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 2021-09-01 to 2025-09-01.)

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	87
Announcements	82
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	76
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	71
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	55
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs	55
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	51
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	41
Phylogenomic Insights into the Evolution and Origin of Nematoda	40
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization	39
How to Validate a Bayesian Evolutionary Model	37
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination	36
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	34
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	33
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	32
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	32
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	31
Announcements	31
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	31
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	31
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	30
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	29
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	29
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	29

Evolutionary Tempo, Supertaxa, and Living Fossils	28
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	27
Announcements	26
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index	26
Estimating Global Biodiversity: The Role of Cryptic Insect Species	26
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial	25
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	25
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	25
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	24
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	24
Robust, Universal Tree Balance Indices	23
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	23
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	22
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	22
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions	22
DEPP: Deep Learning Enables Extending Species Trees using Single Genes	22
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	22
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	22
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	22
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	21
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	21
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	21
PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks	21
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	21
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	20
Relative Time Constraints Improve Molecular Dating	20
New Phylogenetic Markov Models for Inapplicable Morphological Characters	19
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	19
ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing	19
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	19
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	19
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	19
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?	18
Is Over-parameterization a Problem for Profile Mixture Models?	18
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	18
On Information Rank Deficiency in Phenotypic Covariance Matrices	18
Estimation of species divergence times in presence of cross-species gene flow	18
Waves of Colonization and Gene Flow in a Great Speciator	18
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	17
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution	17
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	17
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	17
Announcements	17
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	17
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	16
The Effect of Copy Number Hemiplasy on Gene Family Evolution	16
PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	16
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	16
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	16
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	16

Global climate cooling spurred skipper butterfly diversification	16
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	15
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages	15
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	15
Robust Analysis of Phylogenetic Tree Space	14
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	14
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	14
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	14