DOI: 10.1093/Molbev/Msy200  0.69
2018 Walker JF, Brown JW, Smith SA. Analyzing contentious relationships and outlier genes in phylogenomics. Systematic Biology. PMID 29893968 DOI: 10.1093/Sysbio/Syy043  0.633
2018 Smith SA, Brown JW, Walker JF. So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. Plos One. 13: e0197433. PMID 29772020 DOI: 10.1371/Journal.Pone.0197433  0.623
2018 Smith SA, Brown JW. Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany. 105: 302-314. PMID 29746720 DOI: 10.1002/Ajb2.1019  0.631
2018 Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany. 105: 385-403. PMID 29746719 DOI: 10.1002/Ajb2.1016  0.775
2018 Walker JF, Yang Y, Feng T, Timoneda A, Mikenas J, Hutchison V, Edwards C, Wang N, Ahluwalia S, Olivieri J, Walker-Hale N, Majure LC, Puente R, Kadereit G, Lauterbach M, ... ... Smith SA, et al. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. American Journal of Botany. PMID 29738076 DOI: 10.1002/Ajb2.1069  0.585
2018 Knowles LL, Huang H, Sukumaran J, Smith SA. A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories. American Journal of Botany. PMID 29710372 DOI: 10.1002/Ajb2.1064  0.444
2018 Soltis DE, Moore MJ, Sessa EB, Smith SA, Soltis PS. Using and navigating the plant tree of life. American Journal of Botany. PMID 29702724 DOI: 10.1002/Ajb2.1071  0.353
2018 Folk RA, Sun M, Soltis PS, Smith SA, Soltis DE, Guralnick RP. Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids. American Journal of Botany. PMID 29665035 DOI: 10.1002/Ajb2.1059  0.389
2018 Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM, Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham SW, Soltis PS, et al. 10KP: A phylodiverse genome sequencing plan. Gigascience. 7: 1-9. PMID 29618049 DOI: 10.1093/Gigascience/Giy013  0.395
2018 Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, ... ... Smith SA, et al. A roadmap for global synthesis of the plant tree of life. American Journal of Botany. PMID 29603138 DOI: 10.1002/Ajb2.1041  0.439
2018 Lu LM, Mao LF, Yang T, Ye JF, Liu B, Li HL, Sun M, Miller JT, Mathews S, Hu HH, Niu YT, Peng DX, Chen YH, Smith SA, Chen M, et al. Evolutionary history of the angiosperm flora of China. Nature. 554: 234-238. PMID 29420476 DOI: 10.1038/Nature25485  0.417
2018 Echeverría-Londoño S, Enquist BJ, Neves DM, Violle C, Boyle B, Kraft NJB, Maitner BS, McGill B, Peet RK, Sandel B, Smith SA, Svenning J, Wiser SK, Kerkhoff AJ. Plant Functional Diversity and the Biogeography of Biomes in North and South America Frontiers in Ecology and Evolution. 6. DOI: 10.3389/Fevo.2018.00219  0.397
2017 Brown JW, Parins-Fukuchi C, Stull GW, Vargas OM, Smith SA. Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al. Proceedings. Biological Sciences. 284. PMID 29021179 DOI: 10.1098/Rspb.2017.0986  0.553
2017 Lopez-Nieves S, Yang Y, Timoneda A, Wang M, Feng T, Smith SA, Brockington SF, Maeda HA. Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales. The New Phytologist. PMID 28990194 DOI: 10.1111/Nph.14822  0.517
2017 Brown JW, Smith SA. The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates. Systematic Biology. PMID 28945912 DOI: 10.1093/Sysbio/Syx074  0.614
2017 Yang Y, Moore MJ, Brockington SF, Mikenas J, Olivieri J, Walker JF, Smith SA. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. The New Phytologist. PMID 28944472 DOI: 10.1111/Nph.14812  0.582
2017 Smith SA, Brown JW, Yang Y, Bruenn R, Drummond CP, Brockington SF, Walker JF, Last N, Douglas NA, Moore MJ. Disparity, diversity, and duplications in the Caryophyllales. The New Phytologist. PMID 28892163 DOI: 10.1111/Nph.14772  0.689
2017 Brown JW, Wang N, Smith SA. The development of scientific consensus: analyzing conflict and concordance among avian phylogenies. Molecular Phylogenetics and Evolution. PMID 28797692 DOI: 10.1016/J.Ympev.2017.08.002  0.641
