OOIR: Observatory of International Research

Papers

(The TQCC of Systemic Biology is 16. 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 2021-04-01 to 2025-04-01.)

Article	Citations
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)	175
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	72
Announcements	70
Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity	63
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	58
UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina)	58
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	56
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	51
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics	51
Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification	49
New Phylogenetic Markov Models for Inapplicable Morphological Characters	49
PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models	49
Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis	48
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	48
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	44
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	43
Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression	42
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model	41
Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses	40
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	39
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	36
Correction to: Robust, Universal Tree Balance Indices	33
Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot	33
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	33
Miocene Climate and Habitat Change Drove Diversification inBicyclus, Africa’s Largest Radiation of Satyrine Butterflies	32

Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	32
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	31
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	31
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	30
Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?	29
The Frequency and Topology of Pseudoorthologs	29
Corrigendum to: Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	29
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity	29
Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation	28
Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference	28
Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites	28
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data	28
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	27
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	27
Speciation-by-Extinction	27
Estimation of species divergence times in presence of cross-species gene flow	26
Linking Ecological Specialization to Its Macroevolutionary Consequences: An Example with Passerine Nest Type	25
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	25
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	24
Announcements	24
Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation	24
Announcements	24
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support	24
Correction to: DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	24
Increasing Information Content and Diagnosability in Family-Level Classifications	23
How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).	23
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	23
Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution	23
How Important Is Budding Speciation for Comparative Studies?	22
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage	21
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria	20
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus	20
Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)	20
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees	20
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2	20
Lagrange-NG: The next generation of Lagrange	20
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards	19
Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges	19
Are Skyline Plot-Based Demographic Estimates Overly Dependent on Smoothing Prior Assumptions?	19
How to Validate a Bayesian Evolutionary Model	19
A Linear Time Solution to the Labeled Robinson–Foulds Distance Problem	18
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks	18
Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters	18
Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies	18
Is Over-parameterization a Problem for Profile Mixture Models?	17
Different Evolutionary Pathways Lead to Incomplete Convergence of Elongate Body Shapes in Carnivoran Mammals	17
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	17
Global Patterns of Taxonomic Uncertainty and its Impacts on Biodiversity Research	17
On Information Rank Deficiency in Phenotypic Covariance Matrices	17
Inference of multiple mergers while dating a pathogen phylogeny	17

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles	16
Bayesian Inference of Clonal Expansions in a Dated Phylogeny	16
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	16
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	16
Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations	16
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	16
Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC	16