Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

Objective: Individuals with obesity and type 2 diabetes differ from lean and healthy individuals in their abundance of certain gut microbial species and microbial gene richness. Abundance of Akkermansia muciniphila, a mucin-degrading bacterium, has been inversely associated with bodyfat mass and glucose intolerance in mice, but more evidence is needed in humans. The impact of diet and weight loss on this bacterial species is unknown. Our objective was to evaluate the association between fecal A. muciniphila abundance, fecal microbiome gene richness, diet, host characteristics, and their changes after calorie restriction (CR). Design: The intervention consisted of a 6-week CR period followed by a 6-week weight stabilization (WS) diet in overweight and obese adults (N=49, including 41 women). Fecal A. muciniphila abundance, fecal microbial gene richness, diet and bioclinical parameters were measured at baseline and after CR and WS. Results: At baseline A. muciniphila was inversely related to fasting glucose, waist-to-hip ratio, and subcutaneous adipocyte diameter. Subjects with higher gene richness and A. muciniphila abundance exhibited the healthiest metabolic status, particularly in fasting plasma glucose, plasma triglycerides and body fat distribution. Individuals with higher baseline A. muciniphila displayed greater improvement in insulin sensitivity markers and other clinical parameters after CR. A. muciniphila was associated with microbial species known to be related to health. Conclusion: A. muciniphila is associated with a healthier metabolic status and better clinicaloutcomes after CR in overweight/obese adults, however the interaction between gut microbiota ecology and A. muciniphila has to be taken into account.

Sei whale (Balaenoptera borealis) ecology and management in the North Atlantic

Tese de Doutoramento em Ciências do Mar, especialidade em Ecologia Marinha.

Molecular estimation of dispersal for ecology and population genetics

The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species' dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

Response of bat species to sylvo-pastoral abandonment

We assessed the effect of abandonment of sylvo-pastoral practices in chestnut orchards (Castanea sativa) on bats in southern Switzerland to determine practical recommendations for bat conservation. We compared bat species richness and foraging activities between traditionally managed and unmanaged chestnut orchards, testing the hypothesis that managed orchards provide better foraging opportunities and harbour more bat species. Echolocation calls of foraging bats were sampled simultaneously at paired sites of managed and unmanaged orchards using custom made recorders. Vegetation structure and aerial insect availability were sampled at the recording sites and used as explanatory variables in the model. In a paired sampling design, we found twice the number of bat species (12) and five times higher total foraging activity in the managed chestnut orchards compared to the unmanaged ones. Bat species with low flight manoeuvrability were 14 times more common in managed orchards, whereas bats with medium to high manoeuvrability were only 5 times more common than in abandoned orchards. The vegetation structure was less dense in managed orchards. However, management did not affect relative insect abundance. Bats primarily visited the most open orchards, free of undergrowth. As a result of restricted access into the overgrown forests, the abandonment of chestnut orchards leads to a decline in bat species richness and foraging activities. Continued management of chestnut orchards to maintain an open structure is important for the conservation of endangered bat species in the southern Swiss Alps.

Ecology and neurophysiology of sleep in two wild sloth species

Study Objectives: Interspecific variation in sleep measured in captivity correlates with various physiological and environmental factors, including estimates of predation risk in the wild. However, it remains unclear whether prior comparative studies have been confounded by the captive recording environment. Herein we examine the impact of predation pressure on sleep in sloths living in the wild. Design: Comparison of two closely related sloth species, one exposed to predation and one free from predation. Setting: Panamanian mainland rainforest (predators present) and island mangrove (predators absent). Participants: Mainland (Bradypus variegatus, 5 males and 4 females) and island (Bradypus pygmaeus, 6 males) sloths. Interventions: None. Measurements and Results: EEG and EMG activity were recorded using a miniature data logger. Although both species spent between 9 and 10 hours per day sleeping, the mainland sloths showed a preference for sleeping at night, whereas island sloths showed no preference for sleeping during the day or night. EEG activity during NREM sleep showed lower low-frequency power, and increased spindle and higher frequency power in island sloths when compared to mainland sloths. Conclusions: In sloths sleeping in the wild, predation pressure influenced the timing of sleep, but not the amount of time spent asleep. The preference for sleeping at night in mainland sloths may be a strategy to avoid detection by nocturnal cats. The pronounced differences in the NREM sleep EEG spectrum remain unexplained, but might be related to genetic or environmental factors.

