Systemic Biology

Article	Citations
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	102
Announcements	99
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	97
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	83
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	67
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	48
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	46
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	42
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	42
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	39
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	39
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	39
How to Validate a Bayesian Evolutionary Model	38
Phylogenomic Insights into the Evolution and Origin of Nematoda	37
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	37
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	35
Evolutionary Tempo, Supertaxa, and Living Fossils	35
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	34
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	33
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	32
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	32
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	32
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	32
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	32
Estimating Global Biodiversity: The Role of Cryptic Insect Species	31

Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	31
Announcements	30
Robust, Universal Tree Balance Indices	27
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	27
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	27
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	26
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	26
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	26
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	26
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	25
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	25
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	25
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	25
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of	25
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	24
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	24
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	23
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	23
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	23
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	23
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	23
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	23
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	23
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	23
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	22
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	22
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	22
New Phylogenetic Markov Models for Inapplicable Morphological Characters	22
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	21
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	21
Too Many Numbers?	21
Estimation of species divergence times in presence of cross-species gene flow	21
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	21
Is Over-parameterization a Problem for Profile Mixture Models?	21
Waves of Colonization and Gene Flow in a Great Speciator	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	20
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	20
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	20
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	20
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	20
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	20
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	20
Global climate cooling spurred skipper butterfly diversification	19
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	19
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	19
The Effect of Copy Number Hemiplasy on Gene Family Evolution	19
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	19
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	19
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	19

The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	18
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	17
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	17
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	17
Gene Flow Complicates Phylogenetic Inference in an Archipelago Radiation	17
Correction to: Modeling phylogenetic biome shifts on a planet with a past	17
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	16
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	16
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	16
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	16
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	16
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	16
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	16
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss	15
A Genomic Perspective on the Evolutionary Diversification of Turtles	15
Mechanisms of Community Assembly through the Lens of Phylogenetic Diversity: A Critical Reappraisal	15
Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids	15
The Phylogenetic Limits to Diversity-Dependent Diversification	15
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	15
Social Environment and the Evolution of Delayed Reproduction in Birds	15
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	15
Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera	14
Speciation-by-Extinction	14
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	14
Reducing the Biases in False Correlations Between Discrete Characters	14
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	14
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	14
Systematic Biology ’s Seventy-Five Years	14
Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard ( Varanus tristis )	13
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	13
New Perspectives in Phylogenetic Support Assessment: Using the Relative Contradiction Index to Investigate the Phylogenetic Controversies in Crocodylia	13
Hybridization and Polyploidy Shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes ( Luzula sect.	13
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	13
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	13
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	12
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	12
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	12
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization	12
The Comparative Analysis of Lineage-Pair Traits	12
How Important Is Budding Speciation for Comparative Studies?	12
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and <	12
The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade	12
GroupStruct2: A User-Friendly Graphical User Interface for Statistical and Visual Support in Species Diagnosis	12
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	12
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC	12
Phylogenomics of a Genus of “Great Speciators” Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems	12
Dating the Bacterial Tree of Life Based on Ancient Symbiosis	11
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	11
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants	11
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	11
The Consequences of Budding Speciation on Trees	11
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	11
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	11
Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference	10
Link between the Birth–Death Process and the Kingman Coalescent—Applications to Phylogenetic Epidemiology	10
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	10
Genomic and phenotypic delimitation of species in a temperate aquatic biodiversity hotspot	10
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila	10
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	10
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation	9
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	9
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	9
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information	9
The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics	9
Announcements	9
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)	8
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow	8
Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data	8
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	8
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling	8
Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla)	8
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	7
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	7
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	7
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	7
On the Mkv Model with Among-Character Rate Variation	7
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	7
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	7
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	7
Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)	7

Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	7
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	7
Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera	7
Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai–Tibet Plateau	6
Phylogenetic Inference from Atomised 3D Morphometric Data: a Case Study using Kangaroos	6
The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands	6
Functional Trade-Offs Asymmetrically Promote Phenotypic Evolution	6
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria	6
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	6
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation	6
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC	6
On the Need for New Measures of Phylogenomic Support	6
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	6
Incorporating Continuous Characters in Joint Estimation of Dicynodont Phylogeny	6
Estimating Ancestral States of Complex Characters: A Case Study on the Evolution of Feathers	6
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies	6