Systemic Biology

Article	Citations
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	133
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)	85
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales	77
Ghost Lineages Highly Influence the Interpretation of Introgression Tests	57
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	56
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	52
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow	52
The Legacy of Recurrent Introgression during the Radiation of Hares	51
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	48
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	44
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	42
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	42
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies	41
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	37
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	37
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	36
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data	36
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses	36
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	36
Estimating Global Biodiversity: The Role of Cryptic Insect Species	35
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene	35
Long Branch Attraction Biases in Phylogenetics	34
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses	34
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere	33
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks	32

Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	32
Robust Analysis of Phylogenetic Tree Space	31
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data	31
A New Pipeline for Removing Paralogs in Target Enrichment Data	30
Phylogenomic Insights into the Origin of Primary Plastids	30
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences	30
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	30
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data	28
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	28
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	27
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	27
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance	27
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees	27
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support	25
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	25
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough	24
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution	24
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	23
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	23
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	23
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)	23
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils	23
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	23
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	22
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	22
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)	22
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins	22
Estimation of species divergence times in presence of cross-species gene flow	22
Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology	21
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	21
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	21
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	21
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)	21
Solving the Coral Species Delimitation Conundrum	21
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	20
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	20
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	20
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	20
A Multifunction Trade-Off has Contrasting Effects on the Evolution of Form and Function	19
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	19
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	19
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)	19
Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)	19
A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions	18
Genomics Reveals Widespread Ecological Speciation in Flightless Insects	18
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	18
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent	17
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders	17
Incorporating Hierarchical Characters into Phylogenetic Analysis	17
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models	17

Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae	16
Increasing Information Content and Diagnosability in Family-Level Classifications	16
Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks	16
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	16
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	16
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	16
A Cautionary Note on “A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies”	15
Morphology-Based Identification of Bemisia tabaci Cryptic Species Puparia via Embedded Group-Contrast Convolution Neural Network Analysis	15
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds	15
Mosaic Evolution of the Skull in Labrid Fishes Involves Differences in Both Tempo and Mode of Morphological Change	15
Both Diet and Sociality Affect Primate Brain-Size Evolution	15
Reunion of Australasian Possums by Shared SINE Insertions	15
Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations	15
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	15
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails	14
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	14
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference	14
Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models	14
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model	14
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication	14
Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	14
Deep Learning from Phylogenies for Diversification Analyses	14
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	14
Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models	14
Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?	14
Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae)	13
Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)	13
The Frequency and Topology of Pseudoorthologs	13
Species as a Heuristic: Reconciling Theory and Practice	13
Phylogenetic Signal and Bias in Paleontology	13
Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis	13
Robust, Universal Tree Balance Indices	13
On the Need for New Measures of Phylogenomic Support	13
Reducing the Biases in False Correlations Between Discrete Characters	13
Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?	13
Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy	13
A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth’s Largest Lizards	13
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees	13
Relative Time Constraints Improve Molecular Dating	13
The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology	13
The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation	12
Delayed Adaptive Radiation among New Zealand Stream Fishes: Joint Estimation of Divergence Time and Trait Evolution in a Newly Delineated Island Species Flock	12
Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods	12
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	12
The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from ProgenitorErythroxylum gracilipes	12
Segmental Series and Size: Clade-Wide Investigation of Molar Proportions Reveals a Major Evolutionary Allometry in the Dentition of Placental Mammals	12
Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco)	12
Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales	12
Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)	12
The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation	11
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	11
On Defining and Finding Islands of Trees and Mitigating Large Island Bias	11
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	11
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	11
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution	10
Impact of Ghost Introgression on Coalescent-Based Species Tree Inference and Estimation of Divergence Time	10
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	10
Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla)	10
Divergent Processes Drive Parallel Evolution in Marine and Freshwater Fishes	10
A Phylogenomic Backbone for Gastropod Molluscs	10
Interspecific Gene Flow and Mitochondrial Genome Capture during the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae)	10
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	10
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	9
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	9
Functional Trade-Offs Asymmetrically Promote Phenotypic Evolution	9
New Phylogenetic Markov Models for Inapplicable Morphological Characters	9
Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research a	9
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny	9
Two Notorious Nodes: A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals	9
Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods	9
The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics	8
Temperature-Dependent Evolutionary Speed Shapes the Evolution of Biodiversity Patterns Across Tetrapod Radiations	8
Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere	8
Integrating Fossil Flowers into the Angiosperm Phylogeny Using Molecular and Morphological Evidence	8
Bayesian Morphological Clock versus Parsimony: An Insight into the Relationships and Dispersal Events of Postvacuum Cricetidae (Rodentia, Mammalia)	8
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data	8
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales	8
A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data	8
Compositionally Constrained Sites Drive Long-Branch Attraction	7
Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation	7

Accuracy in Near-Perfect Virus Phylogenies	7
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	7
Modeling the Evolution of Rates of Continuous Trait Evolution	7
Uncertainty in Divergence Time Estimation	7
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	7
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	7
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life	7
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies	7
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification	7
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	6
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	6
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	6
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	6
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	6
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria	6
Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution	6
On Information Rank Deficiency in Phenotypic Covariance Matrices	6
Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites	6
Phylogenomics Reveals that Mitochondrial Capture and Nuclear Introgression Characterize Skua Species Proposed to be of Hybrid Origin	6
The Comparative Method is Not Macroevolution: Across-Species Evidence for Within-Species Process	6
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone	6
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	6
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	6
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)	6
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)	6
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	6
Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation ofAnolisLizards	6