Identification, Abundance and Rearing of Mysids of Gran Canaria: aplication to laboratory and oceanographic respiratory metabolism studies

Programa de doctorado en Oceanografía

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Comparative phylogeography of two co-distributed arctic-alpine freshwater insect species in Europe

The distribution pattern of European arctic-alpine disjunct species is of growing interest among biogeographers due to the arising variety of inferred demographic histories. In this thesis I used the co-distributed mayfly Ameletus inopinatus and the stonefly Arcynopteryx compacta as model species to investigate the European Pleistocene and Holocene history of stream-inhabiting arctic-alpine aquatic insects. I used last glacial maximum (LGM) species distribution models (SDM) to derive hypotheses on the glacial survival during the LGM and the recolonization of Fennoscandia: 1) both species potentially survived glacial cycles in periglacial, extra Mediterranean refugia, and 2) postglacial recolonization of Fennoscandia originated from these refugia. I tested these hypotheses using mitochondrial sequence (mtCOI) and species specific microsatellite data. Additionally, I used future SDM to predict the impact of climate change induced range shifts and habitat loss on the overall genetic diversity of the endangered mayfly A. inopinatus.rnI observed old lineages, deep splits, and almost complete lineage sorting of mtCOI sequences between mountain ranges. These results support the hypothesis that both species persisted in multiple periglacial extra-Mediterranean refugia in Central Europe during the LGM. However, the recolonization of Fennoscandia was very different between the two study species. For the mayfly A. inopinatus I found strong differentiation between the Fennoscandian and all other populations in sequence and microsatellite data, indicating that Fennoscandia was recolonized from an extra European refugium. High mtCOI genetic structure within Fennoscandia supports a recolonization of multiple lineages from independent refugia. However, this structure was not apparent in the microsatellite data, consistent with secondary contact without sexual incompability. In contrast, the stonefly A. compacta exhibited low genetic structure and shared mtCOI haplotypes among Fennoscandia and the Black Forest, suggesting a shared Pleistocene refugium in the periglacial tundrabelt. Again, there is incongruence with the microsatellite data, which could be explained with ancestral polymorphism or female-biased dispersal. Future SDM projects major regional habitat loss for the mayfly A. inopinatus, particularly in Central European mountain ranges. By relating these range shifts to my population genetic results, I identified conservation units primarily in Eastern Europe, that if preserved would maintain high levels of the present-day genetic diversity of A. inopinatus and continue to provide long-term suitable habitat under future climate warming scenarios.rnIn this thesis I show that despite similar present day distributions the underlying demographic histories of the study species are vastly different, which might be due to differing dispersal capabilities and niche plasticity. I present genetic, climatic, and ecological data that can be used to prioritize conservation efforts for cold-adapted freshwater insects in light of future climate change. Overall, this thesis provides a next step in filling the knowledge gap regarding molecular studies of the arctic-alpine invertebrate fauna. However, there is continued need to explore the phenomenon of arctic-alpine disjunctions to help understand the processes of range expansion, regression, and lineage diversification in Europe’s high latitude and high altitude biota.

The nematode parasite fauna in three odontocete species: Phocoena phocoena, Lagenorhynchus albirostris, Lagenorhynchus acutus from Northern Scotland and its relationships with diet composition

