Plant Systematics and Bioinformatics | - CCMAR -

Plant Systematics and Bioinformatics

Short Title 

Systematics, Molecular Phylogenetics, Genomics and Transcriptomics, Biogeography and Ecology, all wrapped up with a healthy dose of Bioinformatics and Computational Biology.




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.





Coordinator Posição
Cymon J. Cox Senior Researcher
Name Posição
Christina Egger MSc Student
Filipe Sousa Postdoc
Gianluca De Moro Researcher
João Brazão PhD Student
Li Yuanshuo MSc Student
Regina L. Cunha Postdoc
Other Past Members 
Blaise Li (Institut Pasteur, Paris)
Peter Civan (Univesity of Manchester)
Joao Sollari Lopes (Instituto Nacional de Estatistica, Lisbon)
Michael Nowak (Natural History Museum, Oslo)
Cristiane Cassiolato Pires Hardoim (UNESP, São Paulo)
Natércia Maria da Silva Conceição (CCMAR, Faro)
Telma Filipa Paulo Franco (75)
View current members by grid
Christina Egger's picture
MSc Student
Filipe Sousa's picture
Gianluca De Moro's picture
João Brazão's picture
PhD Student
Li Yuanshuo's picture
MSc Student
Regina L. Cunha's picture
All Publications 
Coscia I, Castilho R, Massa-Gallucci A, et al. Genetic homogeneity in the deep-sea grenadier Macrourus berglax across the North Atlantic Ocean. Deep sea research Part I: Oceanographic research papers. 2018;132.
Castilho R, Cunha RL, Faria C, Velasco E, Robalo JI. Asymmetrical dispersal and putative isolation-by-distance of an intertidal blenniid across the Atlantic-Mediterranean divide. PeerJ. 2017;5.
Madeira PM, Chefaoui RM, Cunha RL, et al. High-unexpected genetic diversity of a narrow endemic terrestrial mollusc. PeerJ. 2017;5.
Cunha RL, Assis JM, Madeira C, et al. Drivers of Cape Verde archipelagic endemism in keyhole limpets. Scientific Reports. 2017;7. doi:10.1038/srep41817
Cunha RL, Patrão C, Castilho R. Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugs. Scientific Reports. 2017;7. doi:10.1038/s41598-017-16417-y
Silva G, Cunha RL, Ramos AA, Castilho R. Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish. Scientific Reports. 2017;7. doi:10.1038/s41598-017-02945-0
Ranjbar SM, Zolgharnien H, Yavari V, et al. Rising the Persian Gulf black-lip pearl oyster to the species level: fragmented habitat and chaotic genetic patchiness in Pinctada persica. Evolutionary Biology. 2016;43(1). doi:10.1007/s11692-015-9356-1
Cunha RL, Lima FP, Tenorio MJ, Ramos AA, Castilho R, Williams ST. Evolution at a different pace: distinctive phylogenetic patterns of cone snails from two ancient oceanic archipelagos. Syst Biol. 2014;63(6):971-87. doi:10.1093/sysbio/syu059
Cunha RL, Nicastro KR, Costa J, McQuaid CD, Serrão EA, Zardi GI. Wider sampling reveals a non-sister relationship for geographically contiguous lineages of a marine mussel. Ecol Evol. 2014;4(11):2070-81. doi:10.1002/ece3.1033
Teixeira S, Olu K, Decker C, et al. High connectivity across the fragmented chemosynthetic ecosystems of the deep Atlantic Equatorial Belt: efficient dispersal mechanisms or questionable endemism?. Mol Ecol. 2013;22(18):4663-80. doi:10.1111/mec.12419
González EG, Cunha RL, Sevilla RG, Ghanavi HR, Krey G, Bautista JM. Evolutionary history of the genus Trisopterus. Mol Phylogenet Evol. 2012;62(3):1013-8. doi:10.1016/j.ympev.2011.11.032
Decker C, Olu K, Cunha RL, Arnaud-Haond S. Phylogeny and diversification patterns among vesicomyid bivalves. PLoS One. 2012;7(4):e33359. doi:10.1371/journal.pone.0033359
Correia AT, Ramos AA, Barros F, et al. Population structure and connectivity of the European conger eel (Conger conger) across the Northeastern-Atlantic and Western-Mediterranean: integrating molecular and otolith elemental approaches. Marine Biology. 2012;159.
Cunha RL, Coscia I, Madeira C, Mariani S, Stefanni S, Castilho R. Ancient divergence in the trans-oceanic deep-sea shark Centroscymnus crepidater. PLoS One. 2012;7(11):e49196. doi:10.1371/journal.pone.0049196
Cunha RL, Blanc F, Bonhomme F, Arnaud-Haond S. Evolutionary patterns in pearl oysters of the genus Pinctada (Bivalvia: Pteriidae). Mar Biotechnol (NY). 2011;13(2):181-92. doi:10.1007/s10126-010-9278-y
Cunha RL, Verdú JR, Lobo JM, Zardoya R. Ancient origin of endemic Iberian earth-boring dung beetles (Geotrupidae). Mol Phylogenet Evol. 2011;59(3):578-86. doi:10.1016/j.ympev.2011.03.028
Reis DM, Cunha RL, Patrão C, Rebelo R, Castilho R. Salamandra salamandra (Amphibia: Caudata: Salamandridae) in Portugal: not all black and yellow. Genetica. 2011;139(9):1095-105. doi:10.1007/s10709-011-9609-6
Cunha RL, Lopes EP, Reis DM, Castilho R. Genetic structure of Brachidontes puniceus populations in Cape Verde archipelago shows signature of expansion during the last glacial maximum. Journal of Molluscan Studies. 2011;77.
Aires T, Marbà N, Cunha RL, et al. Evolutionary history of the seagrass genus Posidonia. Marine Ecology Progress Series. 2011;421:117 - 130. doi:10.3354/meps08879
Cunha RL, Grande C, Zardoya R. Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol Biol. 2009;9:210. doi:10.1186/1471-2148-9-210
Cunha RL, Tenorio MJ, Afonso CM, Castilho R, Zardoya R. Replaying the tape: recurring biogeographical patterns in Cape Verde Conus after 12 million years. Molecular Ecology. 2008;17(3).
Cunha RL, Castilho R, Rüber L, Zardoya R. Patterns of cladogenesis in the venomous marine gastropod Genus Conus from the Cape Verde islands. Systematic Biology. 2005;54(4).