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	180
Announcements	73
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	73
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	64
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	64
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	59
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	58
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	52
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	52
Phylogenomic Insights into the Evolution and Origin of Nematoda	51
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	51
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	49
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	49
How to Validate a Bayesian Evolutionary Model	49
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	47
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	46
Estimating Global Biodiversity: The Role of Cryptic Insect Species	44
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	43
Announcements	42
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	39
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	36
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	35
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	35
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	34
Accuracy in Near-Perfect Virus Phylogenies	33

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	33
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	32
Announcements	32
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	31
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	31
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	30
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	30
Robust, Universal Tree Balance Indices	29
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	29
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	29
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	29
Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?	28
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	28
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	28
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	28
Aquatic biotas of Sundaland are fragmented but not refugial	27
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	26
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	26
A New Pipeline for Removing Paralogs in Target Enrichment Data	26
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	26
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	25
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	24
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	24
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	24
Relative Time Constraints Improve Molecular Dating	23
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	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
Estimation of species divergence times in presence of cross-species gene flow	21
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	21
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	21
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	20
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	20
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	20
On Information Rank Deficiency in Phenotypic Covariance Matrices	20
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	20
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	19
Announcements	19
Is Over-parameterization a Problem for Profile Mixture Models?	19
Waves of Colonization and Gene Flow in a Great Speciator	19
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	18
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	18
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	18
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	18
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	18
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	18
The Effect of Copy Number Hemiplasy on Gene Family Evolution	18
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	17
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	17

Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	17
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	17
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	17
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	17
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	17
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	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
Robust Analysis of Phylogenetic Tree Space	16
Correction to: Modeling phylogenetic biome shifts on a planet with a past	16
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	16
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	16
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails	16
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	15
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	15
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	15
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	15
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	15
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	15
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	15
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	15
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	14
A Genomic Perspective on the Evolutionary Diversification of Turtles	14
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	13
The Phylogenetic Limits to Diversity-Dependent Diversification	13
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	13
Reducing the Biases in False Correlations Between Discrete Characters	13
Speciation-by-Extinction	13
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	13
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	13
Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	12
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	12
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	12
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	12
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	12
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	12
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	11
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	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
The Consequences of Budding Speciation on Trees	11
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	11
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	11
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	11
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and <	11
How Important Is Budding Speciation for Comparative Studies?	11
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	11
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	11
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	11
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	10
Announcements	10
Dating the bacterial tree of life based on ancient symbiosis	10
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	10
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	10
Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time	10
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	10
How to Render Species Comparable Taxonomic Units Through Deep Time: A Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards	10
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants	10
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	10
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone	10
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	9
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model	9
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation	9
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	9
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	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
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	9
Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data	8
Species as a Heuristic: Reconciling Theory and Practice	8
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	8
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	8
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	8
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	8
Announcements	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
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow	8
Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC	8
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation	8
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	8
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies	8

Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	8
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	8
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	8
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	8
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	8
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)	8
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	7
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria	7
The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands	7
On the Need for New Measures of Phylogenomic Support	7
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	7
Measuring Phylogenetic Information of Incomplete Sequence Data	7
Divergent Processes Drive Parallel Evolution in Marine and Freshwater Fishes	7
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies	7
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	7
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	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
Phylogenomics resolve the systematics and biogeography of the ant tribe Myrmicini and tribal relationships within the hyperdiverse ant subfamily Myrmicinae	7
Functional Trade-Offs Asymmetrically Promote Phenotypic Evolution	7