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 2021-06-01 to 2025-06-01.)

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	76
Announcements	75
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	67
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	67
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	64
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	60
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	55
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	55
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	53
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	51
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	50
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination	47
How to Validate a Bayesian Evolutionary Model	47
Phylogenomic Insights into the Evolution and Origin of Nematoda	45
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	44
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	40
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	39
Accuracy in Near-Perfect Virus Phylogenies	37
Announcements	36
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	36
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	35
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	34
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	32
Evolutionary Tempo, Supertaxa and Living Fossils	31
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	31

Estimating Global Biodiversity: The Role of Cryptic Insect Species	31
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	31
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	31
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	30
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	30
Announcements	30
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
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	29
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	29
Robust, Universal Tree Balance Indices	28
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	28
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	28
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	28
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	27
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	27
Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?	26
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	25
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	25
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	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
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	24
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	24
A New Pipeline for Removing Paralogs in Target Enrichment Data	24
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	23
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	22
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	22
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	21
Relative Time Constraints Improve Molecular Dating	21
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	21
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	20
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	20
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	20
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	20
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	20
Estimation of species divergence times in presence of cross-species gene flow	20
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	20
New Phylogenetic Markov Models for Inapplicable Morphological Characters	20
On Information Rank Deficiency in Phenotypic Covariance Matrices	20
Is Over-parameterization a Problem for Profile Mixture Models?	19
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	19
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	19
Waves of Colonization and Gene Flow in a Great Speciator	18
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	18
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	18
Announcements	18
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	18
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	18
The Effect of Copy Number Hemiplasy on Gene Family Evolution	18
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	18
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	18

ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	17
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	17
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	17
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	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
PickMe: Sample selection for species tree reconstruction using coalescent weighted quartets	17
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	16
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	16
Robust Analysis of Phylogenetic Tree Space	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