OOIR: Observatory of International Research

Papers

(The TQCC of Systemic Biology is 15. 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 2020-11-01 to 2024-11-01.)

Article	Citations
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	133
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)	85
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales	77
Ghost Lineages Highly Influence the Interpretation of Introgression Tests	57
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	56
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	52
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow	52
The Legacy of Recurrent Introgression during the Radiation of Hares	51
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	48
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	44
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	42
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	42
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies	41
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	37
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	37
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	36
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	36
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data	36
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses	36
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene	35
Estimating Global Biodiversity: The Role of Cryptic Insect Species	35
Long Branch Attraction Biases in Phylogenetics	34
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses	34
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere	33
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks	32

Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	32
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data	31
Robust Analysis of Phylogenetic Tree Space	31
A New Pipeline for Removing Paralogs in Target Enrichment Data	30
Phylogenomic Insights into the Origin of Primary Plastids	30
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences	30
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	30
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data	28
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	28
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	27
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	27
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance	27
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees	27
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support	25
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	25
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough	24
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution	24
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils	23
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	23
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	23
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	23
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	23
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)	23
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins	22
Estimation of species divergence times in presence of cross-species gene flow	22
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	22
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	22
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)	22
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)	21
Solving the Coral Species Delimitation Conundrum	21
Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology	21
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference	21
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	21
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	21
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	20
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	20
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	20
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes	20
A Multifunction Trade-Off has Contrasting Effects on the Evolution of Form and Function	19
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	19
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies	19
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)	19
Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)	19
A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions	18
Genomics Reveals Widespread Ecological Speciation in Flightless Insects	18
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process	18
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent	17
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders	17
Incorporating Hierarchical Characters into Phylogenetic Analysis	17
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models	17

Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete	16
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays	16
Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae	16
Increasing Information Content and Diagnosability in Family-Level Classifications	16
Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks	16
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulumComplex)	16
Reunion of Australasian Possums by Shared SINE Insertions	15
Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations	15
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?	15
Morphology-Based Identification of Bemisia tabaci Cryptic Species Puparia via Embedded Group-Contrast Convolution Neural Network Analysis	15
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds	15
A Cautionary Note on “A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies”	15
Mosaic Evolution of the Skull in Labrid Fishes Involves Differences in Both Tempo and Mode of Morphological Change	15
Both Diet and Sociality Affect Primate Brain-Size Evolution	15