Dans un contexte de changement climatique, des dispositifs sont mis en place par les politiques publiques pour permettre le déplacement de la biodiversité et la recolonisation de nouveaux milieux (TVB, trame de vieux bois. . . ). Ces dispositifs semblent adaptés pour les espèces animales les plus mobiles. Or, les espèces ayant une faible capacité de déplacement représentent un enjeu important pour l'e‑cacité des dispositifs mis en place. Un grand nombre de ces espèces demeurent aujourd'hui mal connues. En forêt, les coléoptères saproxyliques aptères de litière sont des espèces ayant des capacités de déplacement et de dispersion limitées en raison de leurs petites tailles, de leurs aptérismes et de leurs exigences trophiques. Ces espèces constituent le modèle biologique de cette étude pour comprendre comment des espèces à faible capacité de déplacement peuvent évoluer dans les forêts et les paysages anthropisés, dans l'espace et le temps. L'échantillonnage par tamisage de litière de dix arbres par peuplement en utilisant un Winkler et une extraction par Berlese, a montré une puissance d'échantillonnage moyenne de 97.2% pour six forêts. Des relevés mensuels sur deux ans ont permis de caractériser la phénologie des espèces, à savoir qu'elles sont i/ présentes dans la litière toute l'année, ii/ davantage abondantes au printemps et en automne et iii/ ne présentent pas de variation interannuelle. Nous avons comparé la richesse spécique et la répartition des espèces, entre les forêts subnaturelles et les peuplements exploités des montagnes Pyrénéennes. Ceci a montré que les espèces sont peu impactées par l'exploitation sylvicole traditionnelle, mais présentent une grande variabilité de répartition qui semble liée à l'impact anthropique passé. Le paysage fragmenté des Coteaux de Gascogne s'est avéré être très pauvre en coléoptères saproxyliques aptères. Étonnamment, dans ce territoire, les répartitions des espèces sont mieux expliquées par les caractéristiques des paysages que celles des forêts. Pour la moitié des espèces, leurs répartitions sont mieux expliquées par la composition du paysage en 1850 que celle d'aujourd'hui. Un seuil critique de 15% de proportion de forêts dans le paysage en 1850 a pu être mis en évidence pour une espèce (Dienerella clathrata). Nous avons montré que les espèces sont capables (au moins) de se déplacer à travers les haies, quelles que soient les caractéristiques de ces dernières. Si les espèces étaient présentes dans la forêt connectée à la haie, elles ont été échantillonnées dans cette dernière. Les capacités de déplacement de trois espèces ont été étudiées en laboratoire et montrent une vitesse moyenne de 1,6m.h-1. Ces deux éléments conrment le fait que ces espèces sont mobiles dans le paysage. L'ensemble de ces résultats, ainsi que le fait que les territoires les moins anthropisés soient les plus riches en coléoptères saproxyliques aptères, nous amènent à conclure que ce groupe taxonomique supporte bien les impacts humains de faible amplitude spatiale et temporelle, mais qu'ils sont peu résilients à une anthropisation importante dans le temps et dans l'espace. / To enable species migration in a global warming context, public policies try to improve European natural network (Green and Blue infrastructure, old trees network...). These measures might be adapted to the high-dispersal species, but there is a lack of knowledge concerning the ability of the low-dispersal species to move using these networks. Lots of these species remain poorly known. Considering forest ecosystems, ightless saproxylic beetles are supposed to be dispersal limited species because of they are small, unable to y and have trophic exigencies. The aim of this study is to understand how dispersal limited species evolve temporally and spatially in the landscape. Flightless saproxylic beetles have been sampled by sieving litter in front of ten trees per stand, using a modied Winkler and extracted through an adapted Berlese. This standardization of the methods lead to sample an average of 97,2% of the species targeted in each forest. A monthly survey during two years has shown that the species are present in the litter throughout the year and that they are stable over two years. The best season to sample them appeared to be autumn and spring. Comparison between old growth forests and harvested stands in the French Pyrénnées has shown that harvesting does not impact signi cantly the target species. Their repartitions were highly dierent between the studied valleys, which is assumed to result from the dierence in the past human impact. In the highly fragmented landscape (Coteaux de Gascogne, SW France), very few ightless saproxylic species have been sampled. Surprisingly, this experiment has shown that the landscape characteristics explain better these dispersal limited species' repartitions than the forest characteristics. For half of them, landscape composition in the 1850's explain better the repartition than the current one. A threshold of 15% of forest cover appeared to be determinant for one species (Dienerella clathrata). We showed that the studied species use the edges (at least to move through them) whatever their characteristics may be. As soon as they are present in the forest, they are in the connected edge. Moving abilities of 3 species have been approached by measuring the running speed in laboratory. This experiment showed a mean of running speed of 1,6m.h -1. These dierent elements lead us to conclude that the ightless saproxylic beetles are mobile in the landscape. All these results, and the fact that species richness is correlated to the landscape anthropisation, leads us to conclude that this taxonomic group can support human impact at small spatial and temporal scale, but are poorly resilient to large and long anthropisation.

