Systemic Biology

Article	Citations
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)	175
Corrigendum to: Delayed Adaptive Radiation among New Zealand Stream Fishes: Joint Estimation of Divergence Time and Trait Evolution in a Newly Delineated Island Species Flock	72
Announcements	70
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	63
UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina)	58
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	58
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	56
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics	51
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	51
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	49
New Phylogenetic Markov Models for Inapplicable Morphological Characters	49
PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models	49
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	48
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	48
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	44
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	43
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	42
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model	41
Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses	40
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	39
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	36
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	33
Correction to: Robust, Universal Tree Balance Indices	33
Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot	33
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	32

Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	32
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	31
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	31
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	30
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	29
Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?	29
The Frequency and Topology of Pseudoorthologs	29
Corrigendum to: Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	29
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data	28
Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation	28
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	28
Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites	28
Speciation-by-Extinction	27
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	27
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	27
Estimation of species divergence times in presence of cross-species gene flow	26
Linking Ecological Specialization to Its Macroevolutionary Consequences: An Example with Passerine Nest Type	25
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	25
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	24
Announcements	24
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	24
Announcements	24
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	24
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	24
Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution	23
Increasing Information Content and Diagnosability in Family-Level Classifications	23
How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).	23
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	23
How Important Is Budding Speciation for Comparative Studies?	22
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	21
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	20
Lagrange-NG: The next generation of Lagrange	20
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria	20
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	20
Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)	20
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees	20
How to Validate a Bayesian Evolutionary Model	19
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards	19
Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges	19
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	19
Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies	18
A Linear Time Solution to the Labeled Robinson–Foulds Distance Problem	18
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	18
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	18
On Information Rank Deficiency in Phenotypic Covariance Matrices	17
Inference of multiple mergers while dating a pathogen phylogeny	17
Is Over-parameterization a Problem for Profile Mixture Models?	17
Different Evolutionary Pathways Lead to Incomplete Convergence of Elongate Body Shapes in Carnivoran Mammals	17
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	17
Global Patterns of Taxonomic Uncertainty and its Impacts on Biodiversity Research	17

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles	16
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	16
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	16
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	16
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	16
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	16
Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC	16
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	15
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	15
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	15
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	15
Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai–Tibet Plateau	15
Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods	15
Both Diet and Sociality Affect Primate Brain-Size Evolution	15
Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates	15
Phylogenomic Insights into the Evolution and Origin of Nematoda	14
Species Tree Estimation from Gene Trees by Minimizing Deep Coalescence and Maximizing Quartet Consistency: A Comparative Study and the Presence of Pseudo Species Tree Terraces	14
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	14
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	13
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	13
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	13
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	13
Announcements	12
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	12
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	12
Announcements	12
Measuring Phylogenetic Information of Incomplete Sequence Data	12
Erratum to: “Lasciate ogni speranza voi chéntrate [Abandon hope, all ye who enter]”	12
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation	12
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference	12
Announcements	12
LoRaD: Marginal likelihood estimation with haste (but no waste)	11
Robust Phylogenetic Regression	11
Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process	11
Phylogenomics of the Ancient and Species-Depauperate Gars Tracks 150 Million Years of Continental Fragmentation in the Northern Hemisphere	11
Functional Trade-Offs Asymmetrically Promote Phenotypic Evolution	11
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	11
Rtapas: An R Package to Assess Cophylogenetic Signal between Two Evolutionary Histories	11
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	11
On the Need for New Measures of Phylogenomic Support	11
The Effect of Copy Number Hemiplasy on Gene Family Evolution	11
The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands	10
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	10
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	10
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	10
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	10
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	10
Caught in the Act: Incipient Speciation at the Southern Limit of Viburnum in the Central Andes	10
Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance inNeodiprionSawflies	10
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	10
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	9
Accuracy in Near-Perfect Virus Phylogenies	9
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	9
Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation	9
The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade	9
Discordance Down Under: Combining Phylogenomics and Fungal Symbioses to Detangle Difficult Nodes in a Diverse Tribe of Australian Terrestrial Orchids	9
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	9
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	9
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	9
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and <	8
The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics	8
Punctuated Versus Gradual Shifts in the Multivariate Evolutionary Process: A Test With Paired Radiations of Scincid Lizards	8
Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)	8
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies	8
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	8
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	8
Phylogenomic Insights into the Origin of Primary Plastids	8
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	8
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny	8
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	8
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	8
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	8
Estimating Global Biodiversity: The Role of Cryptic Insect Species	7
Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance	7
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	7
Divergent Processes Drive Parallel Evolution in Marine and Freshwater Fishes	7
Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny	7
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	7
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	7
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	7

Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic	7
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	7
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	7
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	7
Announcements	7
Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth–Death Epidemiological Models from Phylogenetic Trees	7
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	7
Impact of Ghost Introgression on Coalescent-Based Species Tree Inference and Estimation of Divergence Time	7
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	6
Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations	6
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	6
Evaluating the Impact of Anatomical Partitioning on Summary Topologies Obtained with Bayesian Phylogenetic Analyses of Morphological Data	6
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations	6
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	6
Temperature-Dependent Evolutionary Speed Shapes the Evolution of Biodiversity Patterns Across Tetrapod Radiations	6
Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods	6
Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes	6
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	6
Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences	6
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	6
Inferring Historical Introgression with Deep Learning	6