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 2020-07-01 to 2024-07-01.)

Article	Citations
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	115
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event	83
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)	77
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales	67
Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant GenusPolemonium(Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nucl	66
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	52
Ghost Lineages Highly Influence the Interpretation of Introgression Tests	51
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets	49
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	48
The Legacy of Recurrent Introgression during the Radiation of Hares	47
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	46
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow	44
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	40
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies	40
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent	40
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos	39
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	38
A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data	37
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses	36
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	36
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	35
Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective	34
Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)	33
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?	33
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	32

Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene	32
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	32
Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)	31
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses	31
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data	31
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	31
Phylogeny Estimation Given Sequence Length Heterogeneity	30
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit	30
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	30
Long Branch Attraction Biases in Phylogenetics	30
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data	30
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	29
Defining Species When There is Gene Flow	29
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks	29
A New Pipeline for Removing Paralogs in Target Enrichment Data	29
Modeling Phylogenetic Biome Shifts on a Planet with a Past	28
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	28
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction	28
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere	26
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	26
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences	26
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	25
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance	25
Robust Analysis of Phylogenetic Tree Space	25
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees	25
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy	25
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data	25
Bayesian Inference of Species Trees using Diffusion Models	24
Estimating Global Biodiversity: The Role of Cryptic Insect Species	24
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	24
Phylogenomic Insights into the Origin of Primary Plastids	24
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	22
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough	22
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins	22
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	21
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support	21
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)	21
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	21
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	21
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution	21
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach	21
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	21
An Evolving View of Phylogenetic Support	21
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)	21
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils	20
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	20
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)	20
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	19
Stabilized Morphological Evolution of Spiders Despite Mosaic Changes in Foraging Ecology	19
Estimation of species divergence times in presence of cross-species gene flow	19

Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	19
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)	18
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies	18
Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine Radiation Corvides	18
Solving the Coral Species Delimitation Conundrum	18
A Multifunction Trade-Off has Contrasting Effects on the Evolution of Form and Function	18
Relaxed Random Walks at Scale	18
Genomics Reveals Widespread Ecological Speciation in Flightless Insects	18
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution	17
A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions	17
Incorporating Hierarchical Characters into Phylogenetic Analysis	17
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders	17
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades	17