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	95
Announcements	87
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	84
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	80
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	63
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	60
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	43
How to Validate a Bayesian Evolutionary Model	40
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	40
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	40
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	39
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	38
Phylogenomic Insights into the Evolution and Origin of Nematoda	36
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	35
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	34
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization	34
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	33
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	33
Announcements	32
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	30
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	30
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	29
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	29
Estimating Global Biodiversity: The Role of Cryptic Insect Species	28
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	28

Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	28
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	28
Evolutionary Tempo, Supertaxa, and Living Fossils	28
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	25
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	25
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	25
Announcements	25
Robust, Universal Tree Balance Indices	25
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	25
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	25
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	24
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	24
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	24
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	24
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	23
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	23
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	23
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	22
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	22
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	22
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	21
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	21
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	21
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	21
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	21
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	20
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	20
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	20
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	20
New Phylogenetic Markov Models for Inapplicable Morphological Characters	20
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	20
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	19
On Information Rank Deficiency in Phenotypic Covariance Matrices	19
Estimation of species divergence times in presence of cross-species gene flow	19
Waves of Colonization and Gene Flow in a Great Speciator	19
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	19
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	19
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	18
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	18
Global climate cooling spurred skipper butterfly diversification	18
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	18
Is Over-parameterization a Problem for Profile Mixture Models?	18
PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	18
Too many numbers?	18
The Effect of Copy Number Hemiplasy on Gene Family Evolution	18
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	17
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	17
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	17
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	17
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	17

ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	17
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	17
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	17
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	16
Robust Analysis of Phylogenetic Tree Space	16
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	16
Correction to: Modeling phylogenetic biome shifts on a planet with a past	15
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	15
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	15
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	15
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	15
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	15
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	15
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	15
Social Environment and the Evolution of Delayed Reproduction in Birds	14
A Genomic Perspective on the Evolutionary Diversification of Turtles	14
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	14
Reducing the Biases in False Correlations Between Discrete Characters	14
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	14
Mechanisms of Community Assembly through the Lens of Phylogenetic Diversity: A Critical Reappraisal	14
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	14
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	14
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	13
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss	13
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	13
Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids	13
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	13
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	13
The Phylogenetic Limits to Diversity-Dependent Diversification	13
Hybridization and Polyploidy shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes (Luzula sect. Luzula)	13
Speciation-by-Extinction	13
Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard (Varanus tristis)	12
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	12
New Perspectives in Phylogenetic Support Assessment: Using the Relative Contradiction Index to Investigate the Phylogenetic Controversies in Crocodylia	12
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	12
Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera	12
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	12
The Comparative Analysis of Lineage-Pair Traits	12
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	12
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	12
How Important Is Budding Speciation for Comparative Studies?	12
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	12
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	12
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and <	11
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	11
How to Render Species Comparable Taxonomic Units Through Deep Time: A Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards	11
Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial discordance in island systems	11
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC	11
The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade	11
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization	11
Dating the Bacterial Tree of Life Based on Ancient Symbiosis	11
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	11
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants	10
The Consequences of Budding Speciation on Trees	10
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila	10
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	10
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	10
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	10
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	10
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	9
Site-specific structure and stability constrained substitution models improve phylogenetic inference	9
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information	9
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	9
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
Announcements	9
Link between the Birth–Death Process and the Kingman Coalescent—Applications to Phylogenetic Epidemiology	9
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	9
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)	9
Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla)	8
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	8
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	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
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow	8
On the Mkv Model with Among-Character Rate Variation	8
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling	8
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	8
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	8
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	7
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	7

Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	7
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC	7
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	7
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	7
Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai–Tibet Plateau	7
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	7
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	7