| # | Title | Journal | Year | Citations |
|---|
| 1 | The neighbor-joining method: a new method for reconstructing phylogenetic trees. | Molecular Biology and Evolution | 1987 | 49,040 |
| 2 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | Molecular Biology and Evolution | 2013 | 37,728 |
| 3 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | Molecular Biology and Evolution | 2016 | 36,708 |
| 4 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | Molecular Biology and Evolution | 2011 | 36,550 |
| 5 | CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP | Evolution; International Journal of Organic Evolution | 1985 | 35,356 |
| 6 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | Molecular Biology and Evolution | 2013 | 32,012 |
| 7 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | Molecular Biology and Evolution | 2007 | 25,988 |
| 8 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | Molecular Biology and Evolution | 2018 | 25,630 |
| 9 | Detecting the number of clusters of individuals using the software structure: a simulation study | Molecular Ecology | 2005 | 18,555 |
| 10 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | Molecular Biology and Evolution | 2015 | 16,610 |
| 11 | Confidence Limits on Phylogenies: An Approach Using the Bootstrap | Evolution; International Journal of Organic Evolution | 1985 | 16,574 |
| 12 | Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows | Molecular Ecology Resources | 2010 | 13,484 |
| 13 | ANALYZING TABLES OF STATISTICAL TESTS | Evolution; International Journal of Organic Evolution | 1989 | 13,049 |
| 14 | genalex 6: genetic analysis in Excel. Population genetic software for teaching and research | Molecular Ecology Notes | 2006 | 12,505 |
| 15 | PAML 4: Phylogenetic Analysis by Maximum Likelihood | Molecular Biology and Evolution | 2007 | 11,130 |
| 16 | BEAST: Bayesian evolutionary analysis by sampling trees | BMC Evolutionary Biology | 2007 | 11,072 |
| 17 | ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE | Evolution; International Journal of Organic Evolution | 1984 | 10,475 |
| 18 | Median-joining networks for inferring intraspecific phylogenies | Molecular Biology and Evolution | 1999 | 9,666 |
| 19 | jModelTest: Phylogenetic Model Averaging | Molecular Biology and Evolution | 2008 | 9,343 |
| 20 | micro-checker: software for identifying and correcting genotyping errors in microsatellite data | Molecular Ecology Notes | 2004 | 9,051 |
| 21 | Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | Molecular Biology and Evolution | 2012 | 9,040 |
| 22 | Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | Molecular Biology and Evolution | 2000 | 8,843 |
| 23 | Phylogenies and the Comparative Method | American Naturalist | 1985 | 8,671 |
| 24 | TCS: a computer program to estimate gene genealogies | Molecular Ecology | 2000 | 8,515 |
| 25 | Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. | Molecular Biology and Evolution | 1993 | 8,355 |
| 26 | ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts | Molecular Ecology | 1993 | 8,354 |
| 27 | Genetic Distance between Populations | American Naturalist | 1972 | 8,261 |
| 28 | genepop’007: a complete re‐implementation of the genepop software for Windows and Linux | Molecular Ecology Resources | 2008 | 7,546 |
| 29 | Application of Phylogenetic Networks in Evolutionary Studies | Molecular Biology and Evolution | 2006 | 7,402 |
| 30 | Estimating F-Statistics for the Analysis of Population Structure | Evolution; International Journal of Organic Evolution | 1984 | 7,180 |
| 31 | Arlequin (version 3.0): An integrated software package for population genetics data analysis | Evolutionary Bioinformatics | 2005 | 6,908 |
| 32 | Ecological and Evolutionary Responses to Recent Climate Change | Annual Review of Ecology, Evolution, and Systematics | 2006 | 6,374 |