Food items and nematode parasites were identified from the stomachs of 42 individuals of Phocoena phocoena, 6 of Lagenorhynchus acutus and 8 of L. albirostris stranded off the coastal waters of Northern Scotland between 2004 and 2014. Post-mortem examinations have revealed heavy parasitic worm burdens. Four nematode species complex as Anisakis spp., Contracaeucum spp., Pseudoterronova spp., and Hysterothylacium spp. were recorded. Data on presence of the anisakid species in cetaceans, reported a significative relationship between the presence of Hysterothylacium and the month of host stranding; suggesting a decrease of larval H. aduncum abundance in the period between April and August due to a seasonal effect related to prey availability. Similarly, the parasite burden of the all anisakid genera was related to the year fraction of stranding, and a relationship statistically significant was found just for L. albirostris with an increase between April and October. This finding is explained by a seasonality in occurrence of white-beaked dolphins, with a peak during August, that might be related to movements of shared prey species and competition with other species (Tursiops truncatus). Geographical differences were observed in parasites number of all anisakid species, which was the highest in cetaceans from the East area and lowest in the North coast. The parasites number also increased significantly with the length of the animal and during the year, but with a significant seasonal pattern only for P. phocoena. Regarding diet composition, through a data set consisting of 34 harbour porpoises and 1 Atlantic white-sided dolphins, we found a positive association between parasite number and the cephalopods genus Alloteuthis. This higher level of parasite infection in squid from this area, is probably due to a quantitative distribution of infective forms in squid prey, an abundance of the final host and age or size maturity of squid.

Retrieval simulations of the vertical profiles of water vapour and other chemical species in the Martian atmosphere using PACS

Water vapour, despite being a minor constituent in the Martian atmosphere with its precipitable amount of less than 70 pr. μm, attracts considerable attention in the scientific community because of its potential importance for past life on Mars. The partial pressure of water vapour is highly variable because of its seasonal condensation onto the polar caps and exchange with a subsurface reservoir. It is also known to drive photochemical processes: photolysis of water produces H, OH, HO2 and some other odd hydrogen compounds, which in turn destroy ozone. Consequently, the abundance of water vapour is anti-correlated with ozone abundance. The Herschel Space Observatory provides for the first time the possibility to retrieve vertical water profiles in the Martian atmosphere. Herschel will contribute to this topic with its guaranteed-time key project called "Water and related chemistry in the solar system". Observations of Mars by Heterodyne Instrument for the Far Infrared (HIFI) and Photodetector Array Camera and Spectrometer (PACS) onboard Herschel are planned in the frame of the programme. HIFI with its high spectral resolution enables accurate observations of vertically resolved H2O and temperature profiles in the Martian atmosphere. Unlike HIFI, PACS is not capable of resolving the line-shape of molecular lines. However, our present study of PACS observations for the Martian atmosphere shows that the vertical sensitivity of the PACS observations can be improved by using multiple-line observations with different line opacities. We have investigated the possibility of retrieving vertical profiles of temperature and molecular abundances of minor species including H2O in the Martian atmosphere using PACS. In this paper, we report that PACS is able to provide water vapour vertical profiles for the Martian atmosphere and we present the expected spectra for future PACS observations. We also show that the spectral resolution does not allow the retrieval of several studied minor species, such as H2O2, HCl, NO, SO2, etc.

Island Invasion by a Threatened Tree Species: Evidence for Natural Enemy Release of Mahogany (Swietenia macrophylla) on Dominica, Lesser Antilles

Despite its appeal to explain plant invasions, the enemy release hypothesis (ERH) remains largely unexplored for tropical forest trees. Even scarcer are ERH studies conducted on the same host species at both the community and biogeographical scale, irrespective of the system or plant life form. In Cabrits National Park, Dominica, we observed patterns consistent with enemy release of two introduced, congeneric mahogany species, Swietenia macrophylla and S. mahagoni, planted almost 50 years ago. Swietenia populations at Cabrits have reproduced, with S. macrophylla juveniles established in and out of plantation areas at densities much higher than observed in its native range. Swietenia macrophylla juveniles also experienced significantly lower leaf-level herbivory (~3.0%) than nine co-occurring species native to Dominica (8.4–21.8%), and far lower than conspecific herbivory observed in its native range (11%–43%, on average). These complimentary findings at multiple scales support ERH, and confirm that Swietenia has naturalized at Cabrits. However, Swietenia abundance was positively correlated with native plant diversity at the seedling stage, and only marginally negatively correlated with native plant abundance for stems ≥1-cm dbh. Taken together, these descriptive patterns point to relaxed enemy pressure from specialized enemies, specifically the defoliator Steniscadia poliophaea and the shoot-borer Hypsipyla grandella, as a leading explanation for the enhanced recruitment of Swietenia trees documented at Cabrits.