Master of Science / Department of Biology / Alice Boyle / Species extinctions over the past two centuries have mainly been caused by habitat destruction. Landscape change typically reduces habitat area, and can fragment contiguous habitat into remnant patches that are more subject to anthropogenic disturbance. Furthermore, changes in the landscape matrix and land-use intensification within remaining natural areas can reduce habitat quality and exacerbate the consequences of habitat loss and fragmentation. Accordingly, wildlife conservation requires an understanding of how landscape structure influences habitat selection. However, most studies of habitat selection are conducted at fine spatial scales and fail to account for landscape context. Temperate grasslands are a critically endangered biome, and remaining prairies are threatened by woody encroachment and disruptions to historic fire-grazing regimes. Here, I investigated the effects of habitat area, fragmentation, woody cover, and rangeland management on habitat selection by two species of declining grassland-obligate sparrows: Henslow’s Sparrows (Ammodramus henslowii) and Grasshopper Sparrows (A. savannarum). I conducted >10,000 bird surveys at sites located throughout eastern Kansas, home to North America’s largest remaining tracts of tallgrass prairie, during the breeding seasons of 2015 and 2016. I assessed the relative importance of different landscape attributes in determining occurrence and within-season site-fidelity of Henslow’s Sparrows using dynamic occupancy models. The species was rare, inhabited <1% of sites, and appeared and disappeared from sites within and between seasons. Henslow’s Sparrows only settled in unburned prairie early in spring, but later in the season, inhabited burned areas and responded to landscape structure at larger scales (50-ha area early in spring vs. 200-ha during mid-season). Sparrows usually settled in unfragmented prairie, strongly favored Conservation Reserve Program (CRP) fields embedded within rangeland, avoided trees, and disappeared from hayfields after mowing. Having identified fragmentation as an important determinant of Henslow’s Sparrow occurrence, I used N-mixture models to test whether abundance of the more common Grasshopper Sparrow was driven by total habitat area or core habitat area (i.e. grasslands >60 m from woodlands, croplands, or urbanized areas). Among 50-ha landscapes containing the same total grassland area, sparrows favored landscapes with more core habitat, and like Henslow’s Sparrows, avoided trees; in landscapes containing ~50–70% grassland, abundance decreased more than threefold if half the grassland area was near an edge, and the landscape contained trees. Effective conservation requires ensuring that habitat is suitable at spatial scales larger than that of the territory or home range. Protecting prairie remnants from agricultural conversion and woody encroachment, promoting CRP enrollment, and maintaining portions of undisturbed prairie in working rangelands each year are critical to protecting threatened grassland species. Both Henslow’s Sparrows and Grasshopper Sparrows were influenced by habitat fragmentation, underscoring the importance of landscape features in driving habitat selection by migratory birds. As habitat loss threatens animal populations worldwide, conservation efforts focused on protecting and restoring core habitat could help mitigate declines of sensitive species.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

Humans are modifying the global landscape at an unprecedented scale and pace. As a result, species are declining and going extinct at an alarming rate. Here, I investigate two main aspects of species’ declines: what factors are contributing to their declines and how effective our conservation efforts have been. I assessed one of the main mechanisms for protecting species by looking at the Endangered Species Act (ESA) in the United States. I examined three separate indicators of species declines for different groups of species: range contractions in Canadian imperilled species, declines in abundance in global amphibian populations and increases in temporal variability in abundance in North American breeding birds. I found that change in recovery status of ESA listed species was only very weakly related to the number of years listed, number of years with a recovery plan, and funding. These tools combined explained very little of the variation in recovery status among species. Either these tools are not very effective in promoting species’ recovery, or species recovery data are so poor that it is impossible to tell whether the tools are effective or not. I examined patterns of species’ declines in three different groups in relation to a number of anthropogenic variables. I found high losses of Canadian imperiled bird, mammal, amphibian and reptile species in regions with high proportions of agricultural land cover. However, losses of imperiled species are significantly more strongly related to the proportion of the region treated with agricultural pesticides. This is consistent with the hypothesis that agricultural pesticide use, or something strongly collinear with it (perhaps intensive agriculture more generally), has contributed significantly to the decline of imperiled species in Canada. Global increases in UV radiation do not appear to be a major cause of amphibian population declines. At individual sites, temporal changes in amphibian abundance are not predictably related to changes in UV intensity. Variability in species’ abundance of North American breeding birds, after accounting for mean abundance, is not systematically higher in areas of high human-dominated land cover or climate change. Rather, it appears that areas with a high proportion of human-dominated cover come to have a higher proportion of highly abundant, and thus more variable, species.