How reliable is the monitoring of permanent vegetation plots? A test with multiple observers

Questions: A multiple plot design was developed for permanent vegetation plots. How reliable are the different methods used in this design and which changes can we measure? Location: Alpine meadows (2430 m a.s.l.) in the Swiss Alps. Methods: Four inventories were obtained from 40 m(2) plots: four subplots (0.4 m(2)) with a list of species, two 10m transects with the point method (50 points on each), one subplot (4 m2) with a list of species and visual cover estimates as a percentage and the complete plot (40 m(2)) with a list of species and visual estimates in classes. This design was tested by five to seven experienced botanists in three plots. Results: Whatever the sampling size, only 45-63% of the species were seen by all the observers. However, the majority of the overlooked species had cover < 0.1%. Pairs of observers overlooked 10-20% less species than single observers. The point method was the best method for cover estimate, but it took much longer than visual cover estimates, and 100 points allowed for the monitoring of only a very limited number of species. The visual estimate as a percentage was more precise than classes. Working in pairs did not improve the estimates, but one botanist repeating the survey is more reliable than a succession of different observers. Conclusion: Lists of species are insufficient for monitoring. It is necessary to add cover estimates to allow for subsequent interpretations in spite of the overlooked species. The choice of the method depends on the available resources: the point method is time consuming but gives precise data for a limited number of species, while visual estimates are quick but allow for recording only large changes in cover. Constant pairs of observers improve the reliability of the records.

Trophic ecology of jumbo squid and predatory fishes in the Northern Humboldt Current System

This work provides a contribution to a better understanding of the trophic ecology of important predators in the Northern Humboldt Current System, the jack mackerel (Trachurus murphyi), the chub mackerel (Scomber japonicus) and the jumbo squid (Dosidicus gigas) by the characterization of the highly variable feeding patterns of these species at different spatiotemporal scales. We provided new knowledge on the comparative trophic behaviour of these species, defined as opportunistic in previous investigations. For that purpose we applied a variety of statistical methods to an extensive dataset of 27,188 non-empty stomachs. We defined the spatial organization of the forage fauna of these predators and documented changes in prey composition according to predators’ size and spatiotemporal features of environment. Our results highligh the key role played by the dissolved oxygen. We also deciphered an important paradox on the jumbo squid diet: why do they hardly forage on the huge anchovy (Engraulis ringens) biomass distributed of coastal Peru? We showed that the shallow oxygen minimum zone present off coastal Peru could hamper the co-occurrence of jumbo squids and anchovies. In addition, we proposed a conceptual model on jumbo squid trophic ecology including the ontogenetic cycle, oxygen and prey availability. Moreover we showed that the trophic behaviour of jack mackerel and chub mackerel is adapted to forage on more accessible species such as for example the squat lobster Pleurocondes monodon and Zoea larvae. Besides, both predators present a trophic overlap. But jack mackerel was not as oracious as chub mackerel, contradictorily to what was observed by others authors. Fish diet presented a high spatiotemporal variability, and the shelf break appeared as a strong biogeographical frontier. Diet composition of our fish predators was not necessarily a consistent indicator of changes in prey biomass. El Niño events had a weak effect on the stomach fullness and diet composition of chub mackerel and jack mackerel. Moreover, decadal changes in diet diversity challenged the classic paradigm of positive correlation between species richness and temperature. Finally, the global patterns that we described in this work, illustrated the opportunistic foraging behaviour, life strategies and the high degree of plasticity of these species. Such behaviour allows adaptation to changes in the environment.

Foraging ecology and parental behaviour in the common tern (Sterna hirundo)

