Rute R. da Fonseca

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

A time-calibrated phylogeny of hummingbirds supports stepwise diversification in the Andes

This study reconstructs a time-calibrated hummingbird phylogeny, finding stepwise diversification in the Andes rather than a monophyletic Andean clade.

Ghrelin and Mboat4 are lost in Serpentes

The paper identifies the independent loss of ghrelin and Mboat4 in snakes, chameleons, and toadhead agamas, linking it to adaptations in energy metabolism.

Historic Overexploitation, Genetic Erosion and Local extinction: Palaeogenomic Insights into the Decline of Eubalaena glacialis in the Northeast Atlantic

This study uses ancient DNA to show that the Northeast Atlantic right whale population was historically panmictic but declined sharply in genetic diversity due to whaling, leading to its functional extinction.

DNA from cetariae fish remains confirms sardine (Sardina pilchardus) use and local population continuity in Northwestern Iberia since Roman times

PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era

PseudoChecker2 and PseudoViz automate and visualize gene loss detection across species using genomic data.

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

The paper presents a high-quality genome assembly for the Atlantic chub mackerel, providing a resource for studying its biology and fisheries management.

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

The paper presents the first draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera using Illumina sequencing technologies.

Link Your Sites (LYS) Scripts: Automated search of protein structures and mapping of sites under positive selection detected by PAML

LYS scripts automate the mapping of positively selected sites from PAML analysis onto protein structures and generate publication-quality visualizations.

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

The paper analyzes genomic data from passenger pigeons and their relatives to show that natural selection reduced neutral genetic diversity despite large population size, challenging previous extinction theories.