OOIR: Observatory of International Research

Papers

(The TQCC of Systemic Biology is 17. 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 2022-05-01 to 2026-05-01.)

Article	Citations
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	125
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles	109
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	71
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	61
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	48
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	47
Comparing Partition and Mixture Models with Akaike Information Criteria	47
How to Validate a Bayesian Evolutionary Model	45
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	41
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	39
A Covarion Model for Phylogenetic Estimation Using Discrete Morphological Data Sets	39
Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study	39
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	38
Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes)	37
Phylogenomic Insights into the Evolution and Origin of Nematoda	36
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	36
Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	36
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	35
The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data	35
Stochastic Character Mapping of Continuous Traits on Phylogenies	35
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes	34
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	31
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	31
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	31
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	31

Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	30
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	30
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	30
Evolutionary Tempo, Supertaxa, and Living Fossils	29
Estimating Global Biodiversity: The Role of Cryptic Insect Species	29
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	29
Integrating Fossils Samples with Heterogeneous Diversification Rates: A Combined Multi-Type Fossilized Birth-Death model	28
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	28
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	28
Announcements	28
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	28
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	26
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	26
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	26
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	26
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum	26
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	25
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	25
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	25
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	25
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	25
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	25
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	25
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
On the Utility of Deep Learning for Model Classification and Parameter Estimation on Complex Diversification Scenarios	23
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	23
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	23
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	23
Estimation of species divergence times in presence of cross-species gene flow	23
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	23
Too Many Numbers?	22
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	22
Waves of Colonization and Gene Flow in a Great Speciator	22
The Effect of Copy Number Hemiplasy on Gene Family Evolution	21
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	21
Is Over-parameterization a Problem for Profile Mixture Models?	21
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
Global climate cooling spurred skipper butterfly diversification	21
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	21
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests	20
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels	19
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	19
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	19
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	19
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process	18
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	18
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	18

Gene Flow Complicates Phylogenetic Inference in an Archipelago Radiation	17
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes	17
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	17
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	17
Correction to: Modeling phylogenetic biome shifts on a planet with a past	17
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	17
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	17
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	17