Evolution and Paleontology Studies

Global biogeography of geckos (Squamata: Gekkota) reveals Old-World origins and region-specific heterogeneity in diversification

This study investigates gecko biogeography and diversification, finding Old-World origins and region-specific diversification patterns without evidence of mass extinctions.

Water under the bridge: Aquatic environments and crepuscular-cathemeral intermediates facilitate temporal niche transitions in artiodactyls

The paper tests the crepuscular-cathemeral bridge hypothesis by comparing activity patterns in aquatic and terrestrial artiodactyls, finding support for the bridge and distinct roles of crepuscularity and cathemerality.

Inverse covariation between the neocortex and the limbic system is concentrated at deep evolutionary divergences

The paper shows that the tradeoff between neocortex and limbic system volume is concentrated at deep evolutionary divergences in mammals.

Increase in sea-level and shelf area positively influenced the development of Cenozoic biodiversity hotspots by modulating turnover rate in marine benthos

The paper identifies marine biodiversity hotspots over the past 66 million years and shows that sea-level and shelf area increases boost origination rates in molluscs and cnidaria, contributing to hotspot development.

Phylogenetic estimation of diversity-dependent biogeographic rates using deep learning

DDGeoSSE, a GeoSSE extension in which local species richness modulates speciation, extinction and dispersal, is fit with phyddle neural networks that detect diversity dependence in Anolis and Viburnum.

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

This study examines how localized evolutionary changes affect ancestral state reconstruction and shows that tree partitioning can reduce errors in these reconstructions.

Evolutionary rates in "living fossils" across the Tree of Life

This study examines evolutionary rates in living-fossil lineages and finds reduced morphological but not molecular rates, suggesting morphological conservatism is a key feature.

Insights into the molecular systematics of montane voles of the Western Himalayan Mountains

The paper analyzes mitochondrial and nuclear DNA sequences of Kashmir voles to revise their taxonomy and phylogenetic placement within the arvicoline family.

Ancient mitogenomes reveal unexpected diversity in Madagascar's extinct hippopotamuses

This study uses ancient mitochondrial genomes from Malagasy hippos to reveal unexpected diversity and a complex diversification history, challenging traditional taxonomy and showing a recent radiation of large-bodied island mammals.

Acrean fish diversity back in time: Paleoichthyology of the Rio Acre fossil fauna in Brazil

The paper reports new fossil fish taxa from the Rio Acre locality in Brazil, showing ecological conservatism in Amazonian fish assemblages during the Neogene.

A novel phylogenetic comparative model reveals strong signals for early high disparity in ichthyosaurs

Combining Early Burst and Ornstein-Uhlenbeck processes, an Early High Disparity model best fits ichthyosaur skull length across 108 phylogenies, placing median peak disparity at 231.1 Ma.

REPEATED MARINE-TO-FRESHWATER FISH TRANSITIONS REVEAL PALEOENVIRONMENTAL MODULATION OF ADAPTIVE RADIATION

The paper investigates marine-to-freshwater fish transitions in Sahul rivers, finding that diversification success depends on paleoenvironmental dynamics rather than just ecological opportunity.

On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models

This study maps evolutionary scenarios to governing rules in state-dependent speciation-extinction models and shows that different scenarios can produce identical stationary distributions.

An exact version of Hunt's ancestor-descendant directional random walk model

The paper corrects Hunt's model by using a tridiagonal covariance matrix instead of a diagonal one, improving step size estimation in evolutionary models.

Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process

The paper corrects an overcounting issue in the unresolved FBD model for tip-dating and demonstrates its application to empirical datasets.

Physiology mediates transcontinental radiations of freshwater fishes

The paper shows that saltwater tolerance enabled transcontinental freshwater fish radiations to disperse across marine barriers and diversify in freshwater ecosystems.

Phenotype shift scores reveal the scale and phylogenetic structure of phenotypic differentiation in primates.

This paper introduces the Phenotype Shift Score (PSS) to identify highly differentiated primate species pairs and shows it improves comparative-genomic signal detection.

The macroevolutionary impact of an innovation reversal in ray-finned fishes

This paper shows how swim bladder loss in ray-finned fishes influenced diversification by enabling adaptation to deep sea and Southern Ocean environments, but also acted as a selective filter during past global warming events.

Mammalian returns to the sea reveal broad genomic slowing rather than a fixed adaptive toolkit

The paper analyzes genomic evolution in marine mammals to determine if they share a common adaptive toolkit or exhibit directional genomic slowing.

Modelling a rapid radiation of crown-group placentals

This paper models the rapid radiation of crown-group placentals using the Covariant Evolutionary Tempo (CET) model, showing elevated diversification and molecular evolution rates post-K-Pg boundary.

Accelerated lung evolution associated with end-Permian and end-Triassic mass extinctions

The paper identifies accelerated evolution of lung-related genes in vertebrate lineages surviving end-Permian and end-Triassic mass extinctions, suggesting adaptation to hypoxia.

Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion

The paper introduces a discretized stochastic diffusion approach to model discrete and continuous trait evolution in phylogenetics, exploring multiple new models and their applications.

Phylogenetic reconstruction of trait summary statistics and disparity dynamics

The paper reconstructs the evolution of trait summary statistics and disparity over time using phylogenetic data, showing contrasting patterns in cetacean body length and mammaliaform body mass.

A fossilized birth-death model for fossil records lacking sampled ancestors

The paper introduces a new fossilized birth-death model (FBDT) that handles fossil datasets with only terminal fossils, showing it accurately estimates diversification parameters without bias.

Aridification and habitat shifts are associated with diversification in Australian diplodactylid geckos

This study links environmental change and habitat shifts to diversification in Australian geckos using phylogenetic and ecological analyses.

An Alternative Approach to Compute the Likelihood for the DAISIE (Dynamic Assembly of Island biota through Speciation, Immigration, and Extinction) Model

This paper proposes an alternative method to compute the likelihood for the DAISIE model, improving computational efficiency and enabling state-dependent dynamics in island biodiversity studies.

Phylogenetic inference from an incomplete fossil record

This study investigates how stratigraphic gaps affect phylogenetic inference using a simulation framework and finds that total-evidence analysis is robust to gap distribution but dominated by morphological character data.

Robust evidence for modest neoselachian diversity loss across the K/Pg: Response to Guinot et al.

The paper reanalyzes neoselachian diversity through the K/Pg boundary using new data and methods, finding no diversity collapse during the K/Pg and robust results across different data treatments.

Survivorship Bias Explains Age-Dependent Extinction in Fossil Genera

The paper shows that survivorship bias, not biological changes, explains age-dependent extinction patterns in fossil genera using a one-parameter model.

Of Brobdingnag and Lilliput, or how island area may link body size, genome size and mutation rate

The paper proposes a neutral model linking island area to body size, genome size, and mutation rate, finding modest support for the model across global datasets.