Plant Systematics and Bioinformatics | CCMAR

Plant Systematics and Bioinformatics

Short Title 

The research of the PSB group is focused on the study of plant evolutionary relationships that are reconstructed using molecular data.




The research of the PSB group is focused on the study of plant evolutionary relationships that are reconstructed using molecular data. In a post-genomic era, these data increasingly consist of whole genomes or samples of genes from whole genomes - a field of study often referred to as phylogenomics. The origin of plants from the endosymbiotic union of a heterotrophic eukaryote and a cyanobacterum is perhaps as old as 1.4 billion years ago, while plants did not arrive on land until at least 540 million years ago. Our research is focused on plant plastid (chloroplast) genome evolution, its origin from a cyanobacteria, and its utility in resolving phylogenetic relationships among the main plant lineages (Glaucosystophytes, Rhodophyta, and Chlorophyta) and among 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 is clearly evident from from contemporary data, modeling that change has required the development of complex substitution process models and use of large computational facilities. As part of our research programme, we routinely design and implement novel software to facilitate the phylogenetic analysis of molecular sequence data.



Coordinator Posição
Cymon J. Cox Senior Researcher
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)
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Retrato de Filipe Sousa
Retrato de Gianluca De Moro
Retrato de João Brazão
PhD Student
Retrato de Regina L. Cunha
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).