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 2020-04-01 to 2024-04-01.)

Article	Citations
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life	123
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l	110
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life	103
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event	77
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)	70
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	62
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales	59
Ghost Lineages Highly Influence the Interpretation of Introgression Tests	48
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics	47
The Legacy of Recurrent Introgression during the Radiation of Hares	44
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets	43
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow	43
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes	41
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent	40
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation	40
Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems	39
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution	38
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos	36
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)	36
Repositories for Taxonomic Data: Where We Are and What is Missing	36
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies	35
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses	35
Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification ofViburnum	34
Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)	33
A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data	33

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective	33
Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity	31
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent	31
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)	31
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses	30
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?	30
Phylogeny Estimation Given Sequence Length Heterogeneity	30
Defining Species When There is Gene Flow	29
Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)	29
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit	29
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data	29
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling	28
A New Pipeline for Removing Paralogs in Target Enrichment Data	28
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies	28
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)	27
Modeling Phylogenetic Biome Shifts on a Planet with a Past	27
Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models	27
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data	27
Long Branch Attraction Biases in Phylogenetics	26
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene	26
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation	25
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs	25
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots	25
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees	24
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction	24
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals	24
Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line	24
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere	24
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity	23
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks	23
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences	23
Comparative Phylogenetics of Papilio Butterfly Wing Shape and Size Demonstrates Independent Hindwing and Forewing Evolution	22
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy	22
Bayesian Inference of Species Trees using Diffusion Models	21
Phylogenomic Insights into the Origin of Primary Plastids	21
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution	21
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation	20
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)	20
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)	20
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition	20
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)	20
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa	20
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets	20
Robust Analysis of Phylogenetic Tree Space	20
The Dynamics of Bird Diversity in the New World	20
An Evolving View of Phylogenetic Support	19
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards	19
Estimating Global Biodiversity: The Role of Cryptic Insect Species	19
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation	19
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot	18

Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils	18
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach	18
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)	18
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance	18
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards	18
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough	18
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data	18
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)	17
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa	17
Genomics Reveals Widespread Ecological Speciation in Flightless Insects	17
Relaxed Random Walks at Scale	17
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins	17
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past	17
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders	17
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi	17