Systematic Biology

Long‐Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology‐Based Summary Methods

Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited

A Penalized Likelihood Framework for High‐Dimensional Phylogenetic Comparative Methods and an Application to New‐World Monkeys Brain Evolution

Automated Taxonomic Identification of Insects with Expert-Level Accuracy Using Effective Feature Transfer from Convolutional Networks

Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data

Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors

Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis.

Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications

Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)

Full Bayesian Comparative Phylogeography from Genomic Data

Stochastic Character Mapping of State‐Dependent Diversification Reveals the Tempo of Evolutionary Decline in Self‐Compatible Onagraceae Lineages

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.

Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals

GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments.

Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets

Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data.

True Homoplasy of Retrotransposon Insertions in Primates

Divergence Estimation in the Presence of Incomplete Lineage Sorting and Migration

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction

How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline?

Phylotocol: Promoting Transparency and Overcoming Bias in Phylogenetics

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents.

An Integrative Approach using Phylogenomics and High-resolution X-ray Computed Tomography (CT) for Species Delimitation in Cryptic Taxa.

Lack of signal for the impact of conotoxin gene diversity on speciation rates in cone snails.

Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae)

Homoplasy-Based Partitioning Outperforms Alternatives in Bayesian Analysis of Discrete Morphological Data.

Sex‐Biased Dispersal Obscures Species Boundaries in Integrative Species Delimitation Approaches

A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models.

Species Selection Regime and Phylogenetic Tree Shape.

The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar.

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past.

Inferring Tumour Proliferative Organisation from Phylogenetic Tree Measures in a Computational Model.

Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees

Biogeographical Network Analysis of Cretaceous Terrestrial Tetrapods: A Phylogeny-Based Approach.

The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks.

Metapopulation Vicariance, Age of Island Taxa and Dispersal: A Case Study Using the Pacific Plant Genus Planchonella (Sapotaceae)

Model-based species delimitation: are coalescent species reproductively isolated?

Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum.

A Logical Model of Homology for Comparative Biology

Impossibility Results on Stability of Phylogenetic Consensus Methods.

Using historical biogeography models to study color pattern evolution.