One component of successful parenting is related to efficiency in foraging behaviour. The relationships among chick feeding, the size and type of food package, and length of parental foraging trips has not been well studied in seabirds. In addition, relatively few data have been collected on the activities of seabirds when foraging away from the nest site. The objectives of this study were: (1) to contrast productivity, feeding rate, and attendance patterns of individuals carrying a novel transmitter with a control group of birds; (2) to use radio-telemetry to assess the variability in foraging locations within and between individual male Common Terns; (3) to determine the seasonal variation in chick diet; (4) to determine for each transmittered bird, the relationships among the foraging patterns, parental behaviour, and seasonal reproductive success. The study took place over two years (1990-91) on a concrete breakwater 1 km offshore on Lake Erie near Port Colbome, Ontario. Ten pairs of terns in 1990 and 12 pairs in 1991 were radio-tracked by boat or car during the chick rearing stage. Concurrent behavioural observations documented the time each sex spent foraging or at the nest. The frequency and prey species composition of feeds to chicks were also recorded. The transmitters had negligible effects on the feeding frequency and brood attendance patterns of transmitter carrying birds. Peak nesting transmittered birds in 1990 and 1991 exhibited some inter-individual variability in foraging locations, however intraindividual variability was low. Birds foraged primarily to the west and northwest of the colony. Late nesters exhibited greater inter-individual variability, however intra-individual variability remained low for most birds. Neither group demonstrated sufficient variability to support the regular use of this colony as an "information centre". Individual transmittered birds had unique and predictable foraging patterns, and corresponding differences in feeding frequencies and brood attendance patterns, yet productivity was essentially equal between nests due to the impact and importance of stochastic events. Individuals that were recaptured in 1991 exhibited very similar foraging patterns to 1990, suggesting littie variability between years. Conservation of foraging patterns between years may have potential implications for mate choice decisions in future breeding seasons. Prey species delivered to chicks differed between morning and evening for peak and late nesters in 1990, but not 1991. Peak nesters in 1990 fed significantiy more Rainbow Smelt fOsmerus mordM) than Emerald Shiner (Notropis atherinoidesV this trend was reversed for late nesters who also fed large numbers of unidentified larval fish. No significant differences were found in 1991. Seasonal changes in prey species delivered to chicks is believed to be attributable to the temperature tolerances of the smelt and shiners, and the presence of large schools of larval fish during the late nesting season.

The backwoods of our backyards : Ontario pioneers and the crisis of ecology /

Early in his landmark ecocritical book The Comedy of Survival, Joseph Meeker develops an intriguing hypothesis about human behaviour. He remarks the species Homo sapiens tend to behave like an invasive or pioneering organism, entering a bio-geographical region and aggressively outcompeting all other species for space and resources. Moreover, he suggests, human cultural traditions, at least in the West, have reinforced such behaviour, continually insisting that the impulses he describes are both necessary and right. While Meeker's work goes on to assess a number of literary works in both the tragic and comic modes, his work never fully explores this hypothesis in the context of human pioneers; that is, there is no ~xploration o( how these themes manifest themselves within our culture and what role they might play in the culture of specific pioneering groups. This project is an attempt at just such an analysis, examining the validity of Meeker's hypothesis through a case study of settler literature in Upper Canada/Ontario between the . years 1800-1867. It explores Meeker's work within three main areas: first, Chapter Two situates his book historically within the field of ecocriticism, showing what came before and the explosion of ecocritical inquiry that followed its release. This chapter also delves into the rift between the natural sciences and humanities, arguing that a move towards deeper interdisciplinarity is r:tecessary for the future. Chapter Three examines the biological and ecological ground on which Meeker rests his hypothesis through exploring evolutionary biology as well as invasive and pioneer species behaviour. Lastly, Chapter Four examines how these ecological principles are manifested in the writings of early Canadian settlers, suggesting that Meeker's hypothesis indeed finds itself on stable footing.

Introduced taxa in disturbed ecosystems

In the literature, introduced taxa are assumed to be present, more abundant, and occupy greater physical space in portions of ecosystems disturbed by human activity. This study tested this principle in two sites, Short Hills provincial Park ("SHU) and Backus Woods ("B~l"). spatial distribution of introduced taxa of vegetation, isopods, and earthworms was determined with the runs test along 300m transects encompassing gradients of anthropogenic disturbance severity. The hypothesis was that introduced taxa would be aggregated along these transects; the null hypothesis was that they would not be aggregated. The null hypothesis was rejected for the introduced taxa as a unit, and vegetation and earthworms individually. Introduced taxa were aggregated along 53.33% (N~30) and 57.14% (N~21) of the transects in SH and BW (respectively). Introduced vegetation (90.00%, N~10 and 100.00%, N~7) and earthworms (50.00%, N~10 and 50.00%, N~8) were also significantly aggregated within the sites. Introduced isopods, however, were not significantly aggregated at either place (20. 00%, N-=10 and 16. 67%, ~J~6). This study demonstrated that introduced taxa are aggregated within ecosystems disturbed by human activity. However, since introduced isopods were not significantly aggregated it was also shown that taxa respond differently.

