J. Barido-Sottani

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

This study reconstructs the evolutionary history of true crabs to understand their adaptation to terrestrial environments, finding multiple convergent transitions from marine to terrestrial lifestyles.

Putting the F in FBD analyses: tree constraints or morphological data ?

This study evaluates methods for placing fossils in FBD analyses, finding that divergence times are well recovered across methods, but extant topology is more influenced by molecular data.

Robust phylodynamic analysis of genetic sequencing data from structured populations

The paper improves the bdmm algorithm in BEAST 2 to handle larger genetic datasets, enabling more precise phylodynamic analysis of structured populations.

RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

RevGadgets provides an R package for creating publication-quality figures from Bayesian phylogenetic analyses in RevBayes and other software.

Estimating the age of poorly dated fossil specimens and deposits using a total-evidence approach and the fossilized birth-death process

This study shows that Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model can accurately estimate fossil ages, even when some specimens have poor dating.

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

This paper introduces a skyline birth-death process to infer population size changes over time using occurrence data and phylogenetic trees, applied to epidemiology and macroevolution.

Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference

This study shows that ignoring fossil age uncertainty leads to less accurate tree topologies and divergence times, especially with high character sampling.

Improved multi-type birth-death phylodynamic inference in BEAST 2

The paper improves the multi-type birth-death model in BEAST 2 to handle larger datasets and reports results on Influenza A virus migration and seasonal dynamics.

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

This study shows that ignoring stratigraphic age uncertainty in fossil data leads to biased divergence time estimates under the fossilized birth-death process, and recommends explicitly incorporating age uncertainty.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

The paper introduces a multi-state birth-death model to estimate lineage-specific speciation and extinction rates without requiring prior trait hypotheses, showing its effectiveness on simulated and empirical datasets.