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 2022-01-01 to 2026-01-01.)

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	102
Announcements	99
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	97
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	83
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	67
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	48
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	46
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	42
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	42
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	39
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	39
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	39
How to Validate a Bayesian Evolutionary Model	38
Phylogenomic Insights into the Evolution and Origin of Nematoda	37
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	37
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	35
Evolutionary Tempo, Supertaxa, and Living Fossils	35
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	34
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	33
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	32
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	32
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	32
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	32
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	32
Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	31

Estimating Global Biodiversity: The Role of Cryptic Insect Species	31
Announcements	30
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	27
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	27
Robust, Universal Tree Balance Indices	27
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	26
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	26
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	26
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	26
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	25
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	25
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of	25
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	25
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	25
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	24
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	24
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	23
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	23
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	23
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	23
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	23
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	23
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	23
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	23
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	22
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	22
New Phylogenetic Markov Models for Inapplicable Morphological Characters	22
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
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	21
Is Over-parameterization a Problem for Profile Mixture Models?	21
Waves of Colonization and Gene Flow in a Great Speciator	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	21
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	21
Too Many Numbers?	21
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	20
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	20
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	20
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	20
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	20
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	20
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	20
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	19
The Effect of Copy Number Hemiplasy on Gene Family Evolution	19
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	19
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	19
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	19
Global climate cooling spurred skipper butterfly diversification	19
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	19

The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	18
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	17
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel 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
Correction to: Modeling phylogenetic biome shifts on a planet with a past	17
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	16
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees	16
Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates	16
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	16
Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses	16
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	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