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Jorge Marques da Silva

    Jorge Marques da Silva

    Universidade de Lisboa, Faculdade de Ciências, Faculty Member
    Papers
    Macroevolutionmore
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    ABSTRACT This book is divided in two parts, the first of which shows how, beyond paleontology and systematics, macroevolutionary theories apply key insights from ecology and biogeography, developmental biology, biophysics, molecular... more
    ABSTRACT This book is divided in two parts, the first of which shows how, beyond paleontology and systematics, macroevolutionary theories apply key insights from ecology and biogeography, developmental biology, biophysics, molecular phylogenetics, and even the sociocultural sciences to explain evolution in deep time. In the second part, the phenomenon of macroevolution is examined with the help of real life-history case studies on the evolution of eukaryotic sex, the formation of anatomical form and body-plans, extinction and speciation events of marine invertebrates, hominin evolution and species conservation ethics. The book brings together leading experts, who explain pivotal concepts such as Punctuated Equilibria, Stasis, Developmental Constraints, Adaptive Radiations, Habitat Tracking, Turnovers, (Mass) Extinctions, Species Sorting, Major Transitions, Trends, and Hierarchies – key premises that allow macroevolutionary epistemic frameworks to transcend microevolutionary theories that focus on genetic variation, selection, migration and fitness. Along the way, the contributing authors review ongoing debates and current scientific challenges; detail new and fascinating scientific tools and techniques that allow us to cross the classic borders between disciplines; demonstrate how their theories make it possible to extend the Modern Synthesis; present guidelines on how the macroevolutionary field could be further developed; and provide a rich view of just how it was that life evolved across time and space. In short, this book is a must-read for active scholars and, because the technical aspects are fully explained, it is also accessible for non-specialists. Understanding evolution requires a solid grasp of above-population phenomena. Species are real biological individuals, and abiotic factors impact the future course of evolution. Beyond observation, when the explanation of macroevolution is the goal, we need both evidence and theory that enable us to explain and interpret how life evolves at the grand scale.
    Publication Date: 2015
    Publication Name: Interdisciplinary Evolution Research
    Research Interests:
    The impact of dehydration rate on the production and cellular location of reactive oxygen species in an aquatic mossmore
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    Abstract Background and Aims The aquatic moss Fontinalis antipyretica requires a slow rate of dehydration to survive a desiccation event. The present work examined whether differences in the dehydration rate resulted in corresponding... more
    Abstract Background and Aims The aquatic moss Fontinalis antipyretica requires a slow rate of dehydration to survive a desiccation event. The present work examined whether differences in the dehydration rate resulted in corresponding differences in the production of reactive oxygen species (ROS) and therefore in the amount of cell damage.
    Journal Name: Annals of Botany
    Publication Date: Oct 1, 2012
    Research Interests:
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    Factors involved in spatiotemporal dynamics of submerged macrophytes in a Portuguese coastal lagoon under Mediterranean climate. Estuarine, Coastal and Shelf Sciencmore
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    Publication Name: Estuarine Coastal and Shelf Science
    Research Interests:
    Photosynthesis by six Portuguese maize cultivars during drought stress and recoverymore
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    "Photosynthesis, chlorophyll fluorescence, and leaf water parameters were measured in six Portuguese maize (Zea mays L.) cultivars during and following a period of drought stress. The leaf relative water content (RWC) responded... more
    "Photosynthesis, chlorophyll fluorescence, and
    leaf water parameters were measured in six Portuguese
    maize (Zea mays L.) cultivars during and following a
    period of drought stress. The leaf relative water content
    (RWC) responded differently among cultivars but except
    for cultivar PB369, recovered close to initial values after
    watering was restored. Photosynthetic rate and stomatal
    conductance decreased with drought but more slowly in
    cultivars PB269 and PB260 than in cultivars AD3R, PB64,
    PB304 and PB369. Water use efficiency (WUE) decreased
    during the water stress treatment although with cultivar
    PB260 the decrease was marked only when the RWC fell
    below 40%. Recovery of WUE was seen with all cultivars
    except PB369. The maximum quantum efficiency of photosystem
    II, the photochemical quenching coefficient, the
    electron transport rate in PSII and the estimated functional
    plastoquinone pool tended to decrease with drought, while
    the non-photochemical quenching coefficient increased.
    The parameters estimated from chlorophyll fluorescence
    did not recover in PB369, during re-watering. The results
    show that PB260 and PB269 were the most tolerant and
    PB369 was the least tolerant cultivars to water stress. The variation found among the cultivars tested suggests the
    existence of valuable genetic resources for crop improvement
    in relation to drought tolerance."
