Are Bird Habitat Associations Consistent Across Space and Time?

The concept of the fundamental niche is frequently used in ecology to define the set of environmental conditions needed by a species to survive and reproduce (Hutchinson 1957). In contrast, the realized niche constitutes the locations where a species actually occurred, which is a function of both the environmental (abiotic) conditions and biotic interactions (e.g., predation, competition, mutualisms; Soberon and Peterson 2005). Up to now, the realized niche of most species has been mostly examined during breeding seasons and researchers have long assumed that niches should remain constant across species’ ranges and across the avian annual cycle. If this assumption is valid, then the conservation of each species across their full annual cycle is made easier because each species is associated with a single niche. However, if species have more than one realized niche, then we risk misleading conservation efforts by protecting the wrong habitat in some regions or seasons. In this dissertation, I aim to identify whether most species exhibit a single realized niche, or rather, that species have multiple niches that change depending on age and sex (Ch.2), geographic location (Ch. 3) or the stage of the annual cycle (Ch.4). More specifically, in chapter 2, I assembled a large dataset representing the capture (and release) of Rufous Hummingbirds (Selasphorus rufus) and calculated migration routes and timing across age and sex categories. The data showed that adult males, adult females and juveniles tend to migrate using different migration corridors. A greater number of young birds migrated south through California in comparison to the adults which migrated largely through the Rocky Mountain states. Moreover, migration timing also varied across age and sex categories with adult males departing first and young of both sexes departing last – on average one month after the adult males. Overall, the results of this chapter suggest that Rufous Hummingbirds likely encounter and use slightly different sets of environmental conditions during their fall migration across demographic groups. The goal of chapter 3 was to determine if species exhibit consistent habitat relationships across their breeding range. In other words, are niches sufficiently predictable that predictive models can be readily transferred from one location to another? This property is termed “stationarity”. I used Breeding Bird Survey data from across North America, land cover and climate data from remote sensing, and a model transferability methodology to predict avian abundance across space for 131 species. I also assessed whether species’ traits were correlated with levels of stationarity in distributions. Lastly, I tested whether prediction accuracies between modeled regions decreased with 1) geographical distances, 2) level of extrapolation, and 3) were affected by a ‘core-boundary’ effect. The results suggest that, for most species, habitat relationships change across species’ breeding ranges. Species with large distributions, with distributions in regions with less topographic relief, and species with shorter life spans were more likely to have non-stationary distributions. Moreover, results show that predicting across long geographical distances or to novel environments decreases prediction accuracies. Overall, these results suggest that caution should be used when assuming stationarity in models, because the habitat used by birds across regions sometimes differed in measurable ways within a species’ range. These results are important for conservation planning because many conservation efforts such as forecasts of biological invasions, prioritization of land protection, and translocation of endangered species relies on accurately predicting abundance across space (Guisan et al. 2013). Lastly, in chapter 4, I tested whether 83 migratory bird species are consistent in their niches throughout the annual cycle. Here, I used year-round data from the citizen science program, eBird, along with land cover and weather data from remote-sensing sources to calculate niches for each species in four different seasons in each year (2005 – 2020). I compared niches across years (within season) and across seasons (within years) and calculated the percent niche overlap and the drivers of niche dynamics between pairs of niches. As expected, niche overlap was higher across years than across seasons. Consistent with the niche plasticity hypothesis, the niches of migratory birds were largely stable across species’ annual life cycles, but with some small and significant differences among them. These results suggest that migrants have the most similar niches between spring and fall migrations, and most different niches between breeding and over-wintering grounds. Moreover, migratory birds seem to have the most constrained niches during the breeding season. These results suggest that while most migratory birds may rely on common sets of environmental conditions across seasons, the seasonal niches also contracted and expanded significantly throughout the year. Taken all together, the results of these three chapters suggest that each bird species is associated with differing sets of environmental conditions among demographic groups, and across space and time. As such, species are better represented by multiple realized niches, which overlap to different degrees within their fundamental niche. These results highlight the need to identify each species’ collection of realized niches in order to successfully conserve their populations and protect their habitat throughout their full life cycle. Doing so is likely essential to reversing the negative trends observed in our bird populations (Rosenberg et al. 2019)

Chromatin conformation signatures of cellular differentiation

A suite of computer programs to identify genome-wide chromatin conformation signatures with 5C technology is reported

