Systemic Biology

Papers
(The TQCC of Systemic Biology is 14. 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 2021-08-01 to 2025-08-01.)
ArticleCitations
Corrigendum to: Delayed Adaptive Radiation among New Zealand Stream Fishes: Joint Estimation of Divergence Time and Trait Evolution in a Newly Delineated Island Species Flock83
Announcements75
Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)72
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles69
Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales62
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards53
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations52
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs49
Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models47
Phylogenomic Insights into the Evolution and Origin of Nematoda44
How to Validate a Bayesian Evolutionary Model39
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages39
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method39
The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been accompanied by pervasive hybridization36
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination35
Evolutionary Timelines Help Explain the Evolution of Parental Care Strategies32
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards32
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex31
Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia30
Accuracy in Near-Perfect Virus Phylogenies30
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory30
Announcements29
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI29
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush28
Evolutionary Tempo, Supertaxa and Living Fossils28
The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)28
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution27
Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies27
Estimating Global Biodiversity: The Role of Cryptic Insect Species27
Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index26
Announcements26
Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal25
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of theerato-saraGroup ofHeliconiusButterflies25
Scalable Bayesian Divergence Time Estimation With Ratio Transformations25
Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial24
A Phylogenetic Approach to Delimitate Species in a Probabilistic Way23
A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data23
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations23
Robust, Universal Tree Balance Indices23
A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees22
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions22
Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)22
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating21
DEPP: Deep Learning Enables Extending Species Trees using Single Genes21
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life21
Aquatic Biotas of Sundaland Are Fragmented But Not Refugial21
Relative Time Constraints Improve Molecular Dating20
Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield20
Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process20
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora20
Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors20
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama20
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools19
New Phylogenetic Markov Models for Inapplicable Morphological Characters19
Estimation of species divergence times in presence of cross-species gene flow19
Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?19
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?19
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?18
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses18
Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood18
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution18
On Information Rank Deficiency in Phenotypic Covariance Matrices18
Is Over-parameterization a Problem for Profile Mixture Models?18
Announcements17
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong17
Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions17
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests17
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance17
Waves of Colonization and Gene Flow in a Great Speciator17
The Effect of Copy Number Hemiplasy on Gene Family Evolution17
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages16
Global climate cooling spurred skipper butterfly diversification16
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains16
Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline15
PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets15
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes15
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process15
Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels15
Correction to: Modeling phylogenetic biome shifts on a planet with a past14
Robust Analysis of Phylogenetic Tree Space14
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics14
ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process14
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