D. Pisani

ATP synthase evolution on a cross-braced dated tree of life

This study reconstructs the evolutionary history of ATP synthase using a cross-braced dated tree of life, showing early divergence of F- and A/V-type lineages and timing of eukaryogenesis.

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

This paper uses machine learning and phylogenetic reconciliation to estimate the evolutionary timeline of Bacteria, linking transitions to aerobic lifestyles to the Great Oxidation Event.

Bursts of novel composite gene families at major nodes in animal evolution

The paper identifies composite gene families in animals, showing they emerge abruptly at major evolutionary nodes and are independently evolved in multiple clades.

Resolving tricky nodes in the tree of life through amino acid recoding

This study uses amino acid recoding to improve phylogenetic accuracy at tricky nodes, showing that ctenophores are likely not the first branching animal lineage.

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

The paper uses genome gene content and morphological data to investigate unresolved nodes in animal phylogeny, supporting sponges as the sister group of animals and Xenacoelomorpha as the sister group of Bilateria.

Compositional phylogenomic modelling resolves the 'Zoraptera problem': Zoraptera are sister to all other polyneopteran insects

This study resolves the Zoraptera placement in insect phylogeny, finding Zoraptera as the earliest-diverging polyneopteran order and providing a Devonian origin for winged insects.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

This paper integrates phylogenomic data and fossil records to refine the evolutionary timescale and classification of beetles, revealing a late Carboniferous origin and Cretaceous diversification.

microRNAs as Indicators into the Causes and Consequences of Whole Genome Duplication Events

This study investigates the role of microRNAs in whole genome duplication events, finding that miRNA paralogues are functionally equivalent and that miRNA seed sequence diversity, not WGDs, correlates with morphological complexity.

The role of homology and orthology in the phylogenomic analysis of metazoan gene content

The paper analyzes gene content in 26 animal genomes to show that gene conservation patterns differ based on orthology vs. homology definitions, suggesting new approaches are needed for resolving deep metazoan phylogeny.