    Publication Date: Jul 14, 2011
    Publication Name: Physiologiae Plantarum
    Research Interests:
    Physiological consequences of desiccation in the aquatic bryophyte Fontinalis antipyreticamore
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    The moss Fontinalis antipyretica, an aquatic bryophyte previously described as desiccation-intolerant, is known to survive intermittent desiccation events in Mediterranean rivers. To better understand the mechanisms of desiccation... more
    The moss Fontinalis antipyretica, an aquatic bryophyte previously described as desiccation-intolerant, is known to survive intermittent desiccation events in Mediterranean rivers. To better understand the mechanisms of desiccation tolerance in this species and to reconcile the apparently conflicting evidence between desiccation tolerance classifications and field observations, gross photosynthesis and chlorophyll a fluorescence were measured in field-desiccated bryophyte tips and in bryophyte tips subjected in the laboratory to slow, fast, and very fast drying followed by either a short (30 min) or prolonged (5 days) recovery. Our results show, for the first time, that the metabolic response of F. antipyretica to desiccation, both under field and laboratory conditions, is consistent with a desiccation-tolerance pattern; however, drying must proceed slowly for the bryophyte to regain its pre-desiccation state following rehydration. In addition, the extent of dehydration was found to influence metabolism whereas the drying rate determined the degree of recovery. Photosystem II (PSII) regulation and structural maintenance may be part of the induced desiccation tolerance mechanism allowing this moss to recover from slow drying. The decrease in the photochemical quenching coefficient (qP) immediately following rehydration may serve to alleviate the effects of excess energy on photosystem I (PSI), while low-level non-photochemical quenching (NPQ) would allow an energy shift enabling recovery subsequent to extended periods of desiccation. The findings were confirmed in field-desiccated samples, whose behavior was similar to that of samples slowly dried in the laboratory.
    Publication Date: Mar 12, 2011
    Publication Name: Planta
    Research Interests:
    The impact of dehydration rate on the production and cellular location of reactive oxygen species in an aquatic mossmore
    by , , , and
    "† Background and Aims The aquatic moss Fontinalis antipyretica requires a slow rate of dehydration to survive a desiccation event. The present work examined whether differences in the dehydration rate resulted in corresponding... more
    "† Background and Aims The aquatic moss Fontinalis antipyretica requires a slow rate of dehydration to survive a desiccation event. The present work examined whether differences in the dehydration rate resulted in corresponding differences in the production of reactive oxygen species (ROS) and therefore in the amount of cell damage.

    † Methods Intracellular ROS production by the aquatic moss was assessed with confocal laser microscopy and the ROS-specific chemical probe 2,7-dichlorodihydrofluorescein diacetate. The production of hydrogen peroxide was also quantified and its cellular location was assessed.

    † Key Results The rehydration of slowly dried cells was associated with lower ROS production, thereby reducing the amount of cellular damage and increasing cell survival. A high oxygen consumption burst accompanied the
    initial stages of rehydration, perhaps due to the burst of ROS production.

    †Conclusions A slow dehydration rate may induce cell protection mechanisms that serve to limit ROS production and reduce the oxidative burst, decreasing the number of damaged and dead cells due upon rehydration."
    Publication Date: Aug 7, 2012
    Publication Name: Annals of Botany
    Research Interests:
    Influence of dehydration rate on cell sucrose and water relations parameters in an inducible desiccation tolerant aquatic bryophytemore
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    During desiccation, plant cells are subjected to very low water potentials. Osmoregulation through increase of soluble materials (e.g. soluble sugars, compatible inorganic ions) is a response to the decreasing turgor pressure in the... more
    During desiccation, plant cells are subjected to very low water potentials. Osmoregulation through increase of soluble materials (e.g. soluble sugars, compatible inorganic ions) is a response to the decreasing turgor pressure in the cells. In bryophytes, sucrose acts as an osmolyte and also stabilizing membranes and proteins through vitrification. We used psychrometric measurements in the aquatic bryophyte Fontinalis antipyretica Hedw. to construct pressure–volume isotherms and determine the water relations parameters under fast and slow dehydration rates. Sucrose was also quantified. The starting hypothesis was that a slow dehydration rate would increase sucrose concentration, thereby decreasing the osmotic potential at turgor loss point, and would also increase cell wall elasticity, postponing turgor loss and allowing time for induction of molecular and structural acclimation mechanisms. In fact, we found that slowly dehydrated samples presented more elastic cell walls, allowing cells to shrink and maintain turgor, helping to better preserve their metabolic functions and therefore to induce desiccation tolerance (DT). On the other hand, in fast dehydrated samples the osmotic potential at turgor loss point decreased, indicating the activity of osmoregulation processes, possibly connected to the increase observed in sucrose content. Upon rehydration, fast dried samples lost 50% of the sucrose through leakage due to cell membrane rupture, while slow dehydrated leaves maintained their sucrose content constant. DT appears to be achieved through slow dehydration, meaning that a high sucrose content alone does not contribute to DT establishment. Moreover, in natural conditions external water can be maintained at very high values due to the life form of F. antipyretica, which grows in long and compact floating stems in streams, allowing a slow dehydration rate required for induction of other DT mechanisms.