| 33 | Analyzing Tables of Statistical Tests | Evolution; International Journal of Organic Evolution | 1989 | 6,311 |
| 34 | MEGA11: Molecular Evolutionary Genetics Analysis Version 11 | Molecular Biology and Evolution | 2021 | 6,189 |
| 35 | IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era | Molecular Biology and Evolution | 2020 | 5,960 |
| 36 | UFBoot2: Improving the Ultrafast Bootstrap Approximation | Molecular Biology and Evolution | 2018 | 5,798 |
| 37 | Effects of Habitat Fragmentation on Biodiversity | Annual Review of Ecology, Evolution, and Systematics | 2003 | 5,326 |
| 38 | PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses | Molecular Biology and Evolution | 2012 | 5,083 |
| 39 | SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building | Molecular Biology and Evolution | 2010 | 5,075 |
| 40 | Species Distribution Models: Ecological Explanation and Prediction Across Space and Time | Annual Review of Ecology, Evolution, and Systematics | 2009 | 4,747 |
| 41 | BARCODING: bold: The Barcode of Life Data System (http://www.barcodinglife.org) | Molecular Ecology Notes | 2007 | 4,686 |
| 42 | THE MEASUREMENT OF SELECTION ON CORRELATED CHARACTERS | Evolution; International Journal of Organic Evolution | 1983 | 4,572 |
| 43 | TNT, a free program for phylogenetic analysis | Cladistics | 2008 | 4,493 |
| 44 | Food Web Complexity and Species Diversity | American Naturalist | 1966 | 4,469 |
| 45 | Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment | Molecular Ecology | 2007 | 4,426 |
| 46 | Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory | American Naturalist | 1977 | 4,421 |
| 47 | Sources, Sinks, and Population Regulation | American Naturalist | 1988 | 4,410 |
| 48 | Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. | Molecular Biology and Evolution | 1986 | 4,402 |
| 49 | distruct: a program for the graphical display of population structure | Molecular Ecology Notes | 2003 | 4,229 |
| 50 | FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix | Molecular Biology and Evolution | 2009 | 4,165 |
| 51 | DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets | Molecular Biology and Evolution | 2017 | 4,056 |
| 52 | MITOS: Improved de novo metazoan mitochondrial genome annotation | Molecular Phylogenetics and Evolution | 2013 | 3,919 |
| 53 | Herbivores and the Number of Tree Species in Tropical Forests | American Naturalist | 1970 | 3,886 |
| 54 | Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference | Molecular Biology and Evolution | 1999 | 3,859 |
| 55 | Statistical confidence for likelihood‐based paternity inference in natural populations | Molecular Ecology | 1998 | 3,771 |
| 56 | Population growth makes waves in the distribution of pairwise genetic differences. | Molecular Biology and Evolution | 1992 | 3,711 |
| 57 | The Limiting Similarity, Convergence, and Divergence of Coexisting Species | American Naturalist | 1967 | 3,595 |
| 58 | TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE | Evolution; International Journal of Organic Evolution | 2003 | 3,594 |
| 59 | TESTING SIGNIFICANCE OF INCONGRUENCE | Cladistics | 1994 | 3,589 |
| 60 | On Optimal Use of a Patchy Environment | American Naturalist | 1966 | 3,528 |
| 61 | Mechanisms of Succession in Natural Communities and Their Role in Community Stability and Organization | American Naturalist | 1977 | 3,499 |
| 62 | Homage to Santa Rosalia or Why Are There So Many Kinds of Animals? | American Naturalist | 1959 | 3,465 |
| 63 | Arlequin (version 3.0): an integrated software package for population genetics data analysis | Evolutionary Bioinformatics | 2007 | 3,416 |
| 64 | Intra-sexual selection in Drosophila | Heredity | 1948 | 3,403 |
| 65 | spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels | Molecular Ecology Notes | 2002 | 3,239 |
| 66 | On r- and K-Selection | American Naturalist | 1970 | 3,183 |
| 67 | BUTTERFLIES AND PLANTS: A STUDY IN COEVOLUTION | Evolution; International Journal of Organic Evolution | 1964 | 3,176 |
