| # | Title | Journal | Year | Citations |
|---|
| 1 | MITOS: Improved de novo metazoan mitochondrial genome annotation | Molecular Phylogenetics and Evolution | 2013 | 3,919 |
| 2 | Two Divergent Intragenomic rDNA ITS2 Types within a Monophyletic Lineage of the FungusFusariumAre Nonorthologous | Molecular Phylogenetics and Evolution | 1997 | 1,815 |
| 3 | Ribosomal ITS sequences and plant phylogenetic inference | Molecular Phylogenetics and Evolution | 2003 | 1,592 |
| 4 | An index of substitution saturation and its application | Molecular Phylogenetics and Evolution | 2003 | 1,315 |
| 5 | A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians | Molecular Phylogenetics and Evolution | 2011 | 1,184 |
| 6 | RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography | Molecular Phylogenetics and Evolution | 2015 | 1,049 |
| 7 | Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the compositae | Molecular Phylogenetics and Evolution | 1992 | 866 |
| 8 | The major clades of MADS-box genes and their role in the development and evolution of flowering plants | Molecular Phylogenetics and Evolution | 2003 | 827 |
| 9 | Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora | Molecular Phylogenetics and Evolution | 2011 | 753 |
| 10 | Primers for a PCR-Based Approach to Mitochondrial Genome Sequencing in Birds and Other Vertebrates | Molecular Phylogenetics and Evolution | 1999 | 685 |
| 11 | Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence | Molecular Phylogenetics and Evolution | 1998 | 672 |
| 12 | Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences | Molecular Phylogenetics and Evolution | 2003 | 668 |
| 13 | S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories | Molecular Phylogenetics and Evolution | 2010 | 667 |
| 14 | Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support | Molecular Phylogenetics and Evolution | 2002 | 626 |
| 15 | Evolution of mitochondrial gene content: gene loss and transfer to the nucleus | Molecular Phylogenetics and Evolution | 2003 | 585 |
| 16 | One hundred and seventeen clades of euagarics | Molecular Phylogenetics and Evolution | 2002 | 583 |
| 17 | Functional Diversity, Conservation, and Convergence in the Evolution of the α-, β-, and γ-Carbonic Anhydrase Gene Families | Molecular Phylogenetics and Evolution | 1996 | 579 |
| 18 | Phylogenetic Utility of the External Transcribed Spacer (ETS) of 18S–26S rDNA: Congruence of ETS and ITS Trees ofCalycadenia(Compositae) | Molecular Phylogenetics and Evolution | 1998 | 561 |
| 19 | Phylogeography’s past, present, and future: 10 years after Avise, 2000 | Molecular Phylogenetics and Evolution | 2010 | 535 |
| 20 | Applications of next-generation sequencing to phylogeography and phylogenetics | Molecular Phylogenetics and Evolution | 2013 | 531 |
| 21 | Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species | Molecular Phylogenetics and Evolution | 2016 | 488 |
| 22 | Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales) | Molecular Phylogenetics and Evolution | 2005 | 483 |
| 23 | Split decomposition: A new and useful approach to phylogenetic analysis of distance data | Molecular Phylogenetics and Evolution | 1992 | 472 |
| 24 | Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants | Molecular Phylogenetics and Evolution | 2007 | 460 |
| 25 | Molecular Phylogenetics and Biogeography of Tanagers in the GenusRamphocelus(Aves) | Molecular Phylogenetics and Evolution | 1996 | 442 |
| 26 | FASconCAT: Convenient handling of data matrices | Molecular Phylogenetics and Evolution | 2010 | 442 |
| 27 | Phylogenetic inference based on matrix representation of trees | Molecular Phylogenetics and Evolution | 1992 | 436 |
| 28 | Phylogeny and Biogeography ofPanaxL. (the Ginseng Genus, Araliaceae): Inferences from ITS Sequences of Nuclear Ribosomal DNA | Molecular Phylogenetics and Evolution | 1996 | 423 |
| 29 | Use of rRNA Secondary Structure in Phylogenetic Studies to Identify Homologous Positions: An Example of Alignment and Data Presentation from the Frogs | Molecular Phylogenetics and Evolution | 1995 | 422 |
| 30 | Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies | Molecular Phylogenetics and Evolution | 2008 | 421 |
| 31 | A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai’i | Molecular Phylogenetics and Evolution | 2010 | 420 |
| 32 | Relationship between morphological taxonomy and molecular divergence within Crustacea: Proposal of a molecular threshold to help species delimitation | Molecular Phylogenetics and Evolution | 2006 | 409 |
| 33 | A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach | Molecular Phylogenetics and Evolution | 2007 | 408 |
| 34 | Root Probabilities for Intraspecific Gene Trees under Neutral Coalescent Theory | Molecular Phylogenetics and Evolution | 1994 | 406 |
| 35 | Basal Divergences in Birds and the Phylogenetic Utility of the Nuclear RAG-1 Gene | Molecular Phylogenetics and Evolution | 1999 | 401 |
| 36 | Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory | Molecular Phylogenetics and Evolution | 2004 | 396 |
| 37 | A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches | Molecular Phylogenetics and Evolution | 2008 | 390 |
| 38 | From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem | Molecular Phylogenetics and Evolution | 1997 | 384 |
| 39 | Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes | Molecular Phylogenetics and Evolution | 2003 | 384 |
| 40 | Multiple maternal origins of chickens: Out of the Asian jungles | Molecular Phylogenetics and Evolution | 2006 | 379 |
| 41 | Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide | Molecular Phylogenetics and Evolution | 2009 | 368 |
| 42 | Ancestral Lineages of Arbuscular Mycorrhizal Fungi (Glomales) | Molecular Phylogenetics and Evolution | 2000 | 361 |
| 43 | Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants | Molecular Phylogenetics and Evolution | 2008 | 354 |
| 44 | Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae) | Molecular Phylogenetics and Evolution | 1999 | 353 |
| 45 | Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels | Molecular Phylogenetics and Evolution | 2002 | 353 |
| 46 | Coalescent methods for estimating phylogenetic trees | Molecular Phylogenetics and Evolution | 2009 | 353 |
| 47 | The Interrelationships of Proseriata (Platyhelminthes: Seriata) Tested with Molecules and Morphology | Molecular Phylogenetics and Evolution | 2000 | 346 |
| 48 | Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation | Molecular Phylogenetics and Evolution | 2005 | 344 |
| 49 | Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi) | Molecular Phylogenetics and Evolution | 2007 | 341 |
| 50 | A comprehensive phylogenetic analysis of termites (Isoptera) illuminates key aspects of their evolutionary biology | Molecular Phylogenetics and Evolution | 2007 | 341 |