Conservation is plagued by the issue of prioritization - what to conserve and where to conserve it - which relies on identification and assessment of risks. In this body of work, I identify some of the risks related to climate change impacts on biodiversity, as well as potential solutions. Climate changes are underway across nearly all terrestrial areas and will continue in response to greenhouse gas emissions over centuries. Other extinction drivers, such as habitat loss due to urbanization, commonly operate over localized areas. Urbanization contributes, at most, less than 2% of the total range loss for terrestrial species at risk when averaged within an ecodistrict (Chapter 2). Documented impacts of climate change, to date, include: extinction, population loss, reduction in range area, and decreased abundance for multiple taxonomic groups. Examining species’ and populations’ physiological limits provides insight into the mechanistic basis, as well as geography, of climate change impacts (Chapter 3). Climate changes, and the ecological impacts of climate changes, are scale-dependent. Thus, the biotic implications are more accurately assessed through comparisons of local impacts for populations. Under a scenario of climate change, equatorward margins may be strongly limited by climatic conditions and not by biotic interactions. Yet, geographic responses at poleward margins do not appear directly linked to changes in breeding season temperature (Chapter 4). New ideas on how regions with attenuated climate change (climate refugia) may be used to lower species climate-related extinction risk while simultaneously improving habitat connectivity should be considered in the context of potential future consequences (i.e. range disjunction, alternative biological responses) (Chapter 5). Contemporary climate refugia are identifiable along multiple climatic dimensions, and are similar in size to current protected areas (Chapter 6). Determining how, when, and where species distributions are displaced by climate change as well as methods of reducing climatic displacement involves integrating knowledge from distribution shift rates for populations, occurrence of climate refugia, and dispersal barriers. Such assessments, in the Yellowstone to Yukon region, identify dramatically different pathways for connectivity than assessments that are not informed by considerations of species richness and mobility (Chapter 7).

Earlier studies have found that endangered species recovery is only weakly associated with the tools enabled by the U.S. Endangered Species Act (ESA). With habitat loss often cited as a leading cause of species declines, we tested whether the recovery of ESA-listed species is instead associated with the protection of critical habitat (CH) by protected areas. We tested the relationship for 299 species using recovery indices derived from the biennial status reports to Congress (1990-2010), as well as NatureServe and IUCN population status data. We found no overall relationship between recovery and the extent to which CH is protected. However, restricting the analysis to recovering species, listed species with larger areas of protected (R2 = 0.158) or strictly protected (R2 = 0.194) CH fared better than species with less protected or strictly protected CH areas. Declining species (199 of 273 species studied) fared no better with more protected habitat. We conclude that the abatement of habitat loss alone does not necessarily facilitate recoveries for the majority of ESA-listed species. We also note that the weak relationships we observed in this study may be reflective of poor recovery status estimates.

Orientador: Milton Cezar Ribeiro / Resumo: Alterações antrópicas no nível de paisagens afetam de maneiras distintas os diversos grupos de animais e plantas. Tais alterações afetam a composição de espécies e estrutura de comunidades de mamíferos e aves, resultando na perda de funções ecológicas essenciais para a manutenção das florestas. Dentre os processos que podem ser mais afetados inclui-se a frugivoria e a predação de sementes. Desta forma, avançar os conhecimentos de como a paisagem e os tipos de ambientes influenciam tais processos é essencial para a proposição de estratégias que beneficiem a conservação da biodiversidade e manutenção de processos ecológicos. Este estudo tem por objetivo responder qual a contribuição relativa da proporção de vegetação florestal, do tipo de ambiente e sua interação sobre a predação de sementes e frugivoria. Estudamos quatro tipos de ambientes: interior de floresta continua, fragmento florestal, borda de floresta e corredor florestal. O estudo foi realizado em uma região de ecótono entre os biomas Amazônia e Cerrado no estado de Mato Grosso, Brasil. Nessa região foram selecionadas 17 paisagens, representando um gradiente de quantidade de floresta de 10% a 86% em um raio de 3 km. Nessas paisagens avaliamos a frugivoria utilizando frutos artificiais e a predação de sementes utilizando sementes de amendoim e girassóis. Nossos resultados sugerem que a frugivoria por aves foi positivamente relacionada a proporção florestal para aves de médio e grande porte, bem como para a frugivoria t... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Human changes at the landscape level affect different groups of animals and plants in different ways. Such changes affect species composition and mammal and bird community structure, resulting in the loss of essential ecological functions for forest maintenance. Among the most affected processes are the frugivory and seed predation. Thus, advancing the knowledge of how the landscape and environment types influence such processes is essential for proposing strategies that benefit the conservation of biodiversity and the maintenance of ecological processes. This study aims to assess the relative contribution of forest vegetation proportion, environment type and their interaction on seed predation and frugivory. We studied four environment types: continuous forest interior, forest fragment, forest edge and forest corridor. The study was carried out in an ecotone region between Amazon and Cerrado biomes in Mato Grosso state, Brazil. In this region, 17 landscapes were selected ranging from 10% to 86% of forest cover in a radius of 3 km. In each landscape we evaluated frugivory using artificial fruits and seed predation using peanut and sunflower seeds. Our results suggest that frugivory by birds was positively related to forest proportion for medium and large birds, as well as to total frugivory by birds, however the magnitude of the effect varied according to the group of birds. Frugivory by small mammals, on the other hand, showed a negative relationship with forest proportion, ... (Complete abstract click electronic access below) / Mestre

