Systemic Biology

Article	Citations
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	125
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	109
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	71
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	61
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	48
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	47
Comparing Partition and Mixture Models with Akaike Information Criteria	47
How to Validate a Bayesian Evolutionary Model	45
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	41
Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study	39
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	39
A Covarion Model for Phylogenetic Estimation Using Discrete Morphological Data Sets	39
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	38
Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes)	37
Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	36
Phylogenomic Insights into the Evolution and Origin of Nematoda	36
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	36
Stochastic Character Mapping of Continuous Traits on Phylogenies	35
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	35
The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data	35
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes	34
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	31
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	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)	31

Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	30
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	30
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	30
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	29
Evolutionary Tempo, Supertaxa, and Living Fossils	29
Estimating Global Biodiversity: The Role of Cryptic Insect Species	29
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	28
Integrating Fossils Samples with Heterogeneous Diversification Rates: A Combined Multi-Type Fossilized Birth-Death model	28
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	28
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	28
Announcements	28
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	26
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum	26
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	26
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	26
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	26
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	25
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	25
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	25
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	25
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	25
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	25
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	25
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	24
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	24
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	23
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	23
Estimation of species divergence times in presence of cross-species gene flow	23
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	23
On the Utility of Deep Learning for Model Classification and Parameter Estimation on Complex Diversification Scenarios	23
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	23
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
Waves of Colonization and Gene Flow in a Great Speciator	22
Too Many Numbers?	22
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	22
Global climate cooling spurred skipper butterfly diversification	21
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	21
The Effect of Copy Number Hemiplasy on Gene Family Evolution	21
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	21
Is Over-parameterization a Problem for Profile Mixture Models?	21
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	20
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	19
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	19
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	19
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	19
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	18
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	18
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	18

Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death 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
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	17
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	17
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	17
Correction to: Modeling phylogenetic biome shifts on a planet with a past	17
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	17
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	16
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	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
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	16
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	16
Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids	15
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	15
Systematic Biology ’s Seventy-Five Years	15
The Phylogenetic Limits to Diversity-Dependent Diversification	15
Mechanisms of Community Assembly through the Lens of Phylogenetic Diversity: A Critical Reappraisal	15
Reducing the Biases in False Correlations Between Discrete Characters	15
Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera	15
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	15
Social Environment and the Evolution of Delayed Reproduction in Birds	15
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss	15
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	14
Hybridization and Polyploidy Shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes ( Luzula sect.	14
Automatic Discovery of Optimal Discrete Character Models	14
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	14
New Perspectives in Phylogenetic Support Assessment: Using the Relative Contradiction Index to Investigate the Phylogenetic Controversies in Crocodylia	13
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	13
Speciation-by-Extinction	13
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	13
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	13
Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard ( Varanus tristis )	13
An Evolving View of Species Tree Inference	13
How Important Is Budding Speciation for Comparative Studies?	13
GroupStruct2: A User-Friendly Graphical User Interface for Statistical and Visual Support in Species Diagnosis	13
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	12
Using Gene Trees with Lineage-Specific Duplicates for Phylogenetic Inference Mitigates the Effects of Long-Branch Attraction	12
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC	12
The Comparative Analysis of Lineage-Pair Traits	12
Population Genomics of Endangered Lenoks ( Brachymystax spp.) in China Reveals the Presence of Cryptic Species	12
Soaring Systematics: An Evaluation of Biogeography and Flight Behavior in Dragonflies and Damselflies (Insecta: Odonata) Using Phylogenomics	12
Correction to: Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation	11
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	11
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits	11
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization	11
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: <	11
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	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
Improving the Robustness of Phylogenetic Independent Contrasts: Addressing Abrupt Evolutionary Shifts with Outlier- and Distribution-Guided Correlation	10
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	10
Phylogenomics of a Genus of “Great Speciators” Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems	10
Protracted Speciation under the State-Dependent Speciation and Extinction Approach	9
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	9
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	9
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation	9
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila	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
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information	9
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	9
Genomic and Phenotypic Delimitation of Species in a Temperate Aquatic Biodiversity Hotspot	9
Dating the Bacterial Tree of Life Based on Ancient Symbiosis	9
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	9
The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics	9
Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference	9
An Evolving View of Character Macroevolution	9
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling	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
Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)	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
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	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
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	7
On the Mkv Model with Among-Character Rate Variation	7
Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja	7
Incorporating Continuous Characters in Joint Estimation of Dicynodont Phylogeny	7

Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	7
Phylogenomic discordances reveal conflicting hybridization episodes and widespread lineage-sorting events in temperate Loliinae grasses	7
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	7
Phylogenetic Inference from Atomized 3D Morphometric Data: A Case Study using Kangaroos	7
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	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
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	6
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC	6
Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera	6
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	6
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	6