Systemic Biology

Article	Citations
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life	123
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l	110
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	103
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event	77
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)	70
Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant GenusPolemonium(Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nucl	62
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales	59
Ghost Lineages Highly Influence the Interpretation of Introgression Tests	48
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	47
The Legacy of Recurrent Introgression during the Radiation of Hares	44
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets	43
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow	43
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	41
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	40
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent	40
Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems	39
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	38
Repositories for Taxonomic Data: Where We Are and What is Missing	36
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos	36
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	36
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies	35
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses	35
Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification ofViburnum	34
Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective	33
Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)	33

A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data	33
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	31
Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity	31
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	31
Phylogeny Estimation Given Sequence Length Heterogeneity	30
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses	30
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?	30
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data	29
Defining Species When There is Gene Flow	29
Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)	29
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit	29
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	28
A New Pipeline for Removing Paralogs in Target Enrichment Data	28
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	28
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	27
Modeling Phylogenetic Biome Shifts on a Planet with a Past	27
Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models	27
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data	27
Long Branch Attraction Biases in Phylogenetics	26
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene	26
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	25
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation	25
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	25
Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line	24
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere	24
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees	24
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction	24
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	24
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences	23
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	23
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks	23
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy	22
Comparative Phylogenetics of Papilio Butterfly Wing Shape and Size Demonstrates Independent Hindwing and Forewing Evolution	22
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution	21
Bayesian Inference of Species Trees using Diffusion Models	21
Phylogenomic Insights into the Origin of Primary Plastids	21
Robust Analysis of Phylogenetic Tree Space	20
The Dynamics of Bird Diversity in the New World	20
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	20
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)	20
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)	20
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	20
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	20
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	20
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets	20
An Evolving View of Phylogenetic Support	19
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	19
Estimating Global Biodiversity: The Role of Cryptic Insect Species	19
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	19
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough	18

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data	18
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot	18
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils	18
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach	18
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)	18
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance	18
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	18
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders	17
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	17
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	17
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)	17
Genomics Reveals Widespread Ecological Speciation in Flightless Insects	17
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins	17
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	17
Relaxed Random Walks at Scale	17
Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology	16
Incorporating Hierarchical Characters into Phylogenetic Analysis	16
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support	16
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	16
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	15
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	15
Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics	15
A Multifunction Trade-Off has Contrasting Effects on the Evolution of Form and Function	15
Estimation of species divergence times in presence of cross-species gene flow	15
Solving the Coral Species Delimitation Conundrum	15
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	15
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	15
Global Diversification of Anelosimus Spiders Driven by Long-Distance Overwater Dispersal and Neogene Climate Oscillations	14
Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)	14
Reunion of Australasian Possums by Shared SINE Insertions	14
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	14
Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae	14
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds	13
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	13
Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data	13
Repetitive DNA Profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles	13
A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions	13
Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete	13
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference	12
On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution	12
Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)	12
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	12
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent	12
Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	12
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	12
The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms	12
Segmental Series and Size: Clade-Wide Investigation of Molar Proportions Reveals a Major Evolutionary Allometry in the Dentition of Placental Mammals	12
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails	11
Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco)	11
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	11
Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models	11
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	11
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	11
Morphology-Based Identification of Bemisia tabaci Cryptic Species Puparia via Embedded Group-Contrast Convolution Neural Network Analysis	11
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model	11
Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST	11
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	10
Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees	10
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	10
The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology	10
The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from ProgenitorErythroxylum gracilipes	10
On the Need for New Measures of Phylogenomic Support	10
A Cautionary Note on “A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies”	10
Mosaic Evolution of the Skull in Labrid Fishes Involves Differences in Both Tempo and Mode of Morphological Change	10
A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth’s Largest Lizards	10
Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae)	10
Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)	10
Relative Time Constraints Improve Molecular Dating	10
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication	10
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models	10
Phylogenetic Signal and Bias in Paleontology	9
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	9
Formal Links between Feature Diversity and Phylogenetic Diversity	9
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	9
A Cautionary Note on the Use of Genotype Callers in Phylogenomics	9
A Phylogenomic Backbone for Gastropod Molluscs	9
Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis	9
Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales	9
Both Diet and Sociality Affect Primate Brain-Size Evolution	9
Species as a Heuristic: Reconciling Theory and Practice	9

Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone	9
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	9
The Frequency and Topology of Pseudoorthologs	9
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution	8
Interspecific Gene Flow and Mitochondrial Genome Capture during the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae)	8
Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models	8
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales	8
Impact of Ghost Introgression on Coalescent-Based Species Tree Inference and Estimation of Divergence Time	8
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	8
Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?	8
Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations	8
Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?	8
Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy	7
Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods	7
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification	7
Delayed Adaptive Radiation among New Zealand Stream Fishes: Joint Estimation of Divergence Time and Trait Evolution in a Newly Delineated Island Species Flock	7
On Defining and Finding Islands of Trees and Mitigating Large Island Bias	7
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data	7
Bayesian Morphological Clock versus Parsimony: An Insight into the Relationships and Dispersal Events of Postvacuum Cricetidae (Rodentia, Mammalia)	7
The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment	7
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees	7
Increasing Information Content and Diagnosability in Family-Level Classifications	7
Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla)	6
Reducing the Biases in False Correlations Between Discrete Characters	6
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	6
New Phylogenetic Markov Models for Inapplicable Morphological Characters	6
Modeling Mito-nuclear Compatibility and Its Role in Species Identification	6
The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation	6
The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics	6
Robust, Universal Tree Balance Indices	6
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life	6
Inferring the Effect of Species Interactions on Trait Evolution	6
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)	6
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	6
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)	6
Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods	6
Accuracy in Near-Perfect Virus Phylogenies	6
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	6