Systemic Biology

Article	Citations
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	146
Comparing Partition and Mixture Models with Akaike Information Criteria	75
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	67
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	56
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	52
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	49
Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study	48
A Covarion Model for Phylogenetic Estimation Using Discrete Morphological Data Sets	46
Biased Estimates of Phylogenetic Branch Lengths Resulting from the Discretised Gamma Model of Site Rate Heterogeneity	45
An Empirical Bayes approach for the study of phenotypic evolution from high-dimensional data	44
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	42
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	42
Phylogenomic Insights into the Evolution and Origin of Nematoda	41
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	41
Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes)	41
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	41
How to Validate a Bayesian Evolutionary Model	40
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	39
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	37
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	36
Stochastic Character Mapping of Continuous Traits on Phylogenies	36
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI	35
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	35
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	34
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes	34

Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	33
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	33
The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data	31
Common Ancestry, Contemporary Phylogenetics, and Process Ontology	31
A Novel Phylogenomics Pipeline Reveals Extensive Topological Conflict in the Evolution of the Angiosperm Order Cucurbitales	31
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	30
Evolutionary Tempo, Supertaxa, and Living Fossils	30
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	30
Estimating Global Biodiversity: The Role of Cryptic Insect Species	30
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	29
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	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	29
Integrating Fossils Samples with Heterogeneous Diversification Rates: A Combined Multi-Type Fossilized Birth-Death model	28
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	28
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	27
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	27
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	27
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	27
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum	27
Evolving View on Phylogenetic Networks	27
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	26
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	26
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	26
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	26
Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models	25
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	25
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	25
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	25
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	25
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	24
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
An Evolving View of Phylogenetic Biogeography	23
Estimation of species divergence times in presence of cross-species gene flow	23
On the Utility of Deep Learning for Model Classification and Parameter Estimation on Complex Diversification Scenarios	23
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	23
Too Many Numbers?	23
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	22
The Effects of Hemiplasy and Maintained Polymorphisms in Fossil Clades	22
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
Chromosome Evolution Model Reveals Hidden Variation in Fern Diversification Rates	20
Is Over-parameterization a Problem for Profile Mixture Models?	20
The Effect of Copy Number Hemiplasy on Gene Family Evolution	20
Waves of Colonization and Gene Flow in a Great Speciator	20
Global Climate Cooling Spurred Skipper Butterfly Diversification	19
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	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	18
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	18
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	18

Coalescent-Based Branch Length Estimation Improves Dating of Species Trees	18
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	18
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	17
Gene Flow Complicates Phylogenetic Inference in an Archipelago Radiation	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
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	17
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	16
Correction to: Modeling phylogenetic biome shifts on a planet with a past	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
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	16
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	16
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	16
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	16
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	15
Nuclear Phylogenomic Insights into Relationships, Support, and Conflict Among the Early Diverging Lineages of the Megadiverse Epidendroid Orchids	15
Systematic Biology ’s Seventy-Five Years	15
The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution	15
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	15
Social Environment and the Evolution of Delayed Reproduction in Birds	15
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	15
Phylogenomic Challenges in Polyploid-Rich Lineages: Insights from Paralog Processing and Reticulation Methods Using the Complex Genus Packera (Asteraceae	15
Mechanisms of Community Assembly through the Lens of Phylogenetic Diversity: A Critical Reappraisal	15
Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives	14
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss	14
The Phylogenetic Limits to Diversity-Dependent Diversification	14
Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments	14
Reducing the Biases in False Correlations Between Discrete Characters	14
Evaluating the Robustness of Process-Pattern Links Using Phylogenies—Insights from a Comparison of Eight Simulation Models	14
Speciation-by-Extinction	13
Automatic Discovery of Optimal Discrete Character Models	13
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	13
Hybridization and Polyploidy Shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes ( Luzula sect.	12
New Perspectives in Phylogenetic Support Assessment: Using the Relative Contradiction Index to Investigate the Phylogenetic Controversies in Crocodylia	12
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	12
Diversification Dynamics in the Global Radiation of Gobies	12
An Evolving View of Species Tree Inference	12
Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera	12
How Important Is Budding Speciation for Comparative Studies?	11
The Comparative Analysis of Lineage-Pair Traits	11
Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard ( Varanus tristis )	11
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	11
GroupStruct2: A User-Friendly Graphical User Interface for Statistical and Visual Support in Species Diagnosis	11
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	11
Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)	11
Soaring Systematics: An Evaluation of Biogeography and Flight Behavior in Dragonflies and Damselflies (Insecta: Odonata) Using Phylogenomics	10
Population Genomics of Endangered Lenoks ( Brachymystax spp.) in China Reveals the Presence of Cryptic Species	10
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution	10
Using Gene Trees with Lineage-Specific Duplicates for Phylogenetic Inference Mitigates the Effects of Long-Branch Attraction	10
Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC	10
Improving the Robustness of Phylogenetic Independent Contrasts: Addressing Abrupt Evolutionary Shifts with Outlier- and Distribution-Guided Correlation	9
Phylogenomics of a Genus of “Great Speciators” Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems	9
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood	9
Dating the Bacterial Tree of Life Based on Ancient Symbiosis	9
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)	9
Correction to: Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation	9
Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)	9
The Consequences of Budding Speciation on Trees	9
Correction to: Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: <	9
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization	9
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia	9
Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation	9
The Sequential Direct and Indirect Effects of Mountain Uplift, Climatic Niche, and Floral Trait Evolution on Diversification Dynamics in an Andean Plant Clade	9
Saltwater tolerance and the Holarctic distribution of freshwater percid fishes	8
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information	8
Link between the Birth–Death Process and the Kingman Coalescent—Applications to Phylogenetic Epidemiology	8
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration	8
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila	8
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants	8
Genomic and Phenotypic Delimitation of Species in a Temperate Aquatic Biodiversity Hotspot	8
Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference	7
Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution	7
Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data	7
The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics	7
An Evolving View of Character Macroevolution	7
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow	7
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation	7
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)	7
Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling	7
Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)	6
Phylogenomic Discordances Reveal Conflicting Hybridization Episodes and Widespread Lineage-Sorting Events in Temperate Loliinae Grasses	6

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	6
Phylogenetic Inference from Atomized 3D Morphometric Data: A Case Study using Kangaroos	6
Modeling Site-and-Branch-Heterogeneity with GFmix	6
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	6
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	6
On the Mkv Model with Among-Character Rate Variation	6
Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja	6
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	6
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set	6
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	6