The research of the Plant Systematics and Bioinformatics group is focused on the study of evolutionary relationships. Phylogenetic trees describing the sequence of divergences among a set of taxa are typically reconstructed using molecular data, such as DNA or protein sequences, and used to evaluate the evolution of life-history traits of the organisms. In a post-genomic era, these molecular data used to reconstruct phylogenies increasingly consist of whole genomes or large samples of genes from whole genomes - a field of study often referred to as phylogenomics.

One major focus of our research is on the origin of plants and their transition to terrestrial environments. Plants evolved from the endosymbiotic union of a heterotrophic eukaryote and a cyanobacterum, perhaps as far back as 1.4 billion years ago, and transitioned to land from freshwater approximately 480 million years ago. Our research is part focused on the evolution of the plant plastid (chloroplast) genome, its origin from a cyanobacteria, and its utility in resolving phylogenetic relationships among the main plant lineages (Glaucosystophytes, Rhodophyta, Chlorophyta, and Streptophyta) and among major lineages of land plants (bryophytes and tracheophytes). Such ancient evolutionary origins are especially difficult to reconstruct and require sophisticated modeling of the molecular substitution processes that are inferred from gene sequences of contemporary organisms. Our group is particularly interested in the modeling of heterogeneous substitution processes over time. Although, the observation that the process of molecular change has varied throughout the course of evolution, as is clearly evident from contemporary data, modeling that change has required the development of complex substitution process models and consequently the use of large computational resources.

Besides our interest in plants, we also study a variety of marine organisms including corals, molluscs, and small pelagic fishes, such as the sardine. In particular, we have use molecular data to attempt to delineate species of the endemic Hawaiian coral genus Montipora, which contains taxa that are morphologically diverse and actively speciating. By contrast, we are also studying the diversification of the tiny marine gastropods of the family Caecidae, which although widely distributed, are morphologically and anatomically simple, and likely more diverse genetically than their morphology suggests. These studies of taxa nearer to, or even at, the level of species provide an interesting contrast to our very ancient phylogenetic studies, and bring with them a new set of theoretical and methodological issues. Lastly, we are also interested in developing genomic and genetic resources to be used for monitoring the long-term health and viability of the sardine fisheries stock in Portuguese waters. To this end, we and collaborators have recently published a draft of the nuclear genome of the sardine, and are currently helping develop genetic markers for fisheries monitoring tools.