N. Mongiardino Koch

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

The paper introduces an R package called chronospace to visualize and quantify the sensitivity of divergence time estimates to methodological choices in phylogenetic analysis.

Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea

This study performs the first phylogenomic analysis of sea cucumbers, finding that genome-scale discordance prevents resolving relationships among Neoholothuriida clades.

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

This study uses phylogenomic data to revise the evolutionary history of echinoids, revealing their origin in the Permian and a Cretaceous origin for sand dollars, conflicting with their fossil record.

Phylogenomic subsampling and the search for phylogenetically reliable loci

This paper evaluates phylogenomic subsampling methods across multiple datasets, finding that a multivariate approach outperforms common strategies in selecting phylogenetically useful loci.

Fossils improve phylogenetic analyses of morphological characters

This study shows that fossils improve the accuracy of phylogenetic analyses of morphological data, even with fragmentary fossils, and that tip-dated analyses outperform other methods.

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

This paper constructs a total-evidence dated phylogeny of echinoids by integrating phylogenomic, morphological, and stratigraphic data, revealing convergent evolution in body size across 270 million years.

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

This study shows that paleontological data significantly influence phylogenetic inference, often having greater topological impact than extant taxa and inducing unique rearrangements.

A phylogenomic resolution of the sea urchin tree of life

This study resolves the phylogenetic relationships within echinoids using transcriptomes, revealing discrepancies with current classifications and resolving uncertainties about deep-sea lineages and sand dollar relatives.