2017 Walker JF, Yang Y, Moore MJ, Mikenas J, Timoneda A, Brockington SF, Smith SA. Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. American Journal of Botany. PMID 28634254 DOI: 10.3732/Ajb.1700083  0.575
2017 Yang Y, Moore MJ, Brockington SF, Timoneda A, Feng T, Marx HE, Walker JF, Smith SA. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences. 5. PMID 28337391 DOI: 10.3732/Apps.1600128  0.465
2017 Brown JW, Walker JF, Smith SA. phyx: Phylogenetic tools for Unix. Bioinformatics (Oxford, England). PMID 28174903 DOI: 10.1093/Bioinformatics/Btx063  0.561
2017 Maitner BS, Boyle B, Casler N, Condit R, Donoghue J, Durán SM, Guaderrama D, Hinchliff CE, Jørgensen PM, Kraft NJ, McGill B, Merow C, Morueta‐Holme N, Peet RK, Sandel B, ... ... Smith SA, et al. The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database Methods in Ecology and Evolution. 9: 373-379. DOI: 10.1111/2041-210X.12861  0.787
2016 O'Meara BC, Smith SD, Armbruster WS, Harder LD, Hardy CR, Hileman LC, Hufford L, Litt A, Magallón S, Smith SA, Stevens PF, Fenster CB, Diggle PK. Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity. Proceedings. Biological Sciences / the Royal Society. 283. PMID 27147092 DOI: 10.1098/Rspb.2015.2304  0.342
2016 Smith SA, Pease JB. Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. Briefings in Bioinformatics. PMID 27103098 DOI: 10.1093/Bib/Bbw034  0.739
2015 Zapata F, Goetz FE, Smith SA, Howison M, Siebert S, Church SH, Sanders SM, Ames CL, McFadden CS, France SC, Daly M, Collins AG, Haddock SH, Dunn CW, Cartwright P. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. Plos One. 10: e0139068. PMID 26465609 DOI: 10.1371/Journal.Pone.0139068  0.449
2015 Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD, McTavish EJ, et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences of the United States of America. PMID 26385966 DOI: 10.1073/Pnas.1423041112  0.791
2015 Smith SA, Moore MJ, Brown JW, Yang Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. Bmc Evolutionary Biology. 15: 150. PMID 26239519 DOI: 10.1186/S12862-015-0423-0  0.692
2015 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, et al. Zanne et al. reply. Nature. 521: E6-7. PMID 25993971 DOI: 10.1038/Nature14394  0.67
2015 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, et al. Corrigendum: Three keys to the radiation of angiosperms into freezing environments. Nature. 521: 380. PMID 25993966 DOI: 10.1038/Nature14371  0.692
2015 Brockington SF, Yang Y, Gandia-Herrero F, Covshoff S, Hibberd JM, Sage RF, Wong GK, Moore MJ, Smith SA. Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales. The New Phytologist. PMID 25966996 DOI: 10.1111/Nph.13441  0.53
2015 McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA. Phylesystem: a git-based data store for community-curated phylogenetic estimates. Bioinformatics (Oxford, England). PMID 25940563 DOI: 10.1093/Bioinformatics/Btv276  0.784
2015 Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, Sage RF, Covshoff S, Hibberd JM, Nelson MN, Smith SA. Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing. Molecular Biology and Evolution. 32: 2001-14. PMID 25837578 DOI: 10.1093/Molbev/Msv081  0.615
2015 Smith SA, Moore MJ, Brown JW, Yang Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants Bmc Evolutionary Biology. 15. DOI: 10.1186/s12862-015-0423-0  0.628
2014 Yang Y, Smith SA. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution. 31: 3081-92. PMID 25158799 DOI: 10.1093/Molbev/Msu245  0.584
2014 Hinchliff CE, Smith SA. Some limitations of public sequence data for phylogenetic inference (in plants). Plos One. 9: e98986. PMID 24999823 DOI: 10.1371/Journal.Pone.0098986  0.808
2014 Izquierdo-Carrasco F, Cazes J, Smith SA, Stamatakis A. PUmPER: phylogenies updated perpetually. Bioinformatics (Oxford, England). 30: 1476-7. PMID 24478338 DOI: 10.1093/Bioinformatics/Btu053  0.43