Forest degradation drives widespread avian habitat and population declines

In many regions of the world, forest management has reduced old forest and simplified forest structure and composition. We hypothesized that such forest degradation has resulted in long-term habitat loss for forest-associated bird species of eastern Canada (130,017 km2) which, in turn, has caused bird-population declines. Despite little change in overall forest cover, we found substantial reductions in old forest as a result of frequent clear-cutting and a broad-scale transformation to intensified forestry. Back-cast species distribution models revealed that breeding habitat loss occurred for 66% of the 54 most common species from 1985 to 2020 and was strongly associated with reduction in old age classes. Using a long-term, independent dataset, we found that habitat amount predicted population size for 94% of species, and habitat loss was associated with population declines for old-forest species. Forest degradation may therefore be a primary cause of biodiversity decline in managed forest landscapes

Qu’est-ce que le professionnalisme en ergothérapie ? Étude des représentations d’étudiants et de superviseurs de stagiaires francophones du Québec

Le professionnalisme est une compétence-clé pour les ergothérapeutes, mais des enjeux d’ambiguïté concernant sa définition ont été soulevés par le passé. Une récente étude a permis de proposer une définition contemporaine du professionnalisme en ergothérapie. Or, cette définition est générique et ne tient pas compte des spécificités de la population particulière que sont les étudiants en ergothérapie. Le but de cette étude était d’explorer les représentations sociales qu’ont du professionnalisme des étudiants et des superviseurs de stagiaires en ergothérapie dans le contexte universitaire francophone québécois. Selon un devis descriptif interprétatif, des groupes de discussion ont été menés auprès de 16 étudiants universitaires et des entrevues individuelles ont été conduites avec 16 superviseurs de stagiaires. Les données qualitatives recueillies ont été traitées à l’aide d’une stratégie d’analyse thématique. Il s’agissait de déterminer les antécédents (p. ex. : parcours éducatif), attributs (p. ex. : attitude de juste confiance en soi ou comportement consistant à considérer tous les membres de l’équipe de façon égalitaire) et conséquents (p. ex. : identité professionnelle) du professionnalisme en ergothérapie qui soient spécifiques à la population des étudiants et des superviseurs francophones en ergothérapie au Québec. Il ressort des résultats que le professionnalisme s’inscrit dans un paradigme développemental complexe, que les valeurs propres à la profession sont peu présentes dans les représentations sociales des étudiants et superviseurs de stagiaires rencontrés et que l’organisation du travail peut être une menace pour le professionnalisme en ergothérapie. Enfin, cette étude offre des leviers sur lesquels agir pour faciliter et bonifier l’enseignement et le développement du professionnalisme, notamment en suggérant de miser sur les activités réflexives (p. ex. : portfolio) et d’échange (p. ex. : communauté de pratique) et de bonifier la formation en éthique que reçoivent les étudiants. ______________________________________________________________________________________________________________________________ Professionalism is a key competency for occupational therapists, but issues of ambiguity regarding its definition have arisen in the past. A recent study proposed a contemporary definition of professionalism in occupational therapy. However, this definition is generic and does not consider the specifics of the singular population of occupational therapy students. The purpose of this study was to explore the social representations of professionalism of students and supervisors of occupational therapy interns in the francophone university context in Quebec. According to an interpretative descriptive research design, focus groups were conducted with 16 university students and individual interviews were conducted with 16 supervisors of interns. The qualitative data collected was processed using a thematic analysis strategy. Results suggest antecedents (e.g.: academic background), attributes (e.g.: attitude of fair self-confidence or behavior of considering all team members equally) and consequences (e.g.: professional identity) of professionalism in occupational therapy that are unique to the population of French-speaking occupational therapy students and intern supervisors in Quebec. The interpretation of the results suggests that professionalism is part of a complex developmental paradigm, that the values specific to the profession are not very present in the social representations of the students and intern supervisors we met, and that the work organization may be a threat to professionalism in occupational therapy. Finally, this study offers levers to facilitate and improve the teaching and development of professionalism, notably by suggesting that reflective activities (e.g.: portfolios), exchange activities (e.g.: community of practice) and ethics training for students be enhanced

Qu’est-ce que le professionnalisme en ergothérapie ? Étude des représentations d’étudiants et de superviseurs de stagiaires francophones du Québec

