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 2022-08-01 to 2026-08-01.)

Article	Citations
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)	146
Comparing Partition and Mixture Models with Akaike Information Criteria	75
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations	67
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards	56
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models	52
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales	49
Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study	48
A Covarion Model for Phylogenetic Estimation Using Discrete Morphological Data Sets	46
Biased Estimates of Phylogenetic Branch Lengths Resulting from the Discretised Gamma Model of Site Rate Heterogeneity	45
An Empirical Bayes approach for the study of phenotypic evolution from high-dimensional data	44
The Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompan	42
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method	42
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages	41
Phylogenomic Insights into the Evolution and Origin of Nematoda	41
Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination	41
Dietary specialization drives adaptation, convergence, and integration across the cranial and appendicular skeleton in Waterfowl (Anseriformes)	41
How to Validate a Bayesian Evolutionary Model	40
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory	39
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards	37
Stochastic Character Mapping of Continuous Traits on Phylogenies	36
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia	36
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies	35
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of `BEAGLE` in `RevBayes` With `MPI`	35
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex	34
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes	34

Seventy-Five Years of Systematic Biology: Looking Back, Moving Forward	33
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)	33
The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data	31
Common Ancestry, Contemporary Phylogenetics, and Process Ontology	31
A Novel Phylogenomics Pipeline Reveals Extensive Topological Conflict in the Evolution of the Angiosperm Order Cucurbitales	31
Estimating Global Biodiversity: The Role of Cryptic Insect Species	30
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data	30
Evolutionary Tempo, Supertaxa, and Living Fossils	30
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush	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
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way	29
Scalable Bayesian Divergence Time Estimation With Ratio Transformations	29
Integrating Fossils Samples with Heterogeneous Diversification Rates: A Combined Multi-Type Fossilized Birth-Death model	28
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal	28
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum	27
Evolving View on Phylogenetic Networks	27
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)	27
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial	27
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees	27
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life	27
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors	26
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama	26
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating	26
PhyloFusion—Fast and Easy Fusion of Rooted Phylogenetic Trees into Rooted Phylogenetic Networks	26
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood	25
Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models	25
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield	25
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools	25
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora	25
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing	24
New Phylogenetic Markov Models for Inapplicable Morphological Characters	23
An Evolving View of Phylogenetic Biogeography	23
Estimation of species divergence times in presence of cross-species gene flow	23
On the Utility of Deep Learning for Model Classification and Parameter Estimation on Complex Diversification Scenarios	23
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?	23
Too Many Numbers?	23
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions	22
The Effects of Hemiplasy and Maintained Polymorphisms in Fossil Clades	22
But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating	21
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses	21
The Effect of Copy Number Hemiplasy on Gene Family Evolution	20
Waves of Colonization and Gene Flow in a Great Speciator	20
Chromosome Evolution Model Reveals Hidden Variation in Fern Diversification Rates	20
Is Over-parameterization a Problem for Profile Mixture Models?	20
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong	19
Global Climate Cooling Spurred Skipper Butterfly Diversification	19
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets	19
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
Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection	18

Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance	18
Coalescent-Based Branch Length Estimation Improves Dating of Species Trees	18
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline	17
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process	17
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains	17
Gene Flow Complicates Phylogenetic Inference in an Archipelago Radiation	17
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)	16
Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice	16
Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)	16
Correction to: Modeling phylogenetic biome shifts on a planet with a past	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
Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)	16
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics	16