2014 Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE. Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology. 63: 368-82. PMID 24391149 DOI: 10.1093/Sysbio/Syt108  0.391
2014 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, et al. Three keys to the radiation of angiosperms into freezing environments. Nature. 506: 89-92. PMID 24362564 DOI: 10.1038/Nature12872  0.752
2014 Cornwell WK, Westoby M, Falster DS, Fitzjohn RG, O'Meara BC, Pennell MW, McGlinn DJ, Eastman JM, Moles AT, Reich PB, Tank DC, Wright IJ, Aarssen L, Beaulieu JM, Kooyman RM, ... ... Smith SA, et al. Functional distinctiveness of major plant lineages Journal of Ecology. 102: 345-356. DOI: 10.1111/1365-2745.12208  0.755
2014 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O’Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, et al. Erratum: Corrigendum: Three keys to the radiation of angiosperms into freezing environments Nature. 514: 394-394. DOI: 10.1038/Nature13842  0.686
2013 Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science (New York, N.Y.). 342: 1242592. PMID 24337300 DOI: 10.1126/Science.1242592  0.335
2013 Smith SA, Brown JW, Hinchliff CE. Analyzing and synthesizing phylogenies using tree alignment graphs. Plos Computational Biology. 9: e1003223. PMID 24086118 DOI: 10.1371/Journal.Pcbi.1003223  0.785
2013 Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications. 4: 1958. PMID 23739623 DOI: 10.1038/Ncomms2958  0.759
2013 Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. Bmc Genomics. 14: 328. PMID 23672450 DOI: 10.1186/1471-2164-14-328  0.49
2012 Smith SA, O'Meara BC. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics (Oxford, England). 28: 2689-90. PMID 22908216 DOI: 10.1093/Bioinformatics/Bts492  0.332
2012 Aliscioni S, Bell HL, Besnard G, Christin PA, Columbus JT, Duvall MR, Edwards EJ, Giussani L, Hasenstab-Lehman K, Hilu KW, Hodkinson TR, Ingram AL, Kellogg EA, Mashayekhi S, Morrone O, ... ... Smith SA, et al. New grass phylogeny resolves deep evolutionary relationships and discovers C 4 origins New Phytologist. 193: 304-312. PMID 22115274 DOI: 10.1111/j.1469-8137.2011.03972.x  0.56
2012 Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. Correction: Corrigendum: Resolving the evolutionary relationships of molluscs with phylogenomic tools Nature. 493: 708-708. DOI: 10.1038/Nature11736  0.347
2011 Izquierdo-Carrasco F, Smith SA, Stamatakis A. Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. Bmc Bioinformatics. 12: 470. PMID 22165866 DOI: 10.1186/1471-2105-12-470  0.367
2011 Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SC, Rouse GW, Giribet G, Dunn CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 480: 364-7. PMID 22031330 DOI: 10.1038/Nature10526  0.421
2011 Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. Plos One. 6: e22953. PMID 21829563 DOI: 10.1371/Journal.Pone.0022953  0.326
2011 Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS, Bell CD, Latvis M, Crawley S, Black C, Diouf D, et al. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany. 98: 704-30. PMID 21613169 DOI: 10.3732/Ajb.1000404  0.806
2011 Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ. Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany. 98: 404-14. PMID 21613134 DOI: 10.3732/Ajb.1000481  0.719
2010 Goldberg EE, Kohn JR, Lande R, Robertson KA, Smith SA, Igi? B. Species selection maintains self-incompatibility. Science (New York, N.Y.). 330: 493-5. PMID 20966249 DOI: 10.1126/Science.1194513  0.33
2010 Bendiksby M, Schumacher T, Gussarova G, Nais J, Mat-Salleh K, Sofiyanti N, Madulid D, Smith SA, Barkman T. Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: pliocene vicariance, morphological convergence and character displacement. Molecular Phylogenetics and Evolution. 57: 620-33. PMID 20723606 DOI: 10.1016/J.Ympev.2010.08.005  0.447
