Joseph W. Brown, Ph.D. - Publications

Ecology and Evolutionary Biology University of Michigan, Ann Arbor, Ann Arbor, MI 
phylogenetics; evolution;

35 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
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  0.752
2019 Sarver BAJ, Pennell MW, Brown JW, Keeble S, Hardwick KM, Sullivan J, Harmon LJ. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. Peerj. 7: e6334. PMID 30886768 DOI: 10.7717/Peerj.6334  0.766
2019 Franz NM, Musher LJ, Brown JW, Yu S, Ludäscher B. Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. Plos Computational Biology. 15: e1006493. PMID 30768597 DOI: 10.1371/Journal.Pcbi.1006493  0.342
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, 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  0.757
2018 Walker JF, Brown JW, Smith SA. Analyzing contentious relationships and outlier genes in phylogenomics. Systematic Biology. PMID 29893968 DOI: 10.1093/Sysbio/Syy043  0.75
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  0.75
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  0.57
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  0.725
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  0.499
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  0.581
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  0.755
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  0.59
2017 Brown JW, Walker JF, Smith SA. phyx: Phylogenetic tools for Unix. Bioinformatics (Oxford, England). PMID 28174903 DOI: 10.1093/Bioinformatics/Btx063  0.709
2016 Johnson JA, Brown JW, Fuchs J, Mindell DP. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae). Molecular Phylogenetics and Evolution. PMID 27601346 DOI: 10.1016/J.Ympev.2016.08.025  0.649
2016 Michonneau F, Brown JW, Winter DJ. rotl: an R package to interact with the Open Tree of Life data Methods in Ecology and Evolution. 7: 1476-1481. DOI: 10.1111/2041-210X.12593  0.411
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  0.641
2015 Stein RW, Brown JW, Mooers AØ. A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves). Molecular Phylogenetics and Evolution. PMID 26140861 DOI: 10.1016/J.Ympev.2015.06.005  0.411
2015 Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, Brown JW, Sessa EB, Harmon LJ. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. The New Phytologist. 207: 454-67. PMID 26053261 DOI: 10.1111/Nph.13491  0.743
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  0.777
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  0.544
2014 Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics (Oxford, England). 30: 2216-8. PMID 24728855 DOI: 10.1093/Bioinformatics/Btu181  0.747
2014 Hernández-Hernández T, Brown JW, Schlumpberger BO, Eguiarte LE, Magallón S. Beyond aridification: multiple explanations for the elevated diversification of cacti in the New World Succulent Biome. The New Phytologist. 202: 1382-97. PMID 24611540 DOI: 10.1111/Nph.12752  0.408
2014 Rabosky DL, Grundler M, Anderson C, Title P, Shi JJ, Brown JW, Huang H, Larson JG. BAMMtools: An R package for the analysis of evolutionary dynamics on phylogenetic trees Methods in Ecology and Evolution. 5: 701-707. DOI: 10.1111/2041-210X.12199  0.417
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  0.773
2013 Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, ... ... Brown JW, et al. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. Bmc Bioinformatics. 14: 158. PMID 23668630 DOI: 10.1186/1471-2105-14-158  0.758
2012 Rosenblum EB, Sarver BA, Brown JW, Des Roches S, Hardwick KM, Hether TD, Eastman JM, Pennell MW, Harmon LJ. Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales. Evolutionary Biology. 39: 255-261. PMID 22707806 DOI: 10.1007/S11692-012-9171-X  0.749
2012 Mitchell A, Li R, Brown JW, Schönberger I, Wen J. Ancient divergence and biogeography of Raukaua (Araliaceae) and close relatives in the southern hemisphere Australian Systematic Botany. 25: 432-446. DOI: 10.1071/Sb12020  0.355
2011 Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S, Davis DR, Baixeras J, Brown JW, Parr C. Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)? Systematic Biology. 60: 782-96. PMID 21840842 DOI: 10.1093/Sysbio/Syr079  0.329
2010 Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America. Plos One. 5: e14042. PMID 21124969 DOI: 10.1371/Journal.Pone.0014042  0.571
2010 Brown JW, Sorhannus U. A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages. Plos One. 5. PMID 20862282 DOI: 10.1371/Journal.Pone.0012759  0.406
2010 Qiu YL, Li L, Wang B, Xue JY, Hendry TA, Li RQ, Brown JW, Liu Y, Hudson GT, Chen ZD. Angiosperm phylogeny inferred from sequences of four mitochondrial genes Journal of Systematics and Evolution. 48: 391-425. DOI: 10.1111/J.1759-6831.2010.00097.X  0.412
2009 Howes BJ, Brown JW, Gibbs HL, Herman TB, Mockford SW, Prior KA, Weatherhead PJ. Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding's turtle (Emydoidea blandingii) Conservation Genetics. 10: 407-417. DOI: 10.1007/S10592-008-9607-0  0.384
2008 Brown JW, Rest JS, García-Moreno J, Sorenson MD, Mindell DP. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. Bmc Biology. 6: 6. PMID 18226223 DOI: 10.1186/1741-7007-6-6  0.77
2007 Brown JW, Payne RB, Mindell DP. Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al. Biology Letters. 3: 257-9; discussion 26. PMID 17389215 DOI: 10.1098/Rsbl.2006.0611  0.536
2007 Brown JW, van Coeverden de Groot PJ, Birt TP, Seutin G, Boag PT, Friesen VL. Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus. Molecular Ecology. 16: 327-43. PMID 17217348 DOI: 10.1111/J.1365-294X.2007.03151.X  0.587
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