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	87
Announcements	82
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	76
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	71
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	55
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	55
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	51
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	41
Phylogenomic Insights into the Evolution and Origin of Nematoda	40
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization	39
How to Validate a Bayesian Evolutionary Model	37
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination	36
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	34
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	33
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	32
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	32
Announcements	31
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	31
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	31
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	31
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	30
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	29
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	29
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	29

Evolutionary Tempo, Supertaxa, and Living Fossils	28
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	27
Estimating Global Biodiversity: The Role of Cryptic Insect Species	26
Announcements	26
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	26
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	25
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	25
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	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	24
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	24
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	23
Robust, Universal Tree Balance Indices	23
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	22
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	22
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	22
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	22
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	22
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	22
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	22
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	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
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	21
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	21
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	20
Relative Time Constraints Improve Molecular Dating	20
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	19
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	19
New Phylogenetic Markov Models for Inapplicable Morphological Characters	19
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	19
ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing	19
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	19
Estimation of species divergence times in presence of cross-species gene flow	18
Waves of Colonization and Gene Flow in a Great Speciator	18
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	18
Is Over-parameterization a Problem for Profile Mixture Models?	18
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	18
On Information Rank Deficiency in Phenotypic Covariance Matrices	18
Announcements	17
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	17
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	17
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	17
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	17
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	17
PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	16
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	16
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	16
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	16
Global climate cooling spurred skipper butterfly diversification	16
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	16

The Effect of Copy Number Hemiplasy on Gene Family Evolution	16
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	15
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	15
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	15
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	14
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	14
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	14
Robust Analysis of Phylogenetic Tree Space	14
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	13
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	13
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	13
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	13
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	13
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails	13
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	13
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	13
A Genomic Perspective on the Evolutionary Diversification of Turtles	13
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	13
Correction to: Modeling phylogenetic biome shifts on a planet with a past	13
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	13
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	13
Reducing the Biases in False Correlations Between Discrete Characters	13
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	12
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	12
The Phylogenetic Limits to Diversity-Dependent Diversification	12
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	12
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	12
Social environment and the evolution of delayed reproduction in birds	12
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	12
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	11
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	11
Speciation-by-Extinction	11
Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera	11
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	11
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	11
New perspectives in phylogenetic support assessment: using the new Relative Contradiction Index to investigate the phylogenetic controversies in Crocodylia	11
How Important Is Budding Speciation for Comparative Studies?	11
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	11
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	10
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization	10
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	10
The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade	10
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments using AIC	10
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	10
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	10
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	10
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and <	10
How to Render Species Comparable Taxonomic Units Through Deep Time: A Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards	9
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	9
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	9
Link between the Birth–Death Process and the Kingman Coalescent—Applications to Phylogenetic Epidemiology	9
The Consequences of Budding Speciation on Trees	9
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants	9
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	9
Site-specific structure and stability constrained substitution models improve phylogenetic inference	9
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	9
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	9
Dating the Bacterial Tree of Life Based on Ancient Symbiosis	9
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone	9
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila	9
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	9
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	8
Species as a Heuristic: Reconciling Theory and Practice	8
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow	8
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)	8
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation	8
Announcements	8
Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla)	8
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling	8
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information	8
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	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
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	8
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	7
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	7
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	7
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	7
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	7
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	7
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	7

On the Mkv Model with Among-Character Rate Variation	7
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC	6
Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai–Tibet Plateau	6
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies	6
Functional Trade-Offs Asymmetrically Promote Phenotypic Evolution	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
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
Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic	6
The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands	6
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	6
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	6
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation	6
Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods	6
Measuring Phylogenetic Information of Incomplete Sequence Data	6