A longitudinal study of Besnoitia besnoiti infections and seasonal abundance of Stomoxys calcitrans in a dairy cattle farm of southwest France

Bovine besnoitiosis, caused by the cyst-forming apicomplexan Besnoitia besnoiti, is commonly reported in some restricted regions of South-Western Europe, and in larger regions of Africa and Asia. This infection is thought to be transmitted by blood feeding insects and is responsible for major economic losses in cattle production. A recent emergence in Europe, notified in the Centre of France, Spain and Germany, has attracted more attention to this disease. Clinical signs could appear in some animals; however, many infected cattle remain asymptomatic or show scleral-conjunctival cysts (SCC) only. Recent development of serological methods allows carrying out seroepidemiological field studies. In this respect, a long-term investigation was performed in a dairy cattle farm localized in an enzootic area of besnoitiosis of South-western France between March 2008 and May 2009. The objective was to estimate the seasonal pattern of B. besnoiti infections based on the presence of SCC and serology (ELISA and Western blot). In parallel, an entomological survey was conducted to describe population dynamics of Stomoxys calcitrans and Tabanidae species. The seroprevalence determined by Western blot in a cohort of 57 animals continuously present during the whole survey increased from 30% in March 2008 to 89.5% in May 2009 and was always higher than the prevalence based on clinically assessed SCC. New positive B. besnoitia seroconversions occurred throughout the year with the highest number in spring. In addition, many seroconversions were reported in the two months before turn-out and could be associated with a high indoors activity of S. calcitrans during this period.

Species-specific stomatal response of trees to drought - a link to vegetation dynamics?

Question: Is stomatal regulation specific for climate and tree species, and does it reveal species-specific responses to drought? Is there a link to vegetation dynamics? Location: Dry inner alpine valley, Switzerland Methods: Stomatal aperture (θE) of Pinus sylvestris, Quercus pubescens, Juniperus communis and Picea abies were continuously estimated by the ratio of measured branch sap flow rates to potential transpiration rates (adapted Penman-Monteith single leaf approach) at 10-min intervals over four seasons. Results: θE proved to be specific for climate and species and revealed distinctly different drought responses: Pinus stomata close disproportionately more than neighbouring species under dry conditions, but has a higher θE than the other species when weather was relatively wet and cool. Quercus keeps stomata more open under drought stress but has a lower θE under humid conditions. Juniperus was most drought-tolerant, whereas Picea stomata close almost completely during summer. Conclusions: The distinct microclimatic preferences of the four tree species in terms of θE strongly suggest that climate (change) is altering tree physiological performances and thus species-specific competitiveness. Picea and Pinus currently live at the physiological limit of their ability to withstand increasing temperature and drought intensities at the sites investigated, whereas Quercus and Juniperus perform distinctly better. This corresponds, at least partially, with regional vegetation dynamics: Pinus has strongly declined, whereas Quercus has significantly increased in abundance in the past 30 years. We conclude that θE provides an indication of a species' ability to cope with current and predicted climate.

Effects of native pollinator specialization, selfcompatibility and flowering duration of European plant species on their invasiveness elsewhere

