| # | Title | Journal | Year | Citations |
|---|
| 1 | Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi | Proceedings of the National Academy of Sciences of the United States of America | 2012 | 4,012 |
| 2 | Evolution by gene duplication: an update | Trends in Ecology and Evolution | 2003 | 1,864 |
| 3 | Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level | Molecular Biology and Evolution | 2005 | 1,650 |
| 4 | Phylogenetic distribution and evolution of mycorrhizas in land plants | Mycorrhiza | 2006 | 1,540 |
| 5 | Global food security, biodiversity conservation and the future of agricultural intensification | Biological Conservation | 2012 | 1,414 |
| 6 | A REVIEW OF TRAIT-MEDIATED INDIRECT INTERACTIONS IN ECOLOGICAL COMMUNITIES | Ecology | 2003 | 1,336 |
| 7 | Three keys to the radiation of angiosperms into freezing environments | Nature | 2014 | 1,284 |
| 8 | Seasonality and the dynamics of infectious diseases | Ecology Letters | 2006 | 1,162 |
| 9 | Phylotranscriptomic analysis of the origin and early diversification of land plants | Proceedings of the National Academy of Sciences of the United States of America | 2014 | 1,123 |
| 10 | Spatial autocorrelation in biology: 1. Methodology | Biological Journal of the Linnean Society | 1978 | 1,096 |
| 11 | A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data | Mycologia | 2016 | 1,092 |
| 12 | Inferring Phylogeny Despite Incomplete Lineage Sorting | Systematic Biology | 2006 | 955 |
| 13 | Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence | Nature Reviews Genetics | 2012 | 926 |
| 14 | Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes | Journal of Eukaryotic Microbiology | 2019 | 904 |
| 15 | rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development | Nucleic Acids Research | 2015 | 817 |
| 16 | Ecological Forecasts: An Emerging Imperative | Science | 2001 | 774 |
| 17 | Delimiting Species without Monophyletic Gene Trees | Systematic Biology | 2007 | 657 |
| 18 | Constructing a broadly inclusive seed plant phylogeny | American Journal of Botany | 2018 | 647 |
| 19 | Organic agriculture and the global food supply | Renewable Agriculture and Food Systems | 2007 | 644 |
| 20 | Multispecies coalescent delimits structure, not species | Proceedings of the National Academy of Sciences of the United States of America | 2017 | 640 |
| 21 | Why Do Hubs Tend to Be Essential in Protein Networks? | PLoS Genetics | 2006 | 634 |
| 22 | Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses | Nature | 2016 | 629 |
| 23 | Individual recognition: it is good to be different | Trends in Ecology and Evolution | 2007 | 627 |
| 24 | Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution | Genetics | 2005 | 598 |
| 25 | The changing landscape: ecosystem responses to urbanization and pollution across climatic and societal gradients | Frontiers in Ecology and the Environment | 2008 | 597 |
| 26 | Angiosperm phylogeny: 17 genes, 640 taxa | American Journal of Botany | 2011 | 590 |
| 27 | Data access for the 1,000 Plants (1KP) project | GigaScience | 2014 | 582 |
| 28 | The deepest divergences in land plants inferred from phylogenomic evidence | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 579 |
| 29 | An inverse latitudinal gradient in speciation rate for marine fishes | Nature | 2018 | 579 |
| 30 | The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms | Nature Reviews Genetics | 2011 | 577 |
| 31 | Ecological Lessons from Free-Air CO2 Enrichment (FACE) Experiments | Annual Review of Ecology, Evolution, and Systematics | 2011 | 558 |
| 32 | treePL: divergence time estimation using penalized likelihood for large phylogenies | Bioinformatics | 2012 | 558 |
| 33 | Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation | Nature Communications | 2013 | 531 |
| 34 | Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 530 |
| 35 | The agroecological matrix as alternative to the land-sparing/agriculture intensification model | Proceedings of the National Academy of Sciences of the United States of America | 2010 | 516 |
| 36 | The biology of color | Science | 2017 | 509 |
| 37 | Spatial autocorrelation in biology: 2. Some biological implications and four applications of evolutionary and ecological interest | Biological Journal of the Linnean Society | 1978 | 481 |
| 38 | Subspecific origin and haplotype diversity in the laboratory mouse | Nature Genetics | 2011 | 439 |
| 39 | The impacts of climate change on ecosystem structure and function | Frontiers in Ecology and the Environment | 2013 | 433 |
| 40 | Sunlight controls water column processing of carbon in arctic fresh waters | Science | 2014 | 428 |
| 41 | Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans | Science | 2006 | 423 |
| 42 | THE GROWTH–DEFENSE TRADE-OFF AND HABITAT SPECIALIZATION BY PLANTS IN AMAZONIAN FORESTS | Ecology | 2006 | 404 |
| 43 | Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris | PLoS ONE | 2016 | 403 |
| 44 | Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight‐locus plastid phylogeny | American Journal of Botany | 2011 | 401 |
| 45 | ENVIREM: an expanded set of bioclimatic and topographic variables increases flexibility and improves performance of ecological niche modeling | Ecography | 2018 | 393 |
| 46 | Geological and climatic influences on mountain biodiversity | Nature Geoscience | 2018 | 390 |
| 47 | Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea ( Coprinus cinereus ) | Proceedings of the National Academy of Sciences of the United States of America | 2010 | 389 |
| 48 | Recent Asian origin of chytrid fungi causing global amphibian declines | Science | 2018 | 389 |
| 49 | Ecosystem response to 15 years of chronic nitrogen additions at the Harvard Forest LTER, Massachusetts, USA | Forest Ecology and Management | 2004 | 387 |
| 50 | Inapparent infections and cholera dynamics | Nature | 2008 | 380 |
