Centre for Ecology, Evolution and Environmental Changes

Funder

Organizational Unit

Publications

Novel dynamics and functions of Fibronectin in early vertebrate development

Publication . Gomes De Almeida, Patrícia; Thorsteinsdóttir, Sólveig; Palmeirim, Isabel; Andrade, Raquel P.

The metameric body plan of vertebrates is established during somitogenesis, one of the most complex morphogenetic events during development. Somites epithelialize periodically from the anterior-most presomitic mesoderm, and this rhythmicity is thought to be controlled by cyclic traveling waves of gene expression that sweep the tissue anteriorly. Although the spatial and temporal regulation of somitogenesis has been extensively studied, how the periodicity of genetic oscillations is translated into periodic somite epithelialization remains elusive. Furthermore, while knockout experiments have implicated the extracellular matrix component fibronectin in somite formation, much of the roles of its qualitative features deriving from its assembly state are still unknown. The aim of this thesis is to re-address the role of fibronectin during paraxial mesoderm development, particularly during somite morphogenesis. In Chapter 2, we describe fibronectin production and assembly dynamics during early embryogenesis and found that it is highly dynamic throughout paraxial mesoderm development, as different forms of fibronectin assembly (autocrine vs paracrine) correlate with exquisite morphogenetic events. In Chapter 3 we re-address the role of fibronectin during somite formation in vivo. We show that an intact fibronectin matrix and downstream mechanotransduction signaling are required for correct segmentation clock dynamics and somite morphogenesis. Our results suggest that the fibronectin matrix and its downstream chemical and mechanical cues couple genetic oscillations with timely somite morphogenesis. In Chapter 4 we investigate the role of fibronectin in somite maturation. We demonstrate that normal fibronectin assembly is required for correct Sonic hedgehog signaling in the somite, which in turn controls fibronectin production in this tissue, suggesting that fibronectin and Sonic cooperate to orchestrate somite patterning and differentiation. This thesis demonstrates that fibronectin is a dynamic pivotal player regulating paraxial mesoderm development. It also highlights the previously unappreciated importance of the extracellular matrix and its derived mechanical cues during embryonic development.

2019-02Doctoral thesis

Open access

Diverse bioerosion structures in lower Pliocene deposits from a volcanic oceanic island: Baía de Nossa Senhora section, Santa Maria Island, Azores (central North Atlantic)

Publication . Dávid, Árpád; Uchman, Alfred; Ramalho, Ricardo Dos Santos; Madeira, José; Melo, Carlos; Madeira, Patrícia; Rebelo, Ana Cristina; Berning, Björn; Johnson, Markes E.; Ávila, Sérgio P.

Pliocene body fossils from Santa Maria Island, Azores, have been studied for decades, but only more recently have ichnofossils received their due attention. Calcareous Pliocene deposits from the Baía de Nossa Senhora section contain numerous, diverse, well-preserved natural casts of invertebrate borings. The study of this type of fossils adds to knowledge on the dispersal of benthic faunas across oceans to volcanic oceanic islands. The borings belong to seven ichnogenera and twenty-two ichnotaxa at the ichnospecies level with more than half pertaining to Entobia, which is produced by clionaid sponges. Other borings found were produced by bivalves (Gastrochaenolites), polychaete worms (Caulostrepsis and Maeandropolydora), sipunculid worms (Trypanites), phoronid worms (Talpina) and ctenostome bryozoans (Iramena). The occurrence, ichnogeny, distribution and preservational state of the borings suggest that the bearing bioclasts have been exposed for several years on the sea floor. The borings derive from different bathymetric zones on the shelf, and their formation took place during several bioerosional phases. The association of borings belongs to the Entobia ichnofacies, which is typical of carbonate rocky shores, and shows close similarity to those described from the Paratethys, Mediterranean and partly the eastern Atlantic regions. This fits the idea that most of the Neogene shallow-water marine fauna in the Azores is biogeographically related to the eastern Atlantic shores.

2021-05-01Journal article

Open access

Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems

Publication . Pina-Martins, Francisco; Silva, Diogo N.; Fino, Joana; Paulo, Octávio S.

Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single-threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task-ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios. Furthermore, Structure_threader can perform several automatic and convenient operations, assisting the user in assessing the most biologically likely value of 'K' via implementations such as the "Evanno," or "Thermodynamic Integration" tests and automatically draw the "meanQ" plots (static or interactive) for each value of K (or even combined plots). Structure_threader is written in python 3 and licensed under the GPLv3. It can be downloaded free of charge at https://github.com/StuntsPT/Structure_threader.

2017Journal article

Open access

Mate-choice copying: A fitness-enhancing behavior that evolves by indirect selection

Publication . Santos, Mauro; Sapage, Manuel; Matos, Margarida; Varela, Susana A. M.

A spatially explicit, individual-based simulation model is used to study the spread of an allele for mate-choice copying (MCC) through horizontal cultural transmission when female innate preferences do or do not coevolve with a male viability-increasing trait. Evolution of MCC is unlikely when innate female preferences coevolve with the trait, as copier females cannot express a higher preference than noncopier females for high-fitness males. However, if a genetic polymorphism for innate preference persists in the population, MCC can evolve by indirect selection through hitchhiking: the copying allele hitchhikes on the male trait. MCC can be an adaptive behavior-that is, a behavior that increases a population's average fitness relative to populations without MCC-even though the copying allele itself may be neutral or mildly deleterious.

2017-03-23Journal article

Open access

Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History

Publication . Seabra, Sofia G; De mendonça fragata almeida, Inês; Antunes, Marta; Faria, Gonçalo S; Santos, MA; Sousa, Vitor C; Simões, Pedro; Matos, Margarida

Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.

2018-03Journal article

Open access