Evolutionary lessons from drosophila melanogaster for colonization : how do history, selection and effective population size shape evolution?

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2018Understanding the factors that constrain adaptation, namely in a colonization scenario, has been a major topic in evolutionary biology and was the chief focus of this thesis. Using a highly-replicated experimental evolution design with well-characterized Drosophila melanogaster populations, we aimed to respond to several evolutionary questions relevant for the colonization of a new habitat. First, we showed that reduced effective population size (1) impaired the responses to directional selection, (2) increased between-population differentiation, and (3) shaped the signatures of history and chance, which were overrun by selection in larger populations. Second, we saw that interpopulation hybridization can have strong effects on a population’s subsequent evolution, especially under a sustained bottleneck. Most importantly, the outcome of hybridization is unpredictable, due to the complex genetic architecture of fitness-related traits and the multitude of interfering factors. This calls for caution on the use of hybridization in conservation management, especially in small, endangered populations. Third, we showed that evolutionary history is very important for a population’s subsequent evolution and fate, namely in a reverse colonization scenario. We additionally showed that the evolutionary patterns during reverse evolution are contingent to the trait under study. Finally, we presented the first, while crude, experimental test of the Hamiltonian wave of adaptation. We found that (1) small changes in diet can have significant effects on age-specific mortality but could not determine whether adaptation to a novel diet was greater at earlier than later ages, and (2) the age-specific decrease in differentiation between adapted and non-adapted populations, predicted by the Hamiltonian hypothesis, was not verified in our system. Despite the high replication and complex design of our experiments, many questions remain unanswered. Other studies involving genomic analysis of our populations, other traits, and diets will shed light on how history, selection, and effective population size shape evolution during colonization.A compreensão dos factores que limitam a adaptação, nomeadamente durante a colonização, é um tema importante em evolução, sendo o objectivo principal desta tese. Utilizando populações de Drosophila melanogaster bem caracterizadas, num estudo de evolução experimental altamente replicado, procurámos responder a questões evolutivas relevantes para a colonização de um novo habitat. Primeiro, mostrámos que a redução do efectivo populacional (1) diminuiu as respostas à selecção direccional, (2) aumentou a diferenciação interpopulacional e (3) modelou as assinaturas da história e do acaso, rapidamente superadas pela selecção em populações grandes. Segundo, vimos que a hibridação interpopulacional pode ter fortes efeitos na evolução das populações, especialmente sob Ne reduzido. Sobretudo, verificámos que as consequências da hibridação são imprevisíveis, pela complexa arquitectura genética das características da história da vida e multiplicidade de factores que intervêm na sua evolução. Como tal, alertamos para o uso da hibridização em programas de conservação, especialmente em populações pequenas e ameaçadas. Terceiro, mostrámos que a história evolutiva é fundamental para a subsequente evolução da população, nomeadamente num cenário de colonização reversa, e que os padrões evolutivos durante a evolução reversa são contingentes às características analisadas. Finalmente, apresentámos o primeiro, apesar de rudimentar, teste experimental da onda Hamiltoniana da adaptação. Vimos que (1) alterações pequenas na dieta das populações podem ter efeitos significativos na mortalidade específica de cada idade, mas não pudemos determinar se a adaptação à nova dieta era maior em idades mais precoces e (2) a diminuição da idade-específica na diferenciação entre populações adaptadas e não adaptadas, previstas pela hipótese Hamiltoniana, não foi verificada. Apesar da elevada replicação e do complexo design destas experiências, muitas questões permanecem sem resposta. Outros estudos envolvendo análise genómica, outras características e dietas, dar-nos-ão uma melhor compreensão de como a história, a selecção e o efectivo populacional modelam a evolução durante a colonização

Outcome-Based Education Experiences on Business Administration Courses

This study determined the Outcome-Based Experiences on Business Administration Courses. The study is Descriptive in nature. Survey questionnaire attached with a consent form and Convenience sampling were utilized in data gathering. For the Data treatment and analysis, frequency count, percentages and weighted mean were utilized.  The results of the study revealed that Business Administration students always have Outcome-Based Education experiences on their courses. Though there are factors possible for enhancement

Molecular Tilt on Monolayer-Protected Nanoparticles

The structure of the tilted phase of monolayer-protected nanoparticles is investigated by means of a simple Ginzburg-Landau model. The theory contains two dimensionless parameters representing the preferential tilt angle and the ratio (epsilon) between the energy cost due to spatial variations in the tilt of the coating molecules and that of the van der Waals interactions which favors uniform tilt. We analyze the model for both spherical and octahedral particles. On spherical particles, we find a transition from a tilted phase, at small (epsilon), to a phase where the molecules spontaneously align along the surface normal and tilt disappears. Octahedral particles have an additional phase at small characterized by the presence of six topological defects. These defective configurations provide preferred sites for the chemical functionalization of monolayer-protected nanoparticles via place-exchange reactions and their consequent linking to form molecules and\ud bulk materials

Mesoscopic structure conditions the emergence of cooperation on social networks

We study the evolutionary Prisoner's Dilemma on two social networks obtained from actual relational data. We find very different cooperation levels on each of them that can not be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding perfect agreement with the observations in the real networks. Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.Comment: Largely improved version, includes an artificial network model that fully confirms the explanation of the results in terms of inter- and intra-community structur

Isolation and characterization of Faecalibacterium prausnitzii from calves and piglets.

