D. Arcila

Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments

The paper examines the evolutionary loss and degradation of plaat1 in vertebrates adapted to low-light environments, showing its role in visual acuity and its loss through relaxed selection.

Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes

This study uses phylogenomic and phenotypic data to show that deep-sea anglerfishes have greater diversity and faster diversification rates than shallow-water relatives, challenging expectations about habitat constraints.

Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models

This study uses machine learning to analyze phylogenetic datasets, finding that non-linear models outperform linear ones in capturing complex relationships affecting phylogenomic inference.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

This study identifies cryptic diversity in Panamanian birds using mitochondrial DNA barcodes and finds ecological factors, not geography, drive speciation.

Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy.

This study uses phylogenomic data to resolve the evolutionary relationships and non-monophyly within piranha and pacu families, showing that convergent diets obscure traditional taxonomy.

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

The paper presents seven new exon probe sets and a bioinformatics pipeline for fish phylogenomics, enabling accurate phylogenetic analysis by filtering paralogs and integrating old and new data.