With an increasing worldwide infrastructure more habitats are fragmented by roads and buildings, which can cause a reduction in biodiversity up to 75%. One way to counteract this is by predicting the outcome, with the help of theoretical models, before it happens. In this study I used a Bayesian network model on a fragmented landscape, to test how well trophic metacommunities are able to persist habitat loss, when increasing dispersal between the fragments in the landscapes by implementing corridors. By implementing just three corridors, the species with the highest trophic level went extinct at a considerable later stage, and by just implementing 10 corridors, the metapopulation capacity for all species in all trophic levels increased. Similar results were obtained when changing the way the species extinction probabilities react to their resources being extinct, which further strengthen the efficacy of corridors. The results from this study suggests that increasing connectivity between landscape fragments, and therefore promoting dispersal of organisms, would help the conservation of biodiversity.

Climate change is associated with altered environmental conditions and shifting mosaics of suitable habitats for organisms. Climate change in the form of drought can shift important lake shoreline habitats downslope, altering the lakes chemistry and habitat availability. Additionally, negative biological consequences can occur after a loss of submerged habitat along shorelines, hereafter littoral habitat. The objective of this study is to evaluate whether littoral habitat is lost (cobble, coarse woody habitat (fallen trees; CWH), and aquatic vegetation) under drought conditions across the United States. I used the National Lakes Assessment physical habitat data collected in summer 2012, when 75% of the U.S. experienced drought. I calculated the probability of cobble, CWH, and aquatic vegetation loss with lake level decline. I found cobble and CWH were highly vulnerable, where just 1 meter of lake level loss would result in nearly 100% habitat loss. Aquatic vegetation exhibited vulnerability but at a higher threshold. Multiyear drought will continue into the future with scientists estimating increases in drought frequency and severity, and we do not yet understand how or if aquatic animals will be resilient to a loss of littoral habitat. For example, previous research suggests food webs may be slow to recovery following littoral habitat loss. We must continue to evaluate the biological and environmental consequences of littoral habitat loss under drought conditions to successfully manage lakes and reservoirs into the future.

The pygmy rabbit (Brachylagus idahoensis) is a sagebrush (Artemisia sp.) obligate that depends on sagebrush habitats for food and cover throughout its life cycle. Invasive species, frequent fires, overgrazing, conversion of land to agriculture, energy development, and many other factors have contributed to recent declines in both quantity and quality of sagebrush-steppe habitats required by pygmy rabbits. Because of the many threats to these habitats and the believed decline of pygmy rabbit populations, there is a need to further understand habitat requirements for this species and how they respond to disturbance. This study evaluated habitat selection by pygmy rabbits in Utah and assessed response of this small lagomorph to construction of a large-scale pipeline (i.e. Ruby pipeline) in Utah. We collected habitat data across Utah at occupied sites (pygmy rabbit occupied burrows) and compared these data to similar measurements at unoccupied sites (random locations within sagebrush habitat where pygmy rabbits were not observed). Variables such as horizontal obscurity, elevation, percent understory composed of sagebrush and other shrubs, and sagebrush decadence best described between occupied (active burrow) and unoccupied (randomly selected) sites. Occupied sites had greater amounts of horizontal obscurity, were located at higher elevations, had greater percentage of understory comprised of sagebrush and shrubs, and had less decadent sagebrush. When considering habitat alterations or management these variables should be considered to enhance and protect existing habitat for pygmy rabbits. The Ruby pipeline was a large-scale pipeline project that required the removal of vegetation and the excavation of soil in a continuous linear path for the length of the pipeline. The area that was disturbed is referred to as the right of way (ROW). From our assessment of pygmy rabbit response to construction of the Ruby pipeline, we found evidence for habitat loss and fragmentation as a result of this disturbance. The size of pygmy rabbit space-use areas and home ranges decreased post construction, rabbits shifted core-use areas away from the ROW, and there were fewer movements of collared rabbits across the ROW. Mitigation efforts should consider any action which may reduce restoration time and facilitate movements of rabbits across disturbed areas.