    Publication Date: Jul 6, 2015
    Publication Name: Environmental And Experimental Botany
    Research Interests:
    2015, E. Casetta, J. Marques da Silva, "Facing the Big Sixth: From Prioritizing Species to Conserving Biodiversity". In E. Serrelli, & N. Gontier (Eds.), Macroevolution - Explanation, Interpretation, Evidence, Berlin, Springer: 377-403. more
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    This chapter deals with biodiversity conservation efforts aimed at facing “the Big Sixth”—the new mass extinction we could be entering, the first one involving our own species as a primary cause. Following Michael Soulé (1985), we... more
    This chapter deals with biodiversity conservation efforts aimed at facing “the Big Sixth”—the new mass extinction we could be entering, the first one involving our own species as a primary cause. Following Michael Soulé (1985), we characterize conservation biology as a form of biodiversity surgery and illustrate the main difficulties that this very special kind of surgery has to meet. First of all, we briefly discuss the difficulties that arise in declaring the extinction of a species. We then focus on three challenges that facing extinction requires to take up: How to prioritize species; which conservation targets to focus on; and how to ethically justify species conservation. As we show, matters are complicated by the fact that although species continue to play a central role in policies aimed at preserving the variety of life, biodiversity is not just a matter of species preservation. Finally, based on the analysis of such challenges, we compare two legislations currently in force, namely the Endangered Species Act (the primary legislation providing federal legal protection to endangered species in the United States) and the Habitats Directive (which, together with the Birds Directive, forms the cornerstone of the European Union’s nature conservation policy). We conclude that neither legislation is fully adequate for biodiversity conservation: The Endangered Species Act was not designed to preserve habitats, which constitute the higher level of biodiversity, and the Habitats Directive misses the objective of preserving genes, which constitute the lower level of biodiversity and thereby the evolutionary potential of populations. We therefore suggest that reforms are needed both in North American and European biodiversity conservation policies.
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    2014_E. Casetta, J. Marques da Silva, Biodiversity Surgery: Some Epistemological Challenges in Facing Extinction, Axiomathesmore
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    Biological conservation has a long story, but what distinguishes Conservation Biology from previous conservation fields is its multidisciplinary scope and its character as a mission-oriented crisis discipline. These characteristics... more
    Biological conservation has a long story, but what distinguishes Conservation Biology from previous conservation fields is its multidisciplinary scope and its character as a mission-oriented crisis discipline. These characteristics suggested the introduction of the metaphor of biological conservation as a sort of surgery. This paper is about the initial stages of such surgery. Firstly, some data about the so-called “Big Sixth”—the disease—will be presented together with some information about Conservation Biology—the surgeon. Then epistemic and epistemological difficulties in extinction assessment and conservation prioritization, and triage in particular, will be pointed out. It will be argued that, while data deficiency arising from empirical and practical constraints can in principle be overcome, a different order of difficulties stems from the competition among several species concepts. In this case, it will be suggested that the extent of complications is of such significance to require a thorough re-assessment of the very nature of the patients, i.e., outside the metaphor, of the concept of species.
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    From environmental ethics to nature conservation policymore
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    Publication Date: 2000
    Publication Name: Natura
    Research Interests:
    Contributions of soluble carbohydrates to the osmotic adjustment in the C< sub> 4</sub> grass< i> Setaria sphacelata</i>: A comparison between rapidly and slowly …more
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    Publisher: Elsevier
    Publication Date: 2004
    Publication Name: Journal of plant physiology
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    Photosynthetic responses of three C4 grasses of different metabolic subtypes to water deficitmore
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    Page 1. CSIRO PUBLISHING www.publish.csiro.au/journals/fpb Functional Plant Biology, 2007, 34, 204–213 Photosynthetic responses of three C4 grasses of different metabolic subtypes to water deficit Ana E. Carmo-SilvaA ...