| 68 | Ultrafast Approximation for Phylogenetic Bootstrap | Molecular Biology and Evolution | 2013 | 3,123 |
| 69 | Stacks: an analysis tool set for population genomics | Molecular Ecology | 2013 | 3,077 |
| 70 | Towards a unified paradigm for sequence‐based identification of fungi | Molecular Ecology | 2013 | 2,997 |
| 71 | Inferring weak population structure with the assistance of sample group information | Molecular Ecology Resources | 2009 | 2,931 |
| 72 | Community Structure, Population Control, and Competition | American Naturalist | 1960 | 2,900 |
| 73 | Natural Selection, the Costs of Reproduction, and a Refinement of Lack's Principle | American Naturalist | 1966 | 2,900 |
| 74 | Inference of population structure using multilocus genotype data: dominant markers and null alleles | Molecular Ecology Notes | 2007 | 2,900 |
| 75 | MorphoJ: an integrated software package for geometric morphometrics | Molecular Ecology Resources | 2011 | 2,884 |
| 76 | PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses | Molecular Biology and Evolution | 2017 | 2,854 |
| 77 | A General Hypothesis of Species Diversity | American Naturalist | 1979 | 2,807 |
| 78 | Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences | Molecular Biology and Evolution | 2005 | 2,782 |
| 79 | Some genetic consequences of ice ages, and their role in divergence and speciation | Biological Journal of the Linnean Society | 1996 | 2,749 |
| 80 | An Improved General Amino Acid Replacement Matrix | Molecular Biology and Evolution | 2008 | 2,748 |
| 81 | A DNA test to sex most birds | Molecular Ecology | 1998 | 2,688 |
| 82 | Regime Shifts, Resilience, and Biodiversity in Ecosystem Management | Annual Review of Ecology, Evolution, and Systematics | 2004 | 2,674 |
| 83 | The Paradox of the Plankton | American Naturalist | 1961 | 2,654 |
| 84 | On the Relationship between Abundance and Distribution of Species | American Naturalist | 1984 | 2,647 |
| 85 | Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems | Annual Review of Ecology, Evolution, and Systematics | 2004 | 2,605 |
| 86 | A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach | Molecular Biology and Evolution | 2001 | 2,599 |
| 87 | BRANCH SUPPORT AND TREE STABILITY | Cladistics | 1994 | 2,570 |
| 88 | The Optimal Balance between Size and Number of Offspring | American Naturalist | 1974 | 2,535 |
| 89 | Parasites, Bright Males, and the Immunocompetence Handicap | American Naturalist | 1992 | 2,534 |
| 90 | Comparative phylogeography and postglacial colonization routes in Europe | Molecular Ecology | 1998 | 2,534 |
| 91 | PLEIOTROPY, NATURAL SELECTION, AND THE EVOLUTION OF SENESCENCE | Evolution; International Journal of Organic Evolution | 1957 | 2,516 |
| 92 | ESTIMATING RELATEDNESS USING GENETIC MARKERS | Evolution; International Journal of Organic Evolution | 1989 | 2,493 |
| 93 | Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies | Molecular Biology and Evolution | 1996 | 2,447 |
| 94 | Clumpak: a program for identifying clustering modes and packaging population structure inferences across K | Molecular Ecology Resources | 2015 | 2,411 |
| 95 | ABGD, Automatic Barcode Gap Discovery for primary species delimitation | Molecular Ecology | 2012 | 2,396 |
| 96 | Microsatellite Null Alleles and Estimation of Population Differentiation | Molecular Biology and Evolution | 2007 | 2,333 |
| 97 | Post-glacial re-colonization of European biota | Biological Journal of the Linnean Society | 1999 | 2,330 |
| 98 | Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence | American Naturalist | 2002 | 2,270 |
| 99 | The revolution that wasn't: a new interpretation of the origin of modern human behavior | Journal of Human Evolution | 2000 | 2,269 |
| 100 | Bayesian Inference of Species Trees from Multilocus Data | Molecular Biology and Evolution | 2010 | 2,246 |