1. When entomophilous plants are introduced to a new region, they may leave behind their usual pollinators. In particular, plant species with specialized pollination may then be less likely to establish and spread (i.e. become invasive). Moreover, other reproductive characteristics such as self-compatibility and flowering duration may also affect invasion success. 2. Here, we specifically asked whether plant species' specialization towards pollinator species and families, respectively, as measured in the native range, self-compatibility, flowering duration and their interactions are related to the degree of invasion (i.e. a measure of regional abundance) in non-native regions. 3. We used plant–pollinator interaction data from 119 German grassland sites to calculate unbiased indices of plant specialization towards pollinator species and families for 118 European plant species. We related these specialization indices, flowering duration, self-compatibility and their interactions to the degree of invasion of each species in seven large countries on four non-Eurasian continents. 4. In all models, plant species with long flowering durations had the highest degree of invasion. The best model included the specialization index based on pollinator species instead of the one based on pollinator families. Specialization towards pollinator species had a marginally significant positive effect on the degree of invasion in non-native regions for self-compatible, but not for self-incompatible species. 5. Synthesis. We showed that long flowering duration is related to the degree of invasion in other parts of the world, and a trend that pollinator generalization in the native range may interact with self-compatibility in determining the degree of invasion. Therefore, we conclude that such reproductive characteristics should be considered in risk assessment and management of introduced plant species.

Do invasive species perform better in their new ranges?

A fundamental assumption in invasion biology is that most invasive species exhibit enhanced performance in their introduced range relative to their home ranges. This idea has given rise to numerous hypotheses explaining “invasion success” by virtue of altered ecological and evolutionary pressures. There are surprisingly few data, however, testing the underlying assumption that the performance of introduced populations, including organism size, reproductive output, and abundance, is enhanced in their introduced compared to their native range. Here, we combined data from published studies to test this hypothesis for 26 plant and 27 animal species that are considered to be invasive. On average, individuals of these 53 species were indeed larger, more fecund, and more abundant in their introduced ranges. The overall mean, however, belied significant variability among species, as roughly half of the investigated species (N = 27) performed similarly when compared to conspecific populations in their native range. Thus, although some invasive species are performing better in their new ranges, the pattern is not universal, and just as many are performing largely the same across ranges.

Herbivores equalize the seedling height growth of three dominant tree species in an African tropical rain forest

Determining the impact of insect herbivores on forest tree seedlings and saplings is difficult without experimentation in the field. Moreover, this impact may be heterogeneous in time and space because of seasonal rainfall and canopy disturbances, or ‘gaps’, which can influence both insect abundance and plant performance. In this study we used fine netting to individually protect seedlings of Microberlinia bisulcata, Tetraberlinia bifoliolata and Tetraberlinia korupensis trees (Fabaceae = Leguminosae) from insects in 41 paired gap-understorey locations across 80 ha of primary rain forest (Korup, Cameroon). For all species, growth in height and leaf numbers was negligible in the understorey, where M. bisulcata had the lowest survival after c. 2 years. In gaps, however, all species responded positively with pronounced above-ground growth across seasons. When exposed to herbivores their seedling height growth was similar, but in the absence of herbivores, M. bisulcata significantly outgrew both Tetraberlinia species and matched their leaf numbers. This result suggests that insect herbivores might play an important role in maintaining species coexistence by mitigating sapling abundance of the more palatable M. bisulcata, which in gaps was eaten the most severely. The higher ratio in static leaf damage of control-to-caged M. bisulcata seedlings in gaps than understorey locations was consistent with the Plant Vigour Hypothesis. This result, however, did not apply to either Tetraberlinia species. For M. bisulcata and T. korupensis, but not T. bifoliolata (the most shade-tolerant species), caging improved relative seedling survival in the understory locations compared to gaps, providing restricted support for the Limiting Resource Model. Approximately 2.25 years after treatments were removed, the caged seedlings were taller and had more leaves than controls in all three species, and the effect remained strongest for M. bisulcata. We conclude that in this community the impact of leaf herbivory on seedling growth in gaps is strong for the dominant M. bisulcata, which coupled to a very low shade-tolerance contributes to limiting its regeneration. However, because gaps are common to most forests, insect herbivores may be having impacts upon functionally similar tree species that are also characterized by low sapling recruitment much more widely than currently appreciated. An implication for the restoration and management of M. bisulcata populations in forests outside of Korup is that physical protection from herbivores of new seedlings where the canopy is opened by gaps, or by harvesting, should substantially increase its subcanopy regeneration, and thus, too, its opportunities for adult recruitment.