Le professionnalisme est une compétence-clé pour les ergothérapeutes, mais des enjeux d’ambiguïté concernant sa définition ont été soulevés par le passé. Une récente étude a permis de proposer une définition contemporaine du professionnalisme en ergothérapie. Or, cette définition est générique et ne tient pas compte des spécificités de la population particulière que sont les étudiants en ergothérapie. Le but de cette étude était d’explorer les représentations sociales qu’ont du professionnalisme des étudiants et des superviseurs de stagiaires en ergothérapie dans le contexte universitaire francophone québécois. Selon un devis descriptif interprétatif, des groupes de discussion ont été menés auprès de 16 étudiants universitaires et des entrevues individuelles ont été conduites avec 16 superviseurs de stagiaires. Les données qualitatives recueillies ont été traitées à l’aide d’une stratégie d’analyse thématique. Il s’agissait de déterminer les antécédents (p. ex. : parcours éducatif), attributs (p. ex. : attitude de juste confiance en soi ou comportement consistant à considérer tous les membres de l’équipe de façon égalitaire) et conséquents (p. ex. : identité professionnelle) du professionnalisme en ergothérapie qui soient spécifiques à la population des étudiants et des superviseurs francophones en ergothérapie au Québec. Il ressort des résultats que le professionnalisme s’inscrit dans un paradigme développemental complexe, que les valeurs propres à la profession sont peu présentes dans les représentations sociales des étudiants et superviseurs de stagiaires rencontrés et que l’organisation du travail peut être une menace pour le professionnalisme en ergothérapie. Enfin, cette étude offre des leviers sur lesquels agir pour faciliter et bonifier l’enseignement et le développement du professionnalisme, notamment en suggérant de miser sur les activités réflexives (p. ex. : portfolio) et d’échange (p. ex. : communauté de pratique) et de bonifier la formation en éthique que reçoivent les étudiants. ______________________________________________________________________________________________________________________________ Professionalism is a key competency for occupational therapists, but issues of ambiguity regarding its definition have arisen in the past. A recent study proposed a contemporary definition of professionalism in occupational therapy. However, this definition is generic and does not consider the specifics of the singular population of occupational therapy students. The purpose of this study was to explore the social representations of professionalism of students and supervisors of occupational therapy interns in the francophone university context in Quebec. According to an interpretative descriptive research design, focus groups were conducted with 16 university students and individual interviews were conducted with 16 supervisors of interns. The qualitative data collected was processed using a thematic analysis strategy. Results suggest antecedents (e.g.: academic background), attributes (e.g.: attitude of fair self-confidence or behavior of considering all team members equally) and consequences (e.g.: professional identity) of professionalism in occupational therapy that are unique to the population of French-speaking occupational therapy students and intern supervisors in Quebec. The interpretation of the results suggests that professionalism is part of a complex developmental paradigm, that the values specific to the profession are not very present in the social representations of the students and intern supervisors we met, and that the work organization may be a threat to professionalism in occupational therapy. Finally, this study offers levers to facilitate and improve the teaching and development of professionalism, notably by suggesting that reflective activities (e.g.: portfolios), exchange activities (e.g.: community of practice) and ethics training for students be enhanced

The 20S proteasome core, active within apoptotic exosome-like vesicles, induces autoantibody production and accelerates rejection

Autoantibodies to components of apoptotic cells, such as anti-perlecan antibodies, contribute to rejection in organ transplant recipients. However, mechanisms of immunization to apoptotic components remain largely uncharacterized. We used large-scale proteomics, with validation by electron microscopy and biochemical methods, to compare the protein profiles of apoptotic bodies and apoptotic exosome-like vesicles, smaller extracellular vesicles released by endothelial cells downstream of caspase-3 activation. We identified apoptotic exosome-like vesicles as a central trigger for production of anti-perlecan antibodies and acceleration of rejection. Unlike apoptotic bodies, apoptotic exosome-like vesicles triggered the production of anti-perlecan antibodies in naïve mice and enhanced anti-perlecan antibody production and allograft inflammation in mice transplanted with an MHC (major histocompatibility complex)–incompatible aortic graft. The 20S proteasome core was active within apoptotic exosome-like vesicles and controlled their immunogenic activity. Finally, we showed that proteasome activity in circulating exosome-like vesicles increased after vascular injury in mice. These findings open new avenues for predicting and controlling maladaptive humoral responses to apoptotic cell components that enhance the risk of rejection after transplantation

The three-dimensional architecture of Hox cluster silencing

Spatial chromatin organization is emerging as an important mechanism to regulate the expression of genes. However, very little is known about genome architecture at high-resolution in vivo. Here, we mapped the three-dimensional organization of the human Hox clusters with chromosome conformation capture (3C) technology. We show that computational modeling of 3C data sets can identify candidate regulatory proteins of chromatin architecture and gene expression. Hox genes encode evolutionarily conserved master regulators of development which strict control has fascinated biologists for over 25 years. Proper transcriptional silencing is key to Hox function since premature expression can lead to developmental defects or human disease. We now show that the HoxA cluster is organized into multiple chromatin loops that are dependent on transcription activity. Long-range contacts were found in all four silent clusters but looping patterns were specific to each cluster. In contrast to the Drosophila homeotic bithorax complex (BX-C), we found that Polycomb proteins are only modestly required for human cluster looping and silencing. However, computational three-dimensional Hox cluster modeling identified the insulator-binding protein CTCF as a likely candidate mediating DNA loops in all clusters. Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms