Evolution and Paleontology Studies

Phylogenetic Estimation of branch-specific Shifts in the Tempo of Origination

This paper introduces Pesto, a fast method for estimating branch-specific diversification rates in phylogenies without MCMC, showing high precision but limited power for detecting rate shift events.

Replicated Radiations Reveal Temporally Structured Macroevolutionary Dynamics

The paper examines macroevolutionary dynamics in African cichlid radiations, finding inverse correlation between vertebral count evolution rates and radiation age, but no early burst pattern within individual systems.

A complete and dynamic tree of birds

This paper unites phylogenetic estimates from 262 studies to create a complete, time-scaled bird evolutionary tree, enabling large-scale analyses linking phylogeny with geographic data.

An Eocene Origin of Passerine Birds Estimated Using Bayesian Tip Dating with Fossil Occurrences

This study estimates the origin of passerine birds in the Eocene using Bayesian tip-dating with fossil data, narrowing the gap between molecular and paleontological estimates.

Enhancing Evolutionary Timelines: The Impact of Stratigraphic Range Information on Phylogenetic Inference

This paper introduces the SRFBD model to improve phylogenetic inference by incorporating stratigraphic range data, showing it produces older divergence times and higher sampling proportions compared to the FBD model.

Navigating "tip fog": Embracing uncertainty in tip measurements

The paper introduces 'tip fog' to describe variance between true species means and recorded data in comparative biology, showing its impact on model accuracy and parameter estimates.

Tetrapod species-area relationships across the Cretaceous-Paleogene mass extinction

This study analyzes species-area relationships (SARs) in tetrapods across the Cretaceous-Paleogene extinction, showing changes in SAR slope and intercept that contradict expected patterns of homogenization and diversity loss.

Phenotypic and Developmental Dissection of an Instance of the Island Rule

The paper examines body size evolution in island mice by comparing developmental traits between Gough Island and mainland mice, identifying key periods of weight gain and metabolic shifts.

The extended 'common cause': causal links between punctuated evolution and sedimentary processes

This paper uses computational modeling to show that sedimentary processes can influence microevolutionary trait evolution, producing patterns similar to punctuated equilibria observed in fossil records.

Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

This study uses phylogenomics and deep learning to identify hidden species diversity in talpid moles from Southwest China's sky islands, revealing previously unrecognized species.

The effects of cryptic diversity on diversification dynamics analyses in Crocodylia

This study investigates how incorporating cryptic diversity into diversification dynamics analysis of crocodylians changes speciation rate estimates, finding increased rates toward the present compared to previous studies.

But the clock, tick-tock: the preeminence of relaxed clock models in total-evidence dated phylogenetics

This study evaluates the impact of relaxed clock models on total-evidence dated phylogenetics using echinoid data, showing their influence on divergence times and macroevolutionary inferences.

How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge.

The paper updates the Mammal Diversity Database (MDD2) to include 6,759 mammal species, showing increases in species counts and identifying trends in taxonomic and geographic knowledge over time.

A semiparametric method to test for correlated evolution in a phylogenetic context

This paper introduces a semiparametric method to test for evolutionary correlation between variables in a phylogenetic context, showing it has good statistical properties and comparable power to parametric methods.

PRESENCE OF A LARGE DASYPODIDAE GRAY, 1821 FROM THE CUVIERI CAVE, EASTERN BRAZIL

This study revises two osteoderms from the Cuvieri Cave, identifying them as the first evidence of a large Dasypodidae member in the region.

A flexible Bayesian method for estimating stratigraphic intervals and their co-occurrence in time

This paper introduces a Bayesian method to estimate stratigraphic intervals and their co-occurrence, using empirical examples and a Julia package for implementation.

Selection, Evolution and Persistence of Paleoecological Systems

This paper introduces the Ecological Functional Networks Hypothesis to explain ecological persistence and evolution through functional networks of species, supported by fossil record evidence and proposed tests.

Speciation completion rates have limited impact on macroevolutionary diversification

The paper examines how speciation completion rates affect macroevolutionary diversification by comparing standard birth-death models with a protracted birth-death model.

StratPal: An R package for creating stratigraphic paleobiology modeling pipelines

StratPal is an R package that allows combining stratigraphic, ecological, evolutionary, and taphonomic modules into modeling pipelines to analyze fossil data and account for stratigraphic biases.

Brain size dependent speciation and extinction rates in birds and the cognitive buffer hypothesis

This study models brain size-dependent diversification rates in birds, finding that larger brains reduce extinction rates, supporting the cognitive buffer hypothesis.

Decoding Demosponge Diversity: Bayesian Analysis of Biodiversity, Extinction Events and Environmental Influences throughout the Phanerozoic

This study uses a Bayesian framework to analyze fossil data and identify extinction events and environmental influences on demosponge diversity throughout the Phanerozoic.

Apparent timescaling of fossil diversification rates is caused by sampling bias

This study shows that apparent negative scaling between diversification rates and time in fossils is caused by sampling bias, not real evolutionary trends.

Global plate model choice impacts reconstructions of the latitudinal biodiversity gradient

Across 344,258 Phanerozoic marine invertebrate fossil occurrences, four global plate models often disagree on where latitudinal diversity peaks, with all-model agreement in only ~19% of Palaeozoic stages.

tbea: tools for pre- and post-processing in Bayesian evolutionary analyses

The paper introduces the R package tbea to improve Bayesian divergence time estimation by integrating biological, geological, and palaeontological data for better model specification and reproducibility.

Conflicting Timelines: Exploring patterns of mito-nuclear discordance in divergence estimates among tetrapods

This study quantifies mito-nuclear divergence discordance in four tetrapod groups, finding mitochondrial estimates underestimate basal divergence times and overestimate recent divergences compared to nuclear data.

Variable patterns of phenotypic evolution among canonical 'living fossil' lineages

The paper examines phenotypic evolution in three living fossil lineages, finding varied evolutionary patterns across and within lineages, suggesting idiosyncratic processes rather than uniform change.

The distribution of clade size in a coalescent diversification model

The paper derives a closed-form expression for clade size distribution under the Kingman coalescent model and extends it to time-varying niche numbers.

Evolutionary macroecology: Incorporating phylogenetic information more explicitly into process-based, forward time, simulation models

This paper introduces a spatially-explicit simulation model that integrates phylogenetic information to study the processes shaping biodiversity distribution patterns over time.

Comparative genomics of the world's smallest mammals reveals links to echolocation, metabolism, and body size plasticity

This study identifies shrew-specific genomic variants linked to echolocation, metabolism, and body size plasticity through comparative genomics.

Phylogenetically and ecologically delimited species pool affect the inference of age-dependent extinction

This study examines how phylogenetic and ecological species pool definitions affect age-dependent extinction inference using Canidae fossils and a Bayesian framework.