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 2021-05-01 to 2025-05-01.)

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	180
Announcements	73
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	73
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	64
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	59
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	58
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	52
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	52
Phylogenomic Insights into the Evolution and Origin of Nematoda	51
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	51
How to Validate a Bayesian Evolutionary Model	49
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	49
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	49
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	47
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	46
Estimating Global Biodiversity: The Role of Cryptic Insect Species	44
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	43
Announcements	42
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	39
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	36
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	35
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	35
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	34
Accuracy in Near-Perfect Virus Phylogenies	33

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	33
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	32
Announcements	32
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	31
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	31
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	30
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	30
Robust, Universal Tree Balance Indices	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
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	29
Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?	28
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	28
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	28
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	28
Aquatic biotas of Sundaland are fragmented but not refugial	27
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	26
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	26
A New Pipeline for Removing Paralogs in Target Enrichment Data	26
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	26
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	25
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	24
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	24
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	24
Relative Time Constraints Improve Molecular Dating	23
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	23
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	23
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
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	21
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	21
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	20
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	20
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	20
On Information Rank Deficiency in Phenotypic Covariance Matrices	20
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	20
Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	19
Announcements	19
Is Over-parameterization a Problem for Profile Mixture Models?	19
Waves of Colonization and Gene Flow in a Great Speciator	19
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
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	18
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	18
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	18
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	18
The Effect of Copy Number Hemiplasy on Gene Family Evolution	18
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets	17
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
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	17
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	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
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	17
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails	16
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	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
Robust Analysis of Phylogenetic Tree Space	16
Correction to: Modeling phylogenetic biome shifts on a planet with a past	16
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	16
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	16