OOIR: Observatory of International Research

Papers

(The TQCC of Systemic Biology is 14. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-02-01 to 2025-02-01.)

Article	Citations
Correction to: Robust, Universal Tree Balance Indices	148
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	62
Incorporating Hierarchical Characters into Phylogenetic Analysis	60
Speciation-by-Extinction	55
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	54
Corrigendum to: Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	51
Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation	47
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)	46
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	45
Announcements	42
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	41
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	40
Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)	39
Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?	37
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	36
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model	36
Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	36
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	36
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	35
Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites	34
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	34
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data	32
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	32
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	31
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	30

Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	30
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	30
New Phylogenetic Markov Models for Inapplicable Morphological Characters	28
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	28
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	28
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	27
Segmental Series and Size: Clade-Wide Investigation of Molar Proportions Reveals a Major Evolutionary Allometry in the Dentition of Placental Mammals	27
The Frequency and Topology of Pseudoorthologs	26
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	25
Linking Ecological Specialization to Its Macroevolutionary Consequences: An Example with Passerine Nest Type	25
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	25
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	25
Estimation of species divergence times in presence of cross-species gene flow	24
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	24
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	23
Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot	23
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics	23
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	22
PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models	22
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	22
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	22
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	22
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	22
Is Over-parameterization a Problem for Profile Mixture Models?	21
Announcements	21
Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses	21
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	21
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	21
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	21
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	21
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	20
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	20
Phylogenomic Insights into the Evolution and Origin of Nematoda	20
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	19
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification	19
Announcements	18
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	18
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	17
On Information Rank Deficiency in Phenotypic Covariance Matrices	17
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	17
How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).	17
Both Diet and Sociality Affect Primate Brain-Size Evolution	16
Species Tree Estimation from Gene Trees by Minimizing Deep Coalescence and Maximizing Quartet Consistency: A Comparative Study and the Presence of Pseudo Species Tree Terraces	16
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards	16
How Important Is Budding Speciation for Comparative Studies?	16
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees	16
Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution	16
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	16
A Linear Time Solution to the Labeled Robinson–Foulds Distance Problem	15
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	15

Lagrange-NG: The next generation of Lagrange	15
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	15
Inference of multiple mergers while dating a pathogen phylogeny	15
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	15
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	15
Different Evolutionary Pathways Lead to Incomplete Convergence of Elongate Body Shapes in Carnivoran Mammals	14
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	14
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	14
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation	14
On Defining and Finding Islands of Trees and Mitigating Large Island Bias	14
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	14
Increasing Information Content and Diagnosability in Family-Level Classifications	14
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	14
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	14
Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates	14
How to Validate a Bayesian Evolutionary Model	14