    Publisher: CSIRO
    Publication Date: 2007
    Publication Name: Functional Plant …
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    Physiological responses of the legume model< i> Medicago truncatula</i> cv. Jemalong to water deficitmore
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    Publisher: Elsevier
    Publication Date: 2008
    Publication Name: Environmental and …
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    NONDESTRUCTIVE TRACING OF MIGRATORY RHYTHMS OF INTERTIDAL BENTHIC MICROALGAE USING IN VIVO CHLOROPHYLL A FLUORESCENCE1, 2more
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    ABSTRACT In vivo chlorophyll (Chl) a fluorescence was measured in undisturbed intertidal sediments with the purpose of tracing the vertical migratory rhythms of benthic microalgae. A pulse amplitude fluorometer, an instrument which does... more
    ABSTRACT In vivo chlorophyll (Chl) a fluorescence was measured in undisturbed intertidal sediments with the purpose of tracing the vertical migratory rhythms of benthic microalgae. A pulse amplitude fluorometer, an instrument which does not require physical contact with the sample, was used, thus allowing successive measurements to be taken on the same sample without causing any type of disturbance to the sediment structure. The basis of the method is the possibility to detect changes in the Chl a concentration near the sediment surface ...
    Publisher: Wiley Online Library
    Publication Date: Jan 1, 1997
    Publication Name: Journal of phycology
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    Photosynthesis In the Water‐stressed C4 Grass Setaria Sphacelata is Mainly Limited by Stomata With Both Rapidly and Slowly Imposed Water Deficitsmore
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    Publisher: Wiley Online Library
    Publication Date: Jan 1, 2004
    Publication Name: Physiologia Plantarum
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    Books
    Monitoring Photosynthesis by In Vivo Chlorophyll Fluorescence Application to High Throughput Plant Phenotypingmore
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    In spite of the decrease in the rate of population growth, world population is expected to rise from the current figure (slightly above to 7.2 billion) to reach 9.6 billion in 2050. There is therefore a pressing need to increase food... more
    In spite of the decrease in the rate of population growth, world population is expected to rise from the current figure (slightly above to 7.2 billion) to reach 9.6 billion in 2050. There is therefore a pressing need to increase food production. Since most of the best arable lands are already under production, expanding the agricultural areas would have negative impacts on important natural areas. Thereby, increasing the productivity of the current agricultural areas is the chief objective of agronomical planners, and planting more productive and better adapted plant varieties is crucial to achieve it. In fact, plant breeding is at the forefront of concern of both agronomists and plant biologists. Plant breeding is a millenary activity that deeply changed our world. However, the use of molecular biology techniques jointly with informatics capabilities—giving rise to the omics techniques—deeply accelerated plant breeding, providing new and better plant varieties at an increased pace. The advances in genomics, though, far by-passed the advances in phenomics, and so there is a rising consensus among plant breeders that plant phenotyping is a bottleneck to advancing plant breeding. Therefore, a range of international initiatives in high-throughput plant phenotyping (HTPP) are at course, and new automated equipment is being developed. Phenotyping plants, however, is not a simple matter. To begin with, it has to be decided which parameters to measure in order to extrapolate to the desired goals, plant resistance and plant productivity. For this, as well as for plant breeding, an in-depth knowledge of plant physiology is required. Photosynthesis has been considered as a good indicator of overall plant performance. It is the only energy input in plants and thereby impacts all aspects of plant metabolism and physiology. The cumulative rate of photosynthesis over the growing season is the primary determinant of crop biomass. It largely determines the redox state of plant cells, and therefore, it is at the core of regulatory networks. Therefore, assessing photosynthesis and the photosynthetic apparatus plays a core role on plant phenotyping. Nevertheless, high-throughput phenotyping demands very rapid measurements, and consequently the most common method of photosynthesis measurement—the infra-red gas analysis—is not well suited for this purpose. On the contrary, the techniques based on in vivo chlorophyll (Chl) a fluorescence measurements are perfectly fit. In this chapter, an historical perspective on the development of in vivo Chl a measurement is briefly addressed. Then, the state of the art of the fluorescence-based techniques of photosynthesis assessment is presented, and their potential use in HTPP is evaluated. Finally, the current use of these techniques in the main systems of phenotyping is surveyed.
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