Effects of Habitat Fragmentation on Abundance, Larval Food and Parasitism of a Spider-Hunting Wasp.

Habitat fragmentation strongly affects species distribution and abundance. However, mechanisms underlying fragmentation effects often remain unresolved. Potential mechanisms are (1) reduced dispersal of a species or (2) altered species interactions in fragmented landscapes. We studied if abundance of the spider-hunting and cavity-nesting wasp Trypoxylon figulus Linnaeus (Hymenoptera: Crabronidae) is affected by fragmentation, and then tested for any effect of larval food (bottom up regulation) and parasitism (top down regulation). Trap nests of T. figulus were studied in 30 agricultural landscapes of the Swiss Plateau. The sites varied in the level of isolation from forest (adjacent, in the open landscape but connected, isolated) and in the amount of woody habitat (from 4 % to 74 %). We recorded wasp abundance (number of occupied reed tubes), determined parasitism of brood cells and analysed the diversity and abundance of spiders that were deposited as larval food. Abundances of T. figulus were negatively related to forest cover in the landscape. In addition, T. figulus abundances were highest at forest edges, reduced by 33.1% in connected sites and by 79.4% in isolated sites. The mean number of spiders per brood cell was lowest in isolated sites. Nevertheless, structural equation modelling revealed that this did not directly determine wasp abundance. Parasitism was neither related to the amount of woody habitat nor to isolation and did not change with host density. Therefore, our study showed that the abundance of T. figulus cannot be fully explained by the studied trophic interactions. Further factors, such as dispersal and habitat preference, seem to play a role in the population dynamics of this widespread secondary carnivore in agricultural landscapes.

How does the taxonomic status of allopatric populations influence species richness within African cichlid fish assemblages?

Aim  Current estimates of species richness within rapidly evolving species flocks are often highly dependent on the species status of allopatric populations that differ in phenotypic traits. These traits may be unreliable indicators of biological species status and systematists may have inconsistently assigned species among lineages or locations on the basis of these traits, thus hampering comparative studies of regional species richness and speciation rates. Our aim was to develop a method of generating standardized estimates of regional species richness suitable for comparative analysis, and to use these estimates to examine the extent and consistency of species assignment of allopatric populations within rapidly evolving cichlid fish flocks present in three east African lakes. Location  Lakes Malawi, Victoria and Tanganyika. Methods  Using published taxon co-occurrence data, a novel approach was employed to calculate standardized ‘minimum’ estimates of regional species richness for hard substrate associated complexes of cichlids within each of the lakes. Minimum estimates were based on an explicit assumption that if taxa present on equivalent habitats have disjunct distributions, then they are allopatric forms of the same species. These estimates were compared with current observed ‘high-end’ regional species richness estimates for those complexes to determine the consistency of species assignment of allopatric populations between lineages within a lake. A ‘sympatry’ index was developed to enable comparisons of levels of species assignment of allopatric populations between-lakes to be made. Results  Within each lake, the minimum and high-end estimates for species richness were significantly correlated across complexes, indicating that the complexes that contain more recognized species contain the most genuine biological species. However, comparisons of complexes among lakes revealed considerable differences. For equivalent geographical areas, substantially higher proportions of recognized species were totally allopatric within the studied Lake Malawi and Lake Victoria complexes, than those of Lake Tanganyika. Main Conclusions  Among African lakes, levels of assignment to species status of allopatric populations were found to be distinctly different. It is unclear whether the discrepancies are a consequence of differences between the lake faunas in degrees of phenotypic divergence among allopatric populations, or are simply the result of inconsistent taxonomic practices. In either case, these results have considerable wider relevance for they emphasize that quantitative measures of regional and beta diversity are critically dependent on the species status of allopatric populations, an issue usually neglected in comparative studies of species richness. The technique introduced here can be used to standardize measures of regional diversity of lineages for comparative analyses, potentially enabling more accurate identification of processes influencing rates of speciation.