Foraging ecology and parental care of common terns (Sterna hirundo) nesting in Windermere Basin, Lake Ontario

The relationships among chick feeding, size and type of prey item, and foraging time away from the brood have not been well studied in seabirds. This study investigated spatial and temporal patterns of foraging and chick-provisioning among 23 radio-tagged male common terns nesting at Hamilton Harbour, Lake Ontario during 1991 and 1992. Telemetry data were collected concurrently with behavioural observations from an elevated blind. Terns fitted with transmitters did not differ from controls with respect to either brood attendance, patterns of chick mortality, species and size distributions of prey delivered to offspring, or chick-provisioning rates. There was a clear separation of parental roles: males were primarily responsible for feeding chicks while females allocated more time to brood attendance. The prey species most commonly delivered to chicks by adults were rainbow smelt (Osmerus mordax) and alewife (A/osa pseudoharengus), followed in importance by larval fish, emerald shiner (Notropis antherinoides), salmonids, and fathead minnows (Pimepha/es prome/as). The relative proportions of various fish speCies delivered to chicks by males differed over the course of each breeding season, and there was also much variability in species composition of prey between years. Sizes of prey delivered to chicks also differed between sampling periods. The modal size of fish brought to chicks during Peak 1991 was 1.5 bill lengths, while the majority of prey in Late 1991 were small larval fish. The reverse trend occurred in 1992 when small fish were delivered to chicks predominantly during the Peak nesting period. During periods when predominantly small fish were delivered to chicks, the foraging activity of radio-tagged males was concentrated within a two kilometer radius of the colony. The observed variation in prey composition and foraging locations during the study likely reflects temporal variation in the availability of prey in the vicinity of the colony. Males delivered fish to chicks at a constant rate, while females 4 increased their feeding frequency over the first six to ten brood days. The mean length of fish delivered to chicks by adults increased significantly with increasing chick age. As a group, within each nesting period, transmittered males either foraged predominantly in the same directional bearing (north during Peak 1991, south during Late 1992), or concentrated foraging activity in the immediate vicinity of the colony (Late 1991, Peak 1992). However, individual radio-tagged males exhibited unique and predictable foraging patterns, often favouring specific locations within these areas and differing in their secondary foraging patterns. Overall, the Lake Ontario shoreline between NCB Bay" (3.5 km south of colony) and the lift bridge canal (4 km north of colony) was the foraging area used most frequently by radiotagged males during the chick-rearing period. Foraging patterns of transmittered males at Windermere Basin are similar to patterns of peak-nesting common terns, but differ from those of late-nesters, at a nearby colony (Port Colborne, Lake Erie). Differences between the foraging patterns of late-nesting terns at these colonies likely reflect differences in annual patterns of fish availability between the two locations. No relationship was found between foraging proficiency of adults and survival of offspring. Stochastic factors, such as predation by black-crowned nightherons (Nycticorax nycticorax) and adverse weather conditions during the early stages of chick rearing, may be more important determinants of common tern breeding success than parental quality or fish availability.

Aspects of spatial and habitat ecology of multiple Anopheles species (Diptera: Culicidae): malaria vectors in the highlands and foothills of Ecuador