The goal of our study was to isolate and characterize Faecalibacterium prausnitzii from fecal samples of healthy calves and piglets, in order to develop a novel probiotic for livestock animals. We identified 203 isolates of Faecalibacterium sp., which were clustered in 40 genetically distinct groups. One representative isolate from each cluster was selected for further characterization. The concentrations of the short chain fatty acids (SCFA) acetate, butyrate, propionate and isobutyrate in the culture media were measured by gas chromatography. We observed reduction in the concentration of acetate followed by concomitant increase in the concentration of butyrate, suggesting that the isolates were consuming acetate present in the media and producing butyrate. Butyrate production correlated positively with bacterial growth. Since butyrate has many benefits to the colonic epithelial cells, the selection of strains that produce higher amounts of butyrate is extremely important for the development of this potential probiotic. The effect of pH and concentration of bile salts on bacterial growth was also evaluated in order to mimic the conditions encountered by F. prausnitzii in vivo. The optimal pH for growth ranged between 5.5 and 6.7, while most isolates were inhibited by of the lowest concentration of bile salts tested (0.1%). Antimicrobial resistance profile showed that most isolates of Faecalibacterium sp. were resistant against ciprofloxacin and sulfamethoxazole-trimethoprim. More than 50% of the isolates were resistant to tetracycline, amikacin, cefepime and cefoxitin. A total of 19 different combinations of multidrug resistance were observed among the isolates. Our results provide new insights into the cultural and physiological characteristics of Faecalibacterium prausnitzii illustrating large variability in short chain fatty acid production, in vitro growth, sensitivity to bile salts, and antibiotic resistance and suggesting that future probiotic candidates should be carefully studied before elected for in vivo studies

Suppression of electron spin decoherence in a quantum dot

The dominant source of decoherence for an electron spin in a quantum dot is the hyperfine interaction with the surrounding bath of nuclear spins. The decoherence process may be slowed down by subjecting the electron spin to suitable sequences of external control pulses. We investigate the performance of a variety of dynamical decoupling protocols using exact numerical simulation. Emphasis is given to realistic pulse delays and the long-time limit, beyond the domain where available analytical approaches are guaranteed to work. Our results show that both deterministic and randomized protocols are capable to significantly prolong the electron coherence time, even when using control pulse separations substantially larger than what expected from the {\em upper cutoff} frequency of the coupling spectrum between the electron and the nuclear spins. In a realistic parameter range, the {\em total width} of such a coupling spectrum appears to be the physically relevant frequency scale affecting the overall quality of the decoupling.Comment: 8 pages, 3 figures. Invited talk at the XXXVII Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Jan 2007. Submitted to J. Mod. Op

MAAP Transition from ISO 9001:2015 to ISO 21001:2018 the new quality standard in education organization

Sustainable success has become an ever-more-important future goal in all industries but challenges arise from the advent of fourth industrial revolution and revisions of national and international regulations directly affect the shipping industry trickling down to the Maritime Education and Training Institutions (METI). Thus, a metamorphosis of standards for a maritime school like the Maritime Academy of Asia and the Pacific (MAAP) transitioning to a more tailor-fit Quality Standards is inevitable to manage the changes in educational organizations. ISO 21001:2018 has been published in oder to replace IWA 2:2007. This prompted the Academy to evolve from the traditional ISO 9001:2015 standard. This paper aims to discuss the STCW ’78 (as amended) requirements for Quality Standard System and how the new standard in educational and training organizations complies with it. The paper shall also serve as a resource and reference for those schools that are looking for standards that can attune their management systems gearing towards safer, cleaner, and excellent shipping by having a competent seafarer through a certified Educational Organization Management System. With the vision of the academy to be the leading institution of excellence in maritime and training the Asia-Pacific region and beyond, certification with the standard is indeed a milestone and breakthrough

Interplay of quantum and classical fluctuations near quantum critical points

For a system near a quantum critical point (QCP), above its lower critical dimension $d_L$, there is in general a critical line of second order phase transitions that separates the broken symmetry phase at finite temperatures from the disordered phase. The phase transitions along this line are governed by thermal critical exponents that are different from those associated with the quantum critical point. We point out that, if the effective dimension of the QCP, $d_{eff}=d+z$ ($d$ is the Euclidean dimension of the system and $z$ the dynamic quantum critical exponent) is above its upper critical dimension $d_C$, there is an intermingle of classical (thermal) and quantum critical fluctuations near the QCP. This is due to the breakdown of the generalized scaling relation $\psi=\nu z$ between the shift exponent $\psi$ of the critical line and the crossover exponent $\nu z$, for $d+z>d_C$ by a \textit{dangerous irrelevant interaction}. This phenomenon has clear experimental consequences, like the suppression of the amplitude of classical critical fluctuations near the line of finite temperature phase transitions as the critical temperature is reduced approaching the QCP.Comment: 10 pages, 6 figures, to be published in Brazilian Journal of Physic