Systemic Biology

(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 2020-05-01 to 2024-05-01.)
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life126
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l113
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life107
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event82
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)73
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales63
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 Nucl62
Ghost Lineages Highly Influence the Interpretation of Introgression Tests49
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics48
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets47
The Legacy of Recurrent Introgression during the Radiation of Hares45
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution43
Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes43
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow43
Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation40
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent40
Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems39
Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)38
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies37
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos37
A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data35
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses35
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)34
Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective33
Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)33
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent32
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses31
Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)31
Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity31
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data31
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?31
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit30
Phylogeny Estimation Given Sequence Length Heterogeneity30
Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene29
A New Pipeline for Removing Paralogs in Target Enrichment Data29
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data29
Defining Species When There is Gene Flow29
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling28
Long Branch Attraction Biases in Phylogenetics28
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies28
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation27
Modeling Phylogenetic Biome Shifts on a Planet with a Past27
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)27
Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs27
Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line26
Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots26
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals26
Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa25
Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks24
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere24
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction24
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study onPseudapisBees24
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences24
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity24
Bayesian Inference of Species Trees using Diffusion Models23
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data23
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy22
Phylogenomic Insights into the Origin of Primary Plastids22
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation22
Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)22
Robust Analysis of Phylogenetic Tree Space22
Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution21
Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough21
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)21
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards20
An Evolving View of Phylogenetic Support20
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition20
Estimating Global Biodiversity: The Role of Cryptic Insect Species20
Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation20
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets20
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)20
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support19
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)19
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach19
Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins19
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance18
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi18
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)18
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards18
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils18
Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa18
Relaxed Random Walks at Scale17
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution17
Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders17
Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past17
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies17
Genomics Reveals Widespread Ecological Speciation in Flightless Insects17