The resurgence of malaria in highland regions of Africa, Oceania and recently in South America underlines the importance of the study of the ecology of highland mosquito vectors of malaria. Since the incidence of malaria is limited by the distribution of its vectors, the purpose of this PhD thesis was to examine aspects of the ecology of Anopheles mosquitoes in the Andes of Ecuador, South America. A historical literature and archival data review (Chapter 2) indicated that Anopheles pseudopunctipennis transmitted malaria in highland valleys of Ecuador prior to 1950, although it was eliminated through habitat removal and the use of chemical insecticides. Other anopheline species were previously limited to low-altitude regions, except in a few unconfirmed cases. A thorough larval collection effort (n=438 attempted collection sites) in all road-accessible parts of Ecuador except for the lowland Amazon basin was undertaken between 2008 - 2010 (Chapter 3). Larvae were identified morphologically and using molecular techniques (mitochondrial COl gene), and distribution maps indicated that all five species collected (Anopheles albimanus, An. pseudopunctipennis, Anopheles punctimacula, Anopheles oswaldoi s.l. and Anopheles eiseni) were more widespread throughout highland regions than previously recorded during the 1940s, with higher maximum altitudes for all except An. pseudopunctipennis (1541 m, 1930 m, 1906 m, 1233 m and 1873 m, respectively). During larval collections, to characterize species-specific larval habitat, a variety of abiotic and biotic habitat parameters were measured and compared between species-present and species-absent sites using chi-square tests and stepwise binary logistic regression analyses (Chapter 4). An. albimanus was significantly associated with permanent pools with sand substrates and An. pseudopunctipennis with gravel and boulder substrates. Both species were significantly associated with floating cyanobacterial mats and warmer temperatures, which may limit their presence in cooler highland regions. Anopheles punctimacula was collected more often than expected from algae-free, shaded pools with higher-than-average calculated dissolved oxygen. Anopheles oswaldoi s.l., the species occurring on the Amazonian side of the Andes, was associated with permanent, anthropogenic habitats such as roadside ditches and ponds. To address the hypothesis that human land use change is responsible for the emergence of multiple highland Anopheles species by creating larval habitat, common land uses in the western Andes were surveyed for standing water and potential larval habitat suitability (Chapter 5). Rivers and road edges provided large amounts of potentially suitable anopheline habitat in the western Andes, while cattle pasture also created potentially suitable habitat in irrigation canals and watering ponds. Other common land uses surveyed (banana farms, sugarcane plantations, mixed tree plantations, and empty lots) were usually established on steep slopes and had very little standing water present. Using distribution and larval habitat data, a GIS-based larval habitat distribution model for the common western species was constructed in ArcGIS v.l 0 (ESRI 2010) using derived data layers from field measurements and other sources (Chapter 6). The additive model predicted 76.4 - 97.9% of the field-observed collection localities of An. albimanus, An. pseudopunctipennis and An. punctimacula, although it could not accurately distinguish between species-absent and speciespresent sites due to its coarse scale. The model predicted distributional expansion and/or shift of one or more anopheline species into the following highland valleys with climate warming: Mira/Chota, Imbabura province, Tumbaco, Pichincha province, Pallatanga and Sibambe, Chimborazo province, and Yungilla, Azuay province. These valleys may serve as targeted sites of future monitoring to prevent highland epidemics of malaria. The human perceptions of malaria and mosquitoes in relation to land management practices were assessed through an interview-based survey (n=262) in both highlands and lowlands, of male and female land owners and managers of five property types (Chapter 7). Although respondents had a strong understanding of where the disease occurs in their own country and of the basic relationship among standing water, mosquitoes and malaria, about half of respondents in potential risk areas denied the current possibility of malaria infection on their own property. As well, about half of respondents with potential anopheline larval habitat did not report its presence, likely due to a highly specific definition of suitable mosquito habitat. Most respondents who are considered at risk of malaria currently use at least one type of mosquito bite prevention, most commonly bed nets. In conclusion, this interdisciplinary thesis examines the occurrence of Anopheles species in the lowland transition area and highlands in Ecuador, from a historic, geographic, ecological and sociological perspective.

Impacts des emprises de lignes électriques sur la végétation des tourbières

Les infrastructures linéaires sont reconnues pour faciliter la dispersion de plantes indésirables dans leur emprise et les habitats adjacents. Toutefois, les impacts des emprises de lignes électriques ont été peu étudiés, particulièrement en milieux humides. Cette étude a examiné la végétation des emprises de lignes électriques et de leurs habitats adjacents dans 23 tourbières ombrotrophes (bogs) et 11 minérotrophes (fens). Dans les fens, la dispersion des espèces indésirables est facilitée le long des emprises et certaines espèces peuvent se propager à plus de 43 m dans les habitats adjacents. Au contraire, ces infrastructures ne semblent pas favoriser la dispersion des espèces indésirables dans les bogs puisque leur présence était limitée à la marge des sites et était négligeable dans les habitats tourbeux adjacents. Finalement, les caractéristiques intrinsèques des tourbières, telles leur degré de minérotrophie (bog ou fen) et leur structure végétale (tourbière ouverte, semi-forestière ou forestière) semblent grandement influencer l’envahissement.