2010 Smith SA, Donoghue MJ. Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales). Systematic Biology. 59: 322-41. PMID 20525639 DOI: 10.1093/Sysbio/Syq011  0.58
2010 Edwards EJ, Osborne CP, Strömberg CA, Smith SA, Bond WJ, Christin PA, Cousins AB, Duvall MR, Fox DL, Freckleton RP, Ghannoum O, Hartwell J, Huang Y, Janis CM, et al. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science (New York, N.Y.). 328: 587-91. PMID 20431008 DOI: 10.1126/Science.1177216  0.611
2010 Smith SA, Beaulieu JM, Donoghue MJ. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 107: 5897-902. PMID 20304790 DOI: 10.1073/Pnas.1001225107  0.7
2010 Edwards EJ, Smith SA. Phylogenetic analyses reveal the shady history of C4 grasses. Proceedings of the National Academy of Sciences of the United States of America. 107: 2532-7. PMID 20142480 DOI: 10.1073/Pnas.0909672107  0.614
2010 Beaulieu JM, Smith SA, Leitch IJ. On the Tempo of Genome Size Evolution in Angiosperms Journal of Botany. 2010: 1-8. DOI: 10.1155/2010/989152  0.582
2009 Smith SA, O'Meara BC. Morphogenera, monophyly, and macroevolution. Proceedings of the National Academy of Sciences of the United States of America. 106: E97-8; author reply . PMID 19805242 DOI: 10.1073/Pnas.0906918106  0.366
2009 Smith SA, Beaulieu JM. Life history influences rates of climatic niche evolution in flowering plants. Proceedings. Biological Sciences / the Royal Society. 276: 4345-52. PMID 19776076 DOI: 10.1098/Rspb.2009.1176  0.597
2009 Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. Bmc Evolutionary Biology. 9: 37. PMID 19210768 DOI: 10.1186/1471-2148-9-37  0.726
2009 Evans ME, Smith SA, Flynn RS, Donoghue MJ. Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia). The American Naturalist. 173: 225-40. PMID 19072708 DOI: 10.1086/595757  0.524
2009 Smith SA. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae Journal of Biogeography. 36: 2324-2337. DOI: 10.1111/J.1365-2699.2009.02160.X  0.392
2009 Cellinese N, Smith SA, Edwards EJ, Kim ST, Haberle RC, Avramakis M, Donoghue MJ. Historical biogeography of the endemic Campanulaceae of Crete Journal of Biogeography. 36: 1253-1269. DOI: 10.1111/J.1365-2699.2008.02077.X  0.724
2008 Smith SA, Donoghue MJ. Rates of molecular evolution are linked to life history in flowering plants. Science (New York, N.Y.). 322: 86-9. PMID 18832643 DOI: 10.1126/Science.1163197  0.569
2008 Smith SA, Tank DC, Boulanger LA, Bascom-Slack CA, Eisenman K, Kingery D, Babbs B, Fenn K, Greene JS, Hann BD, Keehner J, Kelley-Swift EG, Kembaiyan V, Lee SJ, Li P, et al. Bioactive endophytes warrant intensified exploration and conservation. Plos One. 3: e3052. PMID 18725962 DOI: 10.1371/Journal.Pone.0003052  0.739
2008 Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452: 745-9. PMID 18322464 DOI: 10.1038/Nature06614  0.445
2008 Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology. 57: 4-14. PMID 18253896 DOI: 10.1080/10635150701883881  0.674
2008 Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics (Oxford, England). 24: 715-6. PMID 18227120 DOI: 10.1093/Bioinformatics/Btm619  0.374
2007 Roulston TH, Smith SA, Brewster AL. Short communication: A comparison of pan trap and intensive net sampling techniques for documenting a bee (Hymenoptera: Apiformes) fauna Journal of the Kansas Entomological Society. 80: 179-181. DOI: 10.2317/0022-8567(2007)80[179:Acopta]2.0.Co;2  0.376
2006 Moore BR, Smith SA, Donoghue MJ. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping. Systematic Biology. 55: 662-76. PMID 16969942 DOI: 10.1080/10635150600920693  0.681
2004 Donoghue MJ, Smith SA. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 359: 1633-44. PMID 15519978 DOI: 10.1098/Rstb